Gene variant activity is surprisingly variable between tissues

Every gene in (almost) every cell of the body is present in two variants - so called alleles: one is deriving from the mother, the other one from the father. In most cases both alleles are active and transcribed by the cells into an RNA message. However, for a few genes, only one allele is expressed, while the other one is silenced. The decision whether the maternal or the paternal version is shut down occurs early in embryonic development - one reason, why for long it was thought that the pattern of active alleles is nearly homogeneous in the various tissues of the organism.

The new study, where CeMM PhD Student Daniel Andergassen is first author (now a PostDoc at Harvard University), uncovers a different picture. By performing the first comprehensive analysis of all active alleles in 23 different tissues and developmental stages of mice, the team of scientists revealed that each tissue showed a specific distribution of active alleles.

For their experiments, the researchers created hybrids of two genetically distinct mouse strains with a fully sequenced genome, allowing gene variants to be clearly assigned to the maternal or paternal allele. To facilitate the analysis, the team developed a user-friendly program called Allelome.PRO, that can easily be applied to similar datasets in mice and other species, a valuable tool for the community to investigate regulation of allele activity. By using this tool to analyze their data the scientists were able to catalogue active alleles in a comprehensive set of mouse tissues, or the mouse “Allelome”, and gain an insight into how this differential gene activity is regulated.

The scientists found that both genetic and epigenetic differences between the maternal and paternal allele contributed to the observed tissue-specific activity patterns. "Our results indicate that a large part of those patterns are induced by so-called 'enhancers'", co-senior author Quanah Hudson, now at IMBA (Institute for molecular Biotechnology of the Austrian Academy of Sciences) explains. "Enhancers are DNA regions that are often located at quite some distance from the observed allele, but nevertheless have a direct influence on their activity."

"This study reveals for the first time a comprehensive picture of all active alleles in different tissues - we have uncovered the first complete allelome" Florian Pauler, now at ISTA (Institute of Science and Technology Austria) and co-senior author, adds. "This is not only valuable to understand basic biological functions, but will also help investigating diseases that involve defective gene regulators."

Some of the genes that contributed to the tissue-specific activity patterns were located on the X chromosome and escaped so-called "X-chromosome inactivation", where one of the two X chromosomes in females gets shut down. Previously it was reported that around 3% of X-chromosomal genes in mice and 15% in humans escape inactivation. However, this study revealed that mice are more similar to humans than previously thought, with an average of around 10% of active genes escaping X-inactivation per tissue. By examining a broad range of organs the researchers showed that the number of escapers varies dramatically between tissues. Most strikingly, muscle showed a surprisingly high rate of escapers, with over 50% of active genes escaping X chromosome activation, a result that may be relevant to some diseases of the muscle.

Finally, the allelome offers a near complete picture of "genomic imprinting", the process that leads to epigenetic silencing of either the maternal or paternal allele that is initiated by an epigenetic mark placed in either the egg or sperm. Previously, it was reported that approximately 100 genes can be subject to imprinted silencing - but in many cases, the tissue specificity was not known. This study led to the discovery of 18 new imprinted genes, validated some known genes and resolved the disputed status of some others to provide a gold standard list of 93 imprinted genes in mouse. The scientists found that those new genes were located near to other imprinted genes, indicating that they were co-regulated. Interestingly, this study demonstrated that Igfr2, the first imprinted gene discovered by Denise Barlow in 1991, is surrounding by a large cluster of imprinted genes that extend over 10% of the chromosome, making it the largest co-regulated domain in the genome outside of the X chromosome. Fittingly, after her lab found the first imprinted gene, and discovered the first imprinted non-coding RNA shown to control imprinted silencing. Giulio Superti-Furga congratulates Denise Barlow who recently went into retirement to her great scientific achievements and for revealing the full picture of imprinted genes in the mouse.

Andergassen D, Dotter CP, Wenzel D, Sigl V, Bammer PC, Muckenhuber M, Mayer D, Kulinski TM, Theussl HC, Penninger JM, Bock C, Barlow DP, Pauler FM, Hudson QJ.
Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression.
Elife. 2017 Aug 14;6. pii: e25125. doi: 10.7554/eLife.25125.

Most Popular Now

Cannabis extract helps reset brain function in psy…

Research from King's College London has found that a single dose of the cannabis extract cannabidiol can help reduce brain function abnormalities seen in people with psyc...

New cancer treatment uses enzymes to boost immune …

Researchers at The University of Texas at Austin have developed a new approach to treating cancer using enzyme therapy. The enzyme, PEG-KYNase, does not directly kill can...

Bayer accelerates six new startups

Changing the experience of health: that's the focus of the six startups which the Bayer G4A team has included in the Accelerator program this year. The young companies fr...

Novartis receives European Commission approval of …

Novartis today announced that the European Commission (EC) has approved Kymriah® (tisagenlecleucel, formerly CTL019). The approved indications are for the treatment of pe...

Antioxidant reduces risk for second heart attack, …

Doctors have long known that in the months after a heart attack or stroke, patients are more likely to have another attack or stroke. Now, a paper in the Journal of the A...

Shire completes sale of oncology franchise

Shire plc (LSE: SHP, NASDAQ: SHPG) announces today that it has completed the sale of its Oncology franchise to Servier S.A.S. for $2.4 billion. The franchise includes the...

Novartis to divest the Sandoz US dermatology busin…

Novartis today announced it has agreed to sell selected portions of its Sandoz US portfolio, specifically the Sandoz US dermatology business and generic US oral solids po...

Tezepelumab granted Breakthrough Therapy Designati…

AstraZeneca and its partner Amgen Inc. (Amgen) today announced that the US Food and Drug Administration (FDA) has granted Breakthrough Therapy Designation for tezepelumab...

New tablet production facility in Ingelheim: Cente…

Boehringer Ingelheim held a groundbreaking ceremony for the construction of a new production facility for innovative drugs. This new Solids Launch facility will focus on ...

Pfizer terminates domagrozumab (PF-06252616) clini…

Pfizer Inc. (NYSE: PFE) announced that it is terminating two ongoing clinical studies evaluating domagrozumab (PF-06252616) for the treatment of Duchenne muscular dystrop...

Pfizer and Astellas amend clinical research protoc…

Pfizer Inc. (NYSE:PFE) and Astellas Pharma Inc. (TSE:4503, President and CEO: Kenji Yasukawa, Ph.D., "Astellas") announced amendments to the protocols for two registratio...

Study links widely-used drug azathioprine to skin …

A drug used to treat inflammatory bowel disease, arthritis and vasculitis as well as to prevent organ rejection in transplant patients has been identified as an important...