Corporate Banner
Satellite Banner
Scientific Communities
Become a Member | Sign in
Home>News>This Article

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

Published: Tuesday, November 27, 2012
Last Updated: Tuesday, November 27, 2012
Bookmark and Share
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."

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,800+ scientific posters on ePosters
  • More Than 4,000+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Imaging Software Could Speed Up Breast Cancer Diagnosis
Researchers use high speed optical microscopy of intact breast tissue specimens to analyze breast tissue.
Friday, August 21, 2015
Detecting and Identifying Candida Species in Blood Samples of Critically Ill Paediatric Patients
The study aimed to develop a multiplex nested PCR method to detect and identify seven Candida species in peripheral blood samples of critically ill paediatric patients.
Wednesday, August 27, 2014
Researchers Identify Urgent Need for Alzheimer's Disease Drug Development
Analysis of clinical trials published in the journal Alzheimer's Research & Therapy shows that the pipeline for potential treatments of AD is small and rate of success is limited.
Friday, July 04, 2014
Showing Your Age: Your DNA Doesn't Lie
Using thousands of tissue samples from open access datasets, a scientist has created a calculator which predicts the age of tissue using chemical changes to DNA.
Monday, October 21, 2013
Leukaemia Drug Could Help Treat Breast Cancer
A drug currently used to treat leukaemia might also help prevent breast cancer from spreading to other parts of the body.
Friday, August 23, 2013
No Place to Hide: Evolutionary Forensics
The rapid molecular evolution of hepatitis C virus (HCV) has been used to help incriminate the source of an outbreak in two Spanish hospitals in the late nineties.
Monday, July 29, 2013
A Possible Blood Test for Alzheimer’s Disease
A new blood test can be used to discriminate between people with Alzheimer's disease and healthy controls.
Monday, July 29, 2013
Is Enough Being Done to Make Drinking Water Safe?
Arsenic in water is threatening the lives of several hundred million people.
Monday, June 03, 2013
Women’s Immune Systems Remain Younger for Longer
The slower decline in a woman’s immune system may contribute to women living longer than men.
Wednesday, May 15, 2013
Testing the Water – Urine Test Identifies Babies at Most Risk of Necrotizing Enterocolitis
Abnormal gut bacteria in premature babies can be found days before the onset of necrotizing enterocolitis (NEC) finds new research in BioMed Central’s open access journal Microbiome.
Tuesday, April 16, 2013
Gene Signature Can Predict Who Will Survive Chemotherapy
An eight gene ‘signature’ can predict length of relapse-free survival after chemotherapy, finds new research in Biomed Central’s open access journal BMC Medicine.
Tuesday, April 16, 2013
The Tulip Tree Reveals Mitochondrial Genome of Ancestral Flowering Plant
The extraordinary level of conservation of the tulip tree mitochondrial genome has redefined our interpretation of evolution of the angiosperms (flowering plants).
Tuesday, April 16, 2013
Organizing Human Specimen Collections: Getting the Best out of Biobanks
The diversity of biobanks, collections of human specimens from a variety of sources, raises questions about the best way to manage and govern them.
Friday, March 22, 2013
Oxygen-Free Energy Designed to Fuel Brain Development Spurs on Growth of Cancer
The metabolic process which fuels the growth of many cancers has its origins in normal brain growth finds a new study published in BioMed Central's open access journal Cancer & Metabolism.
Wednesday, January 23, 2013
What Did Our Ancestors Look Like?
A new method of establishing hair and eye colour from modern forensic samples can also be used to identify details from ancient human remains.
Monday, January 14, 2013
Scientific News
High Throughput Mass Spectrometry-Based Screening Assay Trends
Dr John Comley provides an insight into HT MS-based screening with a focus on future user requirements and preferences.
Revolutionary Technologies Developed to Improve Outcomes for Lung Cancer Patients
Breath test to detect lung cancer brings oxygen directly to the wound.
NIH Supports New Studies to Find Alzheimer’s Biomarkers in Down Syndrome
Initiative will track dementia onset, progress in Down syndrome volunteers.
Dementia Linked to Deficient DNA Repair
Mutant forms of breast cancer factor 1 (BRCA1) are associated with breast and ovarian cancers but according to new findings, in the brain the normal BRCA1 gene product may also be linked to Alzheimer’s disease.
Using Drug-Susceptible Parasites to Fight Drug Resistance
Researchers at the University of Georgia have developed a model for evaluating a potential new strategy in the fight against drug-resistant diseases.
Boosting Breast Cancer Treatment
To more efficiently treat breast cancer, scientists have been researching molecules that selectively bind to cancer cells and deliver a substance that can kill the tumor cells, for several years.
New Gene Map Reveals Cancer’s Achilles’ Heel
Team of researchers switches off almost 18,000 genes
New Discovery Sheds Light on Disease Risk
Gaps between genes interact to influence the risk of acquiring disease.
How Cells ‘Climb’ to Build Fruit Fly Tracheas
Mipp1 protein helps cells sprout “fingers” for gripping.
Research Finding Could Lead to Targeted Therapies for IBD
Findings published online in Cell Reports.
Scroll Up
Scroll Down
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos