Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

Genome Research
Michael S WernerRalf J Sommer

Abstract

Species-specific, new, or "orphan" genes account for 10%-30% of eukaryotic genomes. Although initially considered to have limited function, an increasing number of orphan genes have been shown to provide important phenotypic innovation. How new genes acquire regulatory sequences for proper temporal and spatial expression is unknown. Orphan gene regulation may rely in part on origination in open chromatin adjacent to preexisting promoters, although this has not yet been assessed by genome-wide analysis of chromatin states. Here, we combine taxon-rich nematode phylogenies with Iso-Seq, RNA-seq, ChIP-seq, and ATAC-seq to identify the gene structure and epigenetic signature of orphan genes in the satellite model nematode Pristionchus pacificus Consistent with previous findings, we find young genes are shorter, contain fewer exons, and are on average less strongly expressed than older genes. However, the subset of orphan genes that are expressed exhibit distinct chromatin states from similarly expressed conserved genes. Orphan gene transcription is determined by a lack of repressive histone modifications, confirming long-held hypotheses that open chromatin is important for new gene formation. Yet orphan gene start sites more closely...Continue Reading

References

Nov 10, 1988·Biochimica Et Biophysica Acta·B Wasylyk
Dec 16, 1998·Science·UNKNOWN C. elegans Sequencing Consortium
Aug 24, 1999·Nucleic Acids Research·M Deutsch, M Long
Mar 23, 2002·Cell·Nick J ProudfootMichael J Dye
Aug 18, 2004·Nature Genetics·Justin M O'SullivanNick J Proudfoot
Sep 21, 2004·Nature Genetics·Fabien Burki, Henrik Kaessmann
Nov 16, 2004·Nature Genetics·John ParkinsonMark L Blaxter
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Feb 24, 2006·Proceedings of the National Academy of Sciences of the United States of America·Nicolas VinckenboschHenrik Kaessmann
Oct 16, 2007·Molecular Cell·Patrick Trojer, Danny Reinberg
Dec 1, 2007·WormBook : the Online Review of C. Elegans Biology·Avril Coghlan
Jun 13, 2008·PLoS Biology·Lia RossoHenrik Kaessmann
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 26, 2008·Nature Reviews. Genetics·Henrik KaessmannManyuan Long
Jan 22, 2009·The Plant Journal : for Cell and Molecular Biology·Ling LiEve Syrkin Wurtele
Sep 1, 2009·Trends in Genetics : TIG·Konstantin KhalturinThomas C G Bosch
Nov 26, 2009·Genes & Development·Jean-Philippe LainéMichael Hampsey
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Jul 24, 2010·Genome Research·Henrik Kaessmann
Dec 15, 2010·PLoS Genetics·Joseph K PickrellJonathan K Pritchard
Dec 17, 2010·Nature·Alvaro Rada-IglesiasJoanna Wysocka
Dec 18, 2010·Science·Sidi ChenManyuan Long
Dec 24, 2010·Genome Research·Tao LiuX Shirley Liu
Dec 24, 2010·Genome Research·Arun K RamaniAndrew G Fraser
Dec 29, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kerry A Geiler-SamerotteD Allan Drummond
Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein
Jul 5, 2011·Annual Review of Genetics·Ralf J Sommer, Adrian Streit
Sep 1, 2011·Nature Reviews. Genetics·Diethard Tautz, Tomislav Domazet-Lošo
Sep 8, 2011·Genes & Development·Nick J Proudfoot
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 7, 2012·Molecular Systems Biology·Vladislav GrishkevichItai Yanai
Jun 23, 2012·Nature·Anne-Ruxandra CarvunisMarc Vidal

❮ Previous
Next ❯

Citations

May 24, 2019·PLoS Genetics·Stephen Branden Van Oss, Anne-Ruxandra Carvunis
May 16, 2019·G3 : Genes - Genomes - Genetics·Neel Prabh, Christian Rödelsperger
Dec 18, 2019·Molecular Biology and Evolution·Paco Majic, Joshua L Payne
May 3, 2020·Molecular Biology and Evolution·Rosa FernándezDenis Tagu
Jul 6, 2019·Frontiers in Physiology·Stuart A Newman
Oct 2, 2019·Journal of Developmental Biology·Emily A Baker, Alison Woollard
Aug 14, 2020·Molecular Biology and Evolution·Christian RödelspergerHendrik C Korswagen
Jan 29, 2021·Nature Communications·William R BlevinsM Mar Albà
Jul 1, 2019·G3 : Genes - Genomes - Genetics·Neel Prabh, Christian Rödelsperger
Aug 12, 2021·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Maša LenuzziRalf J Sommer
Sep 7, 2021·Frontiers in Genetics·Jing LiEve Syrkin Wurtele

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.