Rethinking DNA Redux

[Techne]

EDIT:
Bleh, the title should be:
Rethinking Junk DNA Redux

There have been a few thread with regards to the term "junk DNA". For example:
The Wonderful World of non-coding RNAs
Rethinking junk DNA
At risk of being lambasted for necroing threads (if that is even the right slang ), I thought it would be good to start a new thread to discuss it as well as post interesting scientific studies with regards to the concept of junk DNA.

Firstly, an overview:
Junk DNA
The term "junk DNA" was coined by Dr. Susumu Ohno in 1972 in his article So Much ‘Junk DNA' in our Genome. The term was applied to sequences of DNA for which no function has been identified.

In 1976, Dawkins published his selfish gene idea in his book, The Selfish Gene. In the book, Dawkins argues that genomic DNA can be accounted for by two ways:
A) Specific functions of sequences contribute to phenotypic fitness and was thus selected.
B) DNA sequences that do not contribute to fitness are parasitic elements that replicate themselves without any evolutionary function. Selfish elements. These selfish elements were described as non-coding and non-specific sequences, including repetitive sequences, transposons and other degenerate elements.

In 1980, the following article appeared in Nature:
Selfish genes, the phenotype paradigm and genome evolution.

Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only 'function' is survival within genomes. Prokaryotic transposable elements and eukaryotic middle-repetitive sequences can be seen as such DNA's and thus no phenotypic or evolutionary function need be assigned to them.

Initially, it was thought that proteins are the main functional units that contribute to the fitness of an organism. After it was found that about 97-98% of the human genome consists of non-coding DNA (DNA that does not code for mRNA to produce proteins), it was thought that a large portion of this non-coding part of the genome was junk DNA. As Dawkins wrote:

Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, tandem repeats, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.

This of course had the effect of stifling researches about these non-coding junk DNA elements as this article from Scientific American notes:

The term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years.

Still, there are arguments that sequences of DNA that do not contribute to the fitness and phenotype of an organism can be labelled "junk DNA". For example, Megabase deletions of gene deserts result in viable mice or Deletion of Ultraconserved Elements Yields Viable Mice. Basically, these studies remove large chunks of the genome of certain mice and measure the effect that it has on their phenotype and fitness.

Both these studies removed non-coding portions of the genomes of these mice and it had no effect on their fitness and phenotype. This result is of course nothing special. As noted in this article: Surviving a knockout blow, the results of several knockout studies with no apparent effect on fitness and phenotype never get published.

But even with such information, knockout experiments will continue to throw up micethat show no obvious phenotype. Many mouse genes belong to families whose functions overlap, and this ‘redundancy’ may mean that a clear phenotype only emerges when two or more genes are removed.
For example, knocking out the mouse gene Uch-L3,which codes an enzyme involved in breaking down regulatory, misfolded or damaged proteins, creates mice that are indistinguishable from their genetically intact relatives. But mice also lacking the related gene Uch-L1 develop walking difficulties, paralysis and eventually die early from degeneration of nerve cells in the spinal cord.
Although such examples do get reported, many knockout experiments in which no phenotype could be found never see the light of day. “A lot of those things you don’t hear about,” says Barbara Knowles, director of research at the Jackson Laboratory. To address the problem, the journal Molecular and Cellular Biology has, since 1999, given over a section to knockout and other mutant mice that seem perfectly normal.
Many of these animals might reveal their phenotypes — if only researchers knew how to look for them. “I don’t believe there is a single mouse that doesn’t have a phenotype,” says Mario Capecchi of the University of Utah in Salt Lake City, who shared a 2001 Lasker award for his pioneering work in developing the knock-out technique.“We just aren’t asking the right questions.”

Hidden traits
In some cases, a phenotype only becomes apparent when a mouse is exposed to particular environmental conditions...

There is no reason to think that these knocked out elements do not contribute to the phenotype and fitness of an organism for no environmental condition. To put it differently, research has not shown with any confidence that these deleted elements have zero potential to contribute to the fitness and phenotype of a particular organism.

Meanwhile, research is ongoing. It is interesting to note that about >90% of our genomes are in fact transcribed into RNA.

From:
The discovery of eukaryotic genome design and its forgotten corollary—the postulate of gene regulation by nuclear RNA

We now know that much of the genome of creatures like us is copied into RNA. Earlier methods missed this, in part because only the RNA coming from so-called single-copy DNA elements was scored and also because today’s methods are 100–10,000 times more sensitive. The modern tally says that >90% of the genome is copied into RNA (although the current methods do not always define whether these arise from bona fide transcription start sites as opposed to random RNA polymerase binding to DNA).

And researchers say there is no such thing as junk RNA.

There are several classes of non-coding RNAs and Mattick and Makunin describe a few of them:
Non-coding RNA
These include:
1) microRNAs
2) snoRNA
3) Sense and antisense transcripts
4) Other

Those interested can read up here about recent finding regarding these elements:
'Junk' DNA Has Important Role, Researchers Find
Saved By Junk DNA: Vital Role In The Evolution Of Human Genome
Junk DNA may have handed us a gripping future
Shaking up the theory of evolution
RNAs Taking Center Stage
Spare Gene Is Fodder For Fishes' Evolution
Transposons, or Jumping Genes: Not Junk DNA?
'Linc-ing' a noncoding RNA to a central cellular pathway

At best the term "junk DNA" merely applies to DNA that is a provisionally labelled for sequences of DNA for which no function has been identified. It is simply unscientific to imply that junk DNA is actually functionless junk.

 

[Nerfherder]

TL;DR

 

[Techne]

Function of 'Junk DNA' in Human Genes

ScienceDaily (Feb. 28, 2011) — Part of the answer to how and why primates differ from other mammals, and humans differ from other primates, may lie in the repetitive stretches of the genome that were once considered "junk."

A new study by researchers at the University of Iowa Carver College of Medicine finds that when a particular type of repetitive DNA segment, known as an Alu element, is inserted into existing genes, they can alter the rate at which proteins are produced -- a mechanism that could contribute to the evolution of different biological characteristics in different species. The study was published in the Feb. 15 issue of the journal Proceedings of the National Academy of Sciences (PNAS).

"Repetitive elements of the genome can provide a playground for the creation of new evolutionary characteristics," Xing said. "By understanding how these elements function, we can learn more about genetic mechanisms that might contribute to uniquely human traits."

Alu elements are a specific class of repetitive DNA that first appeared about 60 to 70 million years ago during primate evolution. They do not exist in genomes of other mammals. Alu elements are the most common form of mobile DNA in the human genome, and are able to transpose, or jump, to different positions in the genome sequence. When they jump into regions of the genome containing existing genes, these elements can become new exons -- pieces of messenger RNAs that carry the genetic information.

Although scientists have known for more than a decade that these Alu elements are an important source of new exons in the human genome, it has been more difficult to determine if these new exons are biologically important.

"It's been hard to say whether these Alu-derived exons actually do anything on a genome-wide level," said senior study author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the UI Carver College of Medicine and the UI College of Engineering. "Our new study says they do -- they affect protein production by altering the efficiency with which messenger RNA is translated into protein."

Xing noted that in other circumstances, altering the rate of protein production can cause disease, meaning that a mechanism that can affect protein production can have a real impact on the characteristics of an organism.

"This would not be the only mechanism that might differentiate humans from other primates, but our study suggests that the creation of new exons from Alu elements is an important process that contributes to those differences," Xing said.

The UI team, including co-first authors Shihao Shen, doctoral student in the Department of Biostatistics; and Lan Lin, Ph.D., associate in the Department of Internal Medicine, made use of data from a new technology called high throughput RNA sequencing to analyze more than 120 million RNA sequences from human cerebellum. Using this data, the team was able to quantify how often Alu-derived exons were included in the mature RNA sequences, which provide the final blueprint for protein production, and where they were inserted in the genes.

"What we found is that these exons tend to avoid protein-coding regions of the genes and rather they end up in the non-coding region that precedes the protein-coding region, called the five prime untranslated region or 5' UTR," Xing explained. "This is the part of the gene that usually contains regions that help control the stability of the messenger RNA and the efficiency at which the messenger RNA is translated into protein."

Experiments to probe the function of these newly inserted elements proved that Alu exons in this region are able to alter the efficiency of messenger RNA translation, which means they affect how fast protein is produced from the altered genes.

The study also suggests that the effect of the newly created exons might be amplified because of which genes were "targeted" by the Alu exons. The researchers found that Alu exons are highly enriched in genes that code for zinc-finger transcription factors -- proteins that act as master regulators of gene expression and that previously have been linked to human and primate evolution. Because these transcription factors control the expression of thousands of other genes, any changes to the amount of transcription factor available would likely have a cascade effect on the downstream genes.

In addition to Xing, Shen and Lin, the team included UI researchers Peng Jiang, Ph.D.; Elizabeth Kenkel; Mallory Stroik; Seiko Sato; and Beverly Davidson, Ph.D., professor of internal medicine, neurology and molecular physiology and biophysics. The team also included James Cai, Ph.D., assistant professor of veterinary medicine at Texas A&M University.

The study was funded in part by grants from the National Institutes of Health and the Roy J. Carver Trust.

 

[Techne]

More functions for sequences of DNA for which no function has been identified previously.
From Nature:
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

The genome is extensively transcribed into long intergenic noncoding RNAs (lincRNAs), many of which are implicated in gene silencing1, 2. Potential roles of lincRNAs in gene activation are much less understood3, 4, 5. Development and homeostasis require coordinate regulation of neighbouring genes through a process termed locus control6. Some locus control elements and enhancers transcribe lincRNAs7, 8, 9, 10, hinting at possible roles in long-range control. In vertebrates, 39 Hox genes, encoding homeodomain transcription factors critical for positional identity, are clustered in four chromosomal loci; the Hox genes are expressed in nested anterior-posterior and proximal-distal patterns colinear with their genomic position from 3′ to 5′of the cluster11. Here we identify HOTTIP, a lincRNA transcribed from the 5′ tip of the HOXA locus that coordinates the activation of several 5′ HOXA genes in vivo. Chromosomal looping brings HOTTIP into close proximity to its target genes. HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription. Induced proximity is necessary and sufficient for HOTTIP RNA activation of its target genes. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation.

 

[Techne]

Heterochromatin, once regarded as containing mostly "junk" DNA...

Safeguarding Genome Integrity Through Extraordinary DNA Repair

ScienceDaily (Apr. 26, 2011) — DNA is under constant attack, from internal factors like free radicals and external ones like ionizing radiation. About 10 double-strand breaks -- the kind that snap both backbones of the double helix -- occur every time a human cell divides. To prevent not only gene mutations but broken chromosomes and chromosomal abnormalities known to cause cancer, infertility, and other diseases in humans, prompt, precise DNA repair is essential.

Heterochromatin (purple) accounts for a third of the chromatin in both humans and fruit flies. Some heterochromatin forms the telomeres that cap the ends of the chromatids, and much is concentrated near the centromere, where sister chromatids are joined. Accurate repair of double-strand breaks in heterochromatin is challenging, because most of its DNA consists of short, repeated sequences. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)​

Scientists at the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab), working with cell lines of the fruit fly Drosophila melanogaster, have discovered an unsuspected and dramatic process by which double-strand breaks in heterochromatin -- one of the two major kinds of chromatin that make up chromosomes, which accounts for a third of the chromatin in both humans and fruit flies -- are repaired in a series of steps. The repair starts where the break occurs, but stalls until the repair site physically moves away from the original heterochromatin region, before continuing to completion.

Unlike euchromatin, where most of an organism's genes reside and where most DNA consists of long, unrepetitive sequences of base pairs, DNA in heterochromatin consists mostly of short repeated sequences that don't code for proteins; indeed, heterochromatin was long regarded as containing mostly "junk" DNA.

Heterochromatin is now known to be anything but junk, playing a crucial role in organizing chromosomes and maintaining their integrity during cell division. It is concentrated near centromeres, where chromatids are in closest contact, which are required to transmit chromosomes from one generation to the next. Maintaining heterochromatin structure is necessary to the normal growth and functions of cells and organisms.

"Heterochromatin poses more of a problem for DNA repair than euchromatin," says Gary Karpen, whose group in Berkeley Lab's Life Sciences Division discovered the new repair mechanism. "It has lots of short sequences -- many of them only about five base-pairs each -- which are repeated millions of times."

"Repair of simple repeated sequences is particularly challenging," says Irene Chiolo, first author of the group's paper reporting the results in the journal Cell. "They can promote chromosome aberrations, with severe consequences for the genome stability of dividing cells" -- abnormalities that are a hallmark of cancer cells and cause birth defects.

Finding the right path

With the stakes so high, how can cells insure fast, accurate repair of double-strand breaks? Two main repair pathways are available. One method, nonhomologous end-joining, simply cleans up the ends of the broken strands and glues them back together regardless of sequence. This might seem a good choice for heterochromatin: it almost always creates small deletions or mutations, but these are in repetitive, noncoding sequences and do not affect genes.

Far more accurate but more complex is homologous recombination, a mechanism involving many steps where something could go wrong. Upon detecting a double-strand break in DNA, several proteins rush to the damaged area. The protein machinery trims back the ends of the broken strands (called 'resection')to produce single-strand regions recognized by other proteins, including one called ATRIP.

Another protein, Rad51, is recruited to form filaments on the single-stranded DNA. Rad51 and its associated proteins search for a complementary sequence of DNA in a neighboring chromatid or homologous chromosome. They invade and open that DNA to form a "D-loop" -- like untwisting a rope to open and expose its individual strands. Using the exposed complementary sequence as a template, proteins rebuild the broken DNA into a copy of the sequence that was originally damaged; in this way the broken double strand is remade with its damaged section accurately reproduced.

It's an ideal method for repairing breaks in gene-rich euchromatin. In repetitive heterochromatin, however, danger arises because completely different chromosomes lying close to the site of the break may have great lengths of repeated short sequences that look identical to the region around the break itself. What starts as a repair process may end up splicing different chromosomes together, a common abnormality in cancer cells.

For heterochromatin to employ such a potentially risky repair process seemed counterintuitive. In earlier experiments looking for key signs of repair in mouse heterochromatin after irradiation, classic markers of double-strand break repair by either nonhomologous end-joining or homologous recombination were both absent. In fact it seemed possible that, somehow, such breaks didn't occur in heterochromatin.

"There were no signs of repair half an hour after the cells were exposed to ionizing radiation," says Karpen. "But our group looked at Drosophila cells just 10 minutes after radiation exposure. Now the early signs of homologous recombination were clearly evident."

After half an hour, however, these signs too -- signals from modified histones, the component proteins that form the "spools" around which the DNA "thread" is wound in chromatin, as well as signals from ATRIP recruitment -- were missing from the heterochromatin domain. What had become of the repair process?

Now you see it, now you don't

In a series of experiments, Karpen and Chiolo and their colleagues found that in heterochromatin the early stages of homologous recombination -- resection and ATRIP loading -- appear within three minutes after the damage occurs. The next steps in homologous recombination seemed blocked from entering the heterochromatin at this stage. These steps -- the activity of the Rad51 proteins in preparing invasive filaments of single-strand DNA -- are the most dangerous, where mistaken recombination could easily occur.

By 30 minutes after radiation damage was inflicted, the entire domain had swollen and began sending out expanding and contracting 'fingers' of chromatin. Now, after the relocation of the damaged DNA to outside the heterochromatin, the Rad51 proteins did appear; the researchers found them moving with the ends of the heterochromatin 'fingers'. After an hour the whole domain partially contracted again, indicating that the broken DNA had moved to the periphery of the heterochromatin domain in order to load Rad51 protein and complete the repair process.

"There are a lot of moving parts here," says Karpen. "It opens new ways of thinking about DNA repair and investigating the process."

It's common to picture chromosomes as rather floppy tubes of stuff that are tightly cinched in their middles to form X-shaped figures, but in fact this is a condensed state that occurs only briefly during mitosis, when cells divide. Most of the time chromosomes aren't condensed -- instead they exist as somewhat diffuse clouds of DNA.

"In the last 20 years researchers have found that the DNA for each chromosome occupies a separate domain in the nucleus, even when chromosomes are decondensed," says Chiolo. "From these 'chromosomal territories' the DNA moves to accomplish certain functions, for example gene transcription, by going to where the proteins are. We now observe that similar movements occur even during DNA repair."

Says Karpen, "The process we discovered is an extreme version of this dynamism, where the DNA repair process starts in one domain, then the damaged DNA goes elsewhere to complete repair. It would seem that starting repair in one place, then moving elsewhere is risky, and could result in unrepaired damage, which is just as dangerous to the cell as abnormal recombination with a different chromosome."

Says Chiolo, "Stability is the key. The presence of resected DNA ends is extremely dangerous in heterochromatin only if Rad51 is loaded onto broken DNA." Sure enough, the researchers discovered that a protein complex called Smc5/6 blocks Rad51 recruitment until the damaged DNA is moved outside the heterochromatin.

Chiolo says, "This mechanism is crucial for safeguarding the genome by blocking aberrant recombination between different chromosomes, and promoting safe repair from a sister chromatin, or homolog, after the double-strand break has relocated outside the heterochromatin domain."

Homologous recombination is a complex mechanism with multiple steps, but also with many points of regulation to insure accurate recombination at every stage. This could be why this method has been favored during evolution. The machinery that relocalizes the damaged DNA before loading Rad51 might have evolved because the consequences of not having it would be terrible.

Karpen and Chiolo and their colleagues are now at work on the next steps in the research, investigating the many unanswered questions about how this surprisingly dynamic mechanism of DNA repair works and what happens when it fails. Perhaps most important is learning whether the unexpectedly sophisticated approach to homologous recombination in Drosophila heterochromatin is conserved in other organisms, including humans.

 

[Techne]

Novel Regulatory Molecules Called Mirror-microRNAs Control Multiple Aspects of Brain Function

ScienceDaily (Apr. 27, 2012) — Our genes control many aspects of who we are -- from the colour of our hair to our vulnerability to certain diseases -- but how are the genes, and consequently the proteins they make themselves controlled? Researchers have discovered a new group of molecules which control some of the fundamental processes behind memory function and may hold the key to developing new therapies for treating neurodegenerative diseases

The mirror-miRNA (red) is expressed in hippocampal neurons, the nucleus is shown in blue. (Credit: Image courtesy of University of Bristol)​

The research, led by academics from the University of Bristol's Schools of Clinical Sciences, Biochemistry and Physiology & Pharmacology and published in the Journal of Biological Chemistry, has revealed a new group of molecules, called mirror-microRNAs.
MicroRNAs are non-coding genes that often reside within 'junk DNA' and regulate the levels and functions of multiple target proteins -- responsible for controlling cellular processes in the brain. The study's findings have shown that two microRNA genes with different functions can be produced from the same piece (sequence) of DNA -- one is produced from the top strand and another from the bottom complementary 'mirror' strand.
Specifically, the research has shown that a single piece of human DNA gives rise to two fully processed microRNA genes that are expressed in the brain and have different and previously unknown functions. One microRNA is expressed in the parts of nerve cells that are known to control memory function and the other microRNA controls the processes that move protein cargos around nerve cells.
James Uney, Professor of Molecular Neuroscience in the University's School of Clinical Sciences, said: "These findings are important as they show that very small changes in microRNA genes will have a dramatic effect on brain function and may influence our memory function or likelihood of developing neurodegenerative diseases. These findings also suggest that many more human mirror microRNAs will be found and that they could ultimately be used as treatments for human neurodegenerative diseases such as dementia."
MicroRNAs can be seen as a novel regulatory layer within the genome, relying on the interaction between different RNA molecules. Through binding to messenger RNA (mRNA), they adjust the levels of proteins. Due to their small size, they are able to regulate many different RNAs. MicroRNAs have already been found throughout the double helix, lying in between genes or in areas of the code for a single gene that would normally be discarded. Such areas that were once considered "junk DNA" are now revealing a more complex and important role. In addition microRNAs can be produced in conjunction with their genes, within which they lie, or be controlled and produced entirely independently.
Helen Scott and Joanna Howarth, the lead authors on the study, added: "We have now found that both sides of the double helix can each produce a microRNA. These two microRNAs are almost a perfect mirror of each other, but due to slight differences in their sequence, they regulate different sets of protein producing RNAs, which will in turn affect different biological functions. Such mirror-miRNAs are likely to represent a new group of microRNAs with complex roles in coordinating gene expression, doubling the capacity of regulation."
The study, by Helen Scott, Joanna Howarth, Youn Bok Lee, Liang-Fong Wong, Ioannis Bantounas, Leonidas Phylactou, Paul Verkade and James B Uney, was supported by the Wellcome Trust, Medical Research Council (ERA-NET) and Biotechnology and Biological Sciences Research Council (BBSRC).

Luckily the term "junk DNA" no longer repels mainstream researchers from studying noncoding genetic material. The correct and scientific view on junk DNA is that it merely applies to DNA that is a provisionally labelled for sequences of DNA for which no function has been identified. It is simply unscientific to imply that junk DNA is actually functionless junk.

 

[empirex]

A good layman's introduction to the world of junk DNA, or in this case non-junk DNA, is The Myth of Junk DNA.
Wells cites literally hundreds of peer-reviewed articles in the book, clearly demonstrating that the myth has persisted for far too long despite evidence to the contrary.

He covers the whole range, from intronic regions, which the majority of scientists (no matter which side of the fence they be) now accept directly serve in alternate splicing; pseudogenes; repetitive sequences and sequences independent of exact sequence (rather than exact sequence, they are required as exact "filler"). He of course covers the basics of DNA, it's makeup and expression as well.

 

[Techne]

Another function for non-protein coding RNA:
RNA: From Messenger to Guardian of Genome Integrity

ScienceDaily (May 23, 2012) — A new and unexpected role for RNA is identified: the defence of genome integrity and stability. A study published in the scientific journal Nature shows that an until now unknown class of RNA -- the newly christened DDRNA -- plays a key role in activation of the molecular alarms necessary to safeguard our genome when DNA damage from internal or external factors occurs.

DNA molecule unwinding from a chromosome inside the nucleus of a cell. (Credit: National Human Genome Research Institute)​

The discovery described in the pages of Nature emerges from a study conducted by Fabrizio d'Adda di Fagagna at IFOM in Milan, in collaboration with the CNR in Pavia, the IIT at the IFOM-IEO in Milan and the Riken Omics Science Center in Yokohama, Japan.

Given the importance of the cellular DNA damage response in aging, in the repression and control of tumour development, and in therapeutic treatments for cancer, the discovery could open promising interpretive and potentially therapeutic perspectives.

For decades the scientific community has attributed a role to RNA that is subordinate to that of DNA: the functional processes of expression of genetic information into proteins. With some known exceptions, such as the classes of tRNA and rRNA involved in the synthesis of proteins, RNA molecules were considered "fleeting" messengers necessary to carry genetic instructions from the nucleus, site of the genome, to the cytoplasm where proteins, the scaffolding of living organisms, are produced.

In recent years, this simplistic view has given way to an increasingly complex scenario, with the identification of new RNA classes involved in numerous cellular events.

One in particular, however, had never been identified or described to date: it is DDRNA, a class of non protein-coding RNAs that are generated every time the genome is damaged. They originate from the same sequence of DNA damaged and have the essential task of launching the molecular alarms through which the cell detects the problem and resolves it by repairing the damage.

Therefore, the integrity of the genome depends on DDRNA.
The discovery emerges from a study published online May 23 in the journal Nature and coordinated by Fabrizio d'Adda di Fagagna, head of the "Telomeres and senescence" research program at IFOM (FIRC Institute of Molecular Oncology) in Milan and a researcher at the CNR in Pavia.

DDRNA (DNA Damage Response RNAs), were named precisely for their ability to trigger the cellular DNA damage response and are not simply a new class of RNA that is added to other previously found.

"All of the RNAs described so far -- says d'Adda di Fagagna -- although very different in structure, sequence and mechanism of action, have essentially one thing in common: all contribute, at multiple levels, to regulate the functional organization and expression of the genome. The DDRNA are unique because they safeguard genome integrity. For an RNA, it is a novel task that broadens the spectrum of the functional versatility so far proven for this type of molecules."

Therefore, this discovery represents a milestone in the process leading to a significant change in perspective for this area of molecular biology.

Certainly new sequencing technologies are contributing to revolutionise the field by unravelling first the genomes of numerous plant and animal species, and then the so-called transcriptome -- the entire and specific program of RNA expressed by a cell. The DDRNA described today in Nature was identified thanks to the use of advanced genomic technologies, capable of identifying small amounts of RNA, by scientists at IFOM in close collaboration with the team of Piero Carninci of the RIKEN Omics Science Center at the RIKEN Yokohama Institute in Japan.
Experiments were conducted at laboratories in Milan and Yokohama that recreated stress conditions capable of generating DNA damage in cultured cells and then the complete set of RNA expressed from the damaged cells was sequenced.

"The results of these analyzes have clearly demonstrated -- Carninci comments -- that under such circumstances, short RNA molecules are transcribed from the sequence of damaged DNA. This study has very important implications regarding the function of the non-coding RNAs. These RNAs are often considered "genomic rubbish," because in many cases their function is not yet entirely clear. This study demonstrates unequivocally that even short RNA transcripts may play a role in maintaining genome integrity." Further investigations conducted at the IFOM have revealed that cells rely on them to trigger the alarms necessary for the repair of their damaged genomes.

DDRNA: a barrier against tumour development
The DNA Damage Response or DDR is the reaction that a cell triggers to maintain its genomic integrity: when a DNA break is detected, the growth and proliferation of damaged cells are temporarily halted, thus avoiding conditions that cause genome rearrangements and mutations that might predispose to cancer or the accumulation of irreparable DNA damage and cause cellular aging.
Therefore, this system constitutes a very effective barrier to the uncontrolled cell growth that is typical of tumours.

The experimental journey that led the team of d'Adda di Fagagna at IFOM, composed of Sofia France and Flavia Michelini, to the discovery of DDRNA was inspired by the study of cancer cells: "Analysing these cells -- explains Sofia France, first author of this study supported also by the Italian Institute of Technology at the IFOM-IEO Campus in Milan -- we realized that when we blocked the production of a specific class of non- coding RNAs, inside the cell nucleus the molecular alarms that signal the presence of DNA damage were extinguished and the DDR mechanism was not activated; consequently, the tumour cells began to proliferate again."

While pursuing research on this never before seen phenomenon, the scientists at IFOM have identified a novel role for RNA as a mediator of the cellular response to DNA damage and, as such, as a suppressor of tumour growth. And not only: the accumulation of DNA damage and persistent activation of the DDR are also associated with cellular senescence and organism aging, processes in which this new class of RNA may play a key role.

Senescence and malignant transformation are in many ways opposite faces of the same coin. For years, d'Adda di Fagagna and his team have been dedicated to studying these two closely linked cellular processes and their association with impaired genome integrity. Today's discovery reveals another piece of the puzzle that emerges from research conducted by the scientists at IFOM: "This new class of RNA opens a completely new perspective for interpreting the processes of aging and mechanisms of transformation and of tumour progression linked to the generation of DNA damage" says d'Adda di Fagagna. "In particular, we will now investigate if the mechanisms of synthesis of these DDRNAs are altered in cancer and the impact that these changes may have on the onset and development of tumours. It is in this direction -- continues the scientist -- that we will continue our research in a close collaboration between IFOM and the CNR of Pavia, where we have recently established a laboratory dedicated to studying the maintenance of genomic stability."

This work was realized with support from, among others, the FIRC (Italian Foundation for Cancer Research), AIRC (Italian Association for Cancer Research), the Human Frontier Science Program and Telethon.

 

[Swa]

So removing A from the genome appears to do nothing until B is also removed. What happens then if only B is removed?

 

[Techne]

Pseudogenes are not pseudo any more

Recent significant progress toward understanding the function of pseudogenes in protozoa (Trypanosoma brucei), metazoa (mouse) and plants, make it pertinent to provide a brief overview on what has been learned about this fascinating subject. We discuss the regulatory mechanisms of pseudogenes at the post-transcriptional level and advance new ideas toward understanding the evolution of these, sometimes called “garbage genes” or “junk DNA,” seeking to stimulate the interest of scientists and additional research on the subject. We hope this point-of-view can be helpful to scientists working or seeking to work on these and related issues.

 

[Techne]

EDIT, decided to rather make a new thread about the story as it appears to be quite interesting.

 

[Techne]

More functions of non-coding RNA:
Class of RNA Molecules Protects Germ Cells from Damage

ScienceDaily (Nov. 15, 2012) — Passing one's genes on to the next generation is a mark of evolutionary success. So it makes sense that the body would work to ensure that the genes the next generation inherits are exact replicas of the originals.

Following meiosis, many green clumps in a germ cell lacking piRNA indicate massive DNA damage. (Credit: Image courtesy of University of Pennsylvania)

New research by biologists at the University of Pennsylvania School of Veterinary Medicine has now identified one way the body does exactly that. This protective role is fulfilled in part by a class of small RNA molecules called pachytene piwi-interacting RNAs, or piRNAs. Without them, germ-cell development in males comes to a halt. Because these play such an important role in allowing sperm to develop normally, the research indicates that defects in these molecules or the molecules with which they interact may be responsible for some cases of male infertility.

Jeremy Wang, an associate professor of developmental biology and director of the Center for Animal Transgenesis and Germ Cell Research at Penn Vet, and Ke Zheng, a postdoctoral researcher in Wang's lab, authored the study, which appears in PLoS Genetics.

Scientists know of 8 million different piRNAs in existence; they are the most abundant type of small non-coding RNA. The molecule piRNA gets its name because it forms complexes with piwi proteins. Earlier work had indicated that these piwi-piRNA complexes suppress the activity of transposable elements or "jumping genes," which are stretches of DNA that can change position and cause potentially damaging genetic mutations. These sequences are also known as transposons.

"There are about 50 human diseases caused by transposable elements, so it's important for the body to have a way to try to repress them," Wang said.

This transposon-suppressing activity had been confirmed in a group of piRNAs called pre-pachytene piRNAs, which are expressed before meiosis, the unique process by which germ cells divide. But Zheng and Wang wanted to investigate if a separate group of piRNAs that emerge during meiosis, called pachytene piRNAs, were also required for "silencing" transposons.

Working in male mice, the researchers manipulated an enzyme called MOV10L1, which is known to interact with piwi proteins and is believed to help produce piRNA molecules. They created a mutant mouse in which they could selectively inactivate MOV10L1 at specific stages before, during and after meiosis. The mice that lost the function of MOV10L1 before or at the pachytene stage of meiosis were sterile. When Zheng and Wang examined their germ cells more closely, they found that spermatogenesis had apparently come to a halt at the post-meiotic stage: Early stages of the germ cells were present, but the mice completely lacked mature sperm.

Further experiments allowed Zheng and Wang to pinpoint that MOV10L1 was playing a critical role at the pachytene stage. MOV10L1 mutants lacked pachytene piRNAs, but their levels of pre-pachytene piRNAs were unaffected, as the mutation was "turned on" after they had already been produced.

The researchers also found that, in the MOV10L1 mutants, piwi proteins congregated together along with mitochondria, suggesting that mitochondria may be involved in the generation or organization of pachytene piRNAs. Furthermore, the spermatids, or early-stage sperm, of the mutants had severe DNA damage. While the researchers suspected that the damage may have been caused because of transposons that had been freed from repression in the absence of piRNAs, they actually found that two common transposable elements were not de-repressed in the mutants. They also found a build-up of pachytene piRNA precursors in the testes of the mutants. Their findings raise the possibility that there is another mechanism by which damage occurs.

"It could be the accumulation of precursor molecules is causing some of the damage," Wang said.

This new function for MOV10L1, in playing an essential role in producing pachytene piRNAs, gives researchers a greater understanding of germ-cell development.

"This is the first time we've shown that pachtyene piRNA is required for maintaining genome integrity in the post-meiotic germ cells," Wang said. "It turns out that MOV10L1 is a master regulator of the piRNA pathway and is required for the production of all piRNAs, both pre-pachytene and pachytene."

Any disruptions to this "master regulator" role, therefore, could lead to problems.

"I think we're just beginning to appreciate the significance of this pathway," Wang said. "Mutations at various points in the pathway could lead to infertility."

This research was supported by the National Institutes of Health's National Institute of Child Health and Human Development.

Journal Reference:

Ke Zheng, P. Jeremy Wang. Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity. PLoS Genetics, 2012; 8 (11): e1003038 DOI: 10.1371/journal.pgen.1003038

 

[Techne]

Transposable Elements Reveal a Stem Cell Specific Class of Long Noncoding RNAs

ScienceDaily (Nov. 26, 2012) — Over a decade after sequencing the human genome, it has now become clear that the genome is not mostly 'junk' as previously thought. In fact, the ENCODE project consortium of dozens of labs and petabytes of data have determined that these 'noncoding' regions house everything from disease trait loci to important regulatory signals, all the way through to new types of RNA-based genes.

Yet over 70 years ago, it was first proclaimed that all this junk wasn't so junky. Barbara McClintock discovered the first utility of all of this junk DNA: jumping genes, also known as transposable elements. These genes serve only one purpose, which is to replicate themselves and reinsert randomly in the genome, or do they? Ironically, at the same time two other scientists (Roy Britten and Eric Davidson) proposed that jumping genes may be involved in regulating cell specificity. Indeed, in an exciting new study published in Genome Biology, John Rinn and David Kelley based at Harvard University and the Broad Institute in Boston, USA, provide genome-wide evidence that jumping genes may shape when a gene is turned on or off in stem cells.

"We set out to investigate how jumping genes have invaded the genome to potentially give rise to new genes in the 'junk regions'" says Rinn, the senior author of the study. "It has become very clear that there are thousands of long intergenic noncoding RNA genes (lincRNAs) that may herald a new paradigm for human health and disease." Yet how these genes have evolved from such a desert wasteland has remained a burning question. A new clue has emerged from the jumping genes that compose nearly 50% of the human genome.

"I like to think of it as 'on the origins of lincRNAs'" says Rinn. "It doesn't take more than a brief survey of McClintock, Britten and Davidson's work in the 50s and 60s to realize that transposable elements were a great first place to look. The human genome is in a constant battle with transposable elements with them randomly hopping into new locations, for good or for bad." Kelley adds that "In my Ph.D. work assembling genomes from sequence fragments, these repetitive hopping genes were a major nuisance, which got me thinking about what they were doing in the genome." The study published by Rinn and Kelley finds a striking affinity for a class of hopping genes known as endogenous retroviruses, or ERVs, to land in lincRNAs. The study finds that ERVs are not only enriched in lincRNAs, but also often sit at the start of the gene in an orientation to promote transcription. Perhaps more intriguingly, lincRNAs containing an ERV family known as HERVH correlated with expression in stem cells relative to dozens of other tested tissues and cells. According to Rinn, "This strongly suggests that ERV transposition in the genome may have given rise to stem cell-specific lincRNAs. The observation that HERVHs landed at the start of dozens of lincRNAs was almost chilling; that this appears to impart a stem cell-specific expression pattern was simply stunning!"

These results also raise the tantalizing question of why transposable elements, derived from viruses, regulate stem cell-specific expression in mammals. Rinn hypothesizes that "transposable elements may not be limited to giving rise to new lincRNA genes, but may also provide an engine for the evolution of RNA-encoding genes. I like to think of it as the 'genome getting dirty': in the same way that kids that play in the dirt develop better immune systems, the genome may be 'getting dirty' with transposable elements, and once in a while, this has an advantageous effect of producing a new lincRNA gene."

What is clear is that transposable elements may control the tissue-specific expression of lincRNAs, thereby affecting the evolution and function of lincRNAs with important regulatory roles. Following on from these results, it will be interesting to determine other ways hopping genes may have shaped lincRNA evolution. Kelley notes that "This study merely scratches the surface of the possible roles of transposable elements influencing lincRNA function."

Journal Reference:
David Kelley and John Rinn. Transposable elements reveal a stem cell specific class of long noncoding RNAs. Genome Biology, 2012 (in press) [link]

Not so junky afterall.

 

[Techne]

How Some Unusual RNA Molecules Home in On Targets

July 5, 2013 — The genes that code for proteins -- more than 20,000 in total -- make up only about 1 percent of the complete human genome. That entire thing -- not just the genes, but also genetic junk and all the rest -- is coiled and folded up in any number of ways within the nucleus of each of our cells. Think, then, of the challenge that a protein or other molecule, like RNA, faces when searching through that material to locate a target gene.

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. Here, we investigate the localization mechanisms of the Xist lncRNA during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maintenance of XCI, Xist binds broadly across the X-chromosome. During initiation of XCI, Xist initially transfers to distal regions across the X-chromosome that are not defined by specific sequences. Instead, Xist identifies these regions by exploiting the three-dimensional conformation of the X-chromosome. Xist requires its silencing domain to spread across actively transcribed regions and thereby access the entire chromosome. This suggests a model where Xist coats the X-chromosome by searching in three dimensions, modifying chromosome structure, and spreading to newly accessible locations.

 

[Techne]

Research suggest that "a large proportion of the mammalian genome is functional".
Widespread purifying selection on RNA structure in mammals

Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1. This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.

 

[Techne]

How 'Junk DNA' Can Control Cell Development

Aug. 2, 2013 — Researchers from the Gene and Stem Cell Therapy Program at Sydney's Centenary Institute have confirmed that, far from being "junk," the 97 per cent of human DNA that does not encode instructions for making proteins can play a significant role in controlling cell development.

And in doing so, the researchers have unravelled a previously unknown mechanism for regulating the activity of genes, increasing our understanding of the way cells develop and opening the way to new possibilities for therapy.

Using the latest gene sequencing techniques and sophisticated computer analysis, a research group led by Professor John Rasko AO and including Centenary's Head of Bioinformatics, Dr William Ritchie, has shown how particular white blood cells use non-coding DNA to regulate the activity of a group of genes that determines their shape and function. The work is published today in the scientific journal Cell.

"This discovery, involving what was previously referred to as "junk," opens up a new level of gene expression control that could also play a role in the development of many other tissue types," Rasko says. "Our observations were quite surprising and they open entirely new avenues for potential treatments in diverse diseases including cancers and leukemias."

The researchers reached their conclusions through studying introns -- non-coding sequences which are located inside genes.

As part of the normal process of generating proteins from DNA, the code for constructing a particular protein is printed off as a strip of genetic material known as messenger RNA (mRNA). It is this strip of mRNA which carries the instructions for making the protein from the gene in the nucleus to the protein factories or ribosomes in the body of the cell.

But these mRNA strips need to be processed before they can be used as protein blueprints. Typically, any non-coding introns must be cut out to produce the final sequence for a functional protein. Many of the introns also include a short sequence -- known as the stop codon -- which, if left in, stops protein construction altogether. Retention of the intron can also stimulate a cellular mechanism which breaks up the mRNA containing it.

Dr Ritchie was able to develop a computer program to sort out mRNA strips retaining introns from those which did not. Using this technique the lead molecular biologist of the team, Dr Justin Wong, found that mRNA strips from many dozens of genes involved in white blood cell function were prone to intron retention and consequent break down. This was related to the levels of the enzymes needed to chop out the intron. Unless the intron is excised, functional protein products are never produced from these genes. Dr Jeff Holst in the team went a step further to show how this mechanism works in living bone marrow.

So the researchers propose intron retention as an efficient means of controlling the activity of many genes. "In fact, it takes less energy to break up strips of mRNA, than to control gene activity in other ways," says Rasko. "This may well be a previously-overlooked general mechanism for gene regulation with implications for disease causation and possible therapies in the future."

Journal Reference:
Justin J.-L. Wong, William Ritchie, Olivia A. Ebner, Matthias Selbach, Jason W.H. Wong, Yizhou Huang, Dadi Gao, Natalia Pinello, Maria Gonzalez, Kinsha Baidya, Annora Thoeng, Teh-Liane Khoo, Charles G. Bailey, Jeff Holst, John E.J. Rasko. Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation. Cell, 2013; 154 (3): 583 DOI: 10.1016/j.cell.2013.06.052

 

[Swa]

Genetic compilers. We have come a long way.

 

[Techne]

Origins of Genomic 'Dark Matter' Discovered

Sep. 18, 2013 — A duo of scientists at Penn State University has achieved a major milestone in understanding how genomic "dark matter" originates. This "dark matter" -- called non-coding RNA -- does not contain the blueprint for making proteins and yet it comprises more than 95 percent of the human genome. The researchers have discovered that essentially all coding and non-coding RNA originates at the same types of locations along the human genome. The team's findings eventually may help to pinpoint exactly where complex-disease traits reside, since the genetic origins of many diseases reside outside of the coding region of the genome.

​

A duo of scientists at Penn State University has achieved a major milestone in understanding genomic "dark matter" -- called non-coding RNA. This "dark matter" is difficult to detect and no one knows exactly what it is doing or why it is there in our genome, but scientists suspect it may be the source of inherited diseases. This research achievement may help to pinpoint exactly where complex-disease traits reside in the human genome. This illustration shows, in the upper left corner, a chromosome -- a densely compressed package containing one long, continuous strand of DNA. The DNA is pervasively transcribed into RNA, but only a very small fraction of the RNA has the instructions (or codes) for making proteins. The green circles in this illustration represent places along the strand of DNA where transcription originates. New research led by B. Franklin Pugh of Penn State University shows that essentially all RNA, whether or not it codes for proteins, originates at the same types of locations along the strand of DNA. The findings eventually may help to pinpoint exactly where complex-disease traits reside, since the genetic origins of many diseases reside outside of the coding region of the genome. (Credit: National Institutes of Health and B. Franklin Pugh, Penn State University)​

The research, which will be published as an Advance Online Publication in the journal Nature on 18 September 2013, was performed by B. Franklin Pugh, holder of the Willaman chair in Molecular Biology at Penn State, and postdoctoral scholar Bryan Venters, who now holds a faculty position at Vanderbilt University.

In their research, Pugh and Venters set out to identify the precise location of the beginnings of transcription -- the first step in the expression of genes into proteins. "During transcription, DNA is copied into RNA -- the single-stranded genetic material that is thought to have preceded the appearance of DNA on Earth -- by an enzyme called RNA polymerase and, after several more steps, genes are encoded and proteins eventually are produced," Pugh explained. He added that, in their quest to learn just where transcription begins, other scientists had looked directly at RNA. However, Pugh and Venters instead determined where along human chromosomes the proteins that initiate transcription of the non-coding RNA were located.

"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"

Pugh added that the implications of this research could represent one step towards solving the problem of "missing heritability" -- a concept that describes how most traits, including many diseases, cannot be accounted for by individual genes and seem to have their origins in regions of the genome that do not code for proteins. "It is difficult to pin down the source of a disease when the mutation maps to a region of the genome with no known function," Pugh said. "However, if such regions produce RNA then we are one step closer to understanding that disease."

Journal Reference:
Bryan J. Venters, B. Franklin Pugh. Genomic organization of human transcription initiation complexes. Nature, 2013; DOI: 10.1038/nature12535

 

[Techne]

No longer junk: Role of long noncoding RNAs in autism risk

Summary:
RNA acts as the intermediary between genes and proteins, but the function of pieces of RNA that do not code for protein has, historically, been less clear. Researchers have ignored these noncoding RNAs until recently for not complying with the central dogma of biology -- that a straight line runs from gene to RNA (transcription) to protein (translation). However, noncoding RNAs are emerging as important regulators of diverse cellular processes with implications for numerous human disorders.

In the past decade, long noncoding RNAs (lncRNAs), which extend longer than 200 nucleotides, have emerged as additional important players in the control of gene expression. They fine-tune the expression of numerous genes and direct the activity of complex regulatory pathways, often in a cell- and developmental-stage-specific manner.​

RNA acts as the intermediary between genes and proteins, but the function of pieces of RNA that do not code for protein has, historically, been less clear. Researchers have ignored these noncoding RNAs until recently for not complying with the central dogma of biology -- that a straight line runs from gene to RNA (transcription) to protein (translation). However, noncoding RNAs are emerging as important regulators of diverse cellular processes with implications for numerous human disorders.



Extensive research has already examined the function of microRNAs, a category of small evolutionarily conserved noncoding RNAs about 22 to 24 nucleotides in length that target protein-coding genes in a sequence-specific manner. A plethora of microRNAs are important for brain function and neuropsychiatric diseases, including autism1.
In the past decade, long noncoding RNAs (lncRNAs), which extend longer than 200 nucleotides, have emerged as additional important players in the control of gene expression. They fine-tune the expression of numerous genes and direct the activity of complex regulatory pathways, often in a cell- and developmental-stage-specific manner.
They are found in many places in the genome: within genes, near gene regulatory regions or by themselves (intergenic noncoding RNAs). lncRNAs may overlap with the genetic code for a protein or be expressed in the opposite, or antisense, direction.

In addition to the diversity in their biogenesis, lncRNAs exhibit an impressive versatility of molecular functions. These range from passive influence on the transcription of nearby genes to limiting expression to a paternal or maternal chromosome, a process called imprinting, and inactivating one copy of the X chromosome.
They also interact with chromatin-modifying complexes, which regulate gene expression by changing the packaging of DNA, and with transcription factors that directly regulate gene expression. They may influence RNA splicing, stability and localization and play a role in the translation of RNA to protein and in protein activation. Finally, they may 'sponge' up certain microRNAs, thus blocking their function.

Molecular multitaskers:
The ability of lncRNAs to engage in such molecular multitasking may allow them to link multiple risk factors for genetic disorders into functional networks. This makes them attractive candidates for autism spectrum disorders, which are characterized either by interactions of multiple genes or by disruptions in a single gene that influences numerous molecular pathways.
Whether whole-genome DNA sequencing data will reveal strong genetic links with lncRNAs, as it has for microRNAs, is not yet clear. One thing, though, remains certain: We can no longer overlook such a substantial and active chunk of the transcriptome and characterize it as 'junk' or 'transcriptional noise' if we hope to fully understand complex disorders such as autism.
In the past few years, studies have found alterations in lncRNAs in brains from people with autism, suggesting that they contribute to autism risk. For example, MSNP1AS, a lncRNA transcribed from a region of chromosome 5 that carries an autism-associated variant, is elevated in the cortex of people with autism who also carry the disease-related variant. MSNP1AS may regulate moesin, a gene important for the structure of neurons' signal-receiving branches, or dendrites, and immune system activation.
Last year, a carefully conducted study identified numerous lncRNAs that are robustly dysregulated in autism postmortem brain samples. Impressively, some disease-altered lncRNAs are found near important autism-linked genes such as BDNF and SHANK2.
Another lncRNA with potential implications for autism is LOC389023, which regulates DPP10, a gene linked to autism and other neurodevelopmental disorders. DPP10 controls the structure and function of neuronal junctions, or synapses, via its effects on potassium ion channels3.
Last year, researchers used a similar approach to study the expression of lncRNAs in a mouse model of Rett syndrome. One lncRNA (AK081227) that is expressed at abnormal levels in these mice controls the expression of its host protein-coding gene, the gamma-aminobutyric acid receptor subunit Rho 2 (GABRR2), which has also been linked to autism.
Additional reports have linked other lncRNAs to autism, such those that travel antisense to the FMR1 and UBE3A genes. Mutations in these genes underlie fragile X syndrome and Angelman syndrome, respectively. Other studies have also uncovered a subset of lncRNAs expressed from the autism-linked PTCHD1 gene and the 7q31 chromosomal region.
In addition, the lncRNA ZNF127AS has altered expression in the brains of people with Prader-Willi syndrome. On a similar note, a cluster of small nucleolar RNAs -- which despite their name are a category of lncRNAs -- are encoded by the paternally inherited microdeletion at 15q11.2 that is also linked to Prader-Willi syndrome.

Brain builders:
Previous work has identified a subset of lncRNAs that are important for regulating the birth of new neurons, or neurogenesis, and the process by which synapses adapt to experience, called synaptic plasticity.
Of particular importance is the finding that the intergenic noncoding RNA MALAT1, one of the most highly expressed lncRNAs in the brain, can regulate the formation of new synapses, or synaptogenesis. It does this by associating inside the nucleus with multiple RNA splicing factors and influencing the expression of autism-linked genes, such as NLGN1.

Intriguingly, there are several other links between MALAT1 and autism-associated factors. For example, beta-catenin -- an important component of the WNT signaling pathway that has been linked to multiple neuropsychiatric disorders -- activates MALAT1 transcription. CREB, another transcription factor known for its role in activity-dependent gene expression, also binds to MALAT1. Notably, CREB may control MALAT1 transcription following exposure to the peptide hormone oxytocin, which has also been linked to autism.

MALAT1 and another lncRNA, BDNFOS, which has the antisense, or opposite, code to that of the autism-linked BDNF gene, are expressed in conjunction with neuronal activity. On the other hand, GOMAFU, a lncRNA whose levels are dampened in postmortem brains from people with schizophrenia, is significantly suppressed following the activation of mouse cortical neurons.

Other lncRNAs run antisense to important synaptic plasticity-related genes, such as NRGN, CAMK2N1 and CAMKK1. lncRNAs are also associated with genes linked to changes in the synapse that occur after exposure to cocaine. Interestingly, a novel subset of lncRNAs are expressed from the regulatory elements of genes, such as c-FOS and ARC, that regulate gene transcription in response to neuronal activity.

Adding to their important role in brain plasticity, lncRNAs are highly expressed during prenatal neurogenesis and are important for maintaining and differentiating the precursors to neurons: neural stem cells and neuronal progenitors. Of particular interest is the lncRNA EVF2, which runs antisense to the regulator gene DLX5,6 and plays a crucial role in the birth of neurons that dampen brain activity. This adds another layer to the role of lncRNAs in cell-type-specific neuronal functions.

Despite these many threads, much more work is needed to determine the exact mechanisms of action and the physiological significance of lncRNAs for autism and other neurodevelopmental disorders.

Reference.

 

[Techne]

Regulation of metabolism by long, non-coding RNAs

Abstract:
Our understanding of genomic regulation was revolutionized by the discovery that the genome is pervasively transcribed, giving rise to thousands of mostly uncharacterized non-coding ribonucleic acids (ncRNAs). Long, ncRNAs (lncRNAs) have thus emerged as a novel class of functional RNAs that impinge on gene regulation by a broad spectrum of mechanisms such as the recruitment of epigenetic modifier proteins, control of mRNA decay and DNA sequestration of transcription factors. We review those lncRNAs that are implicated in differentiation and homeostasis of metabolic tissues and present novel concepts on how lncRNAs might act on energy and glucose homeostasis. Finally, the control of circadian rhythm by lncRNAs is an emerging principles of lncRNA-mediated gene regulation.