A distal enhancer and an ultraconserved exon are derived from a novel retroposon

Nature
Gill BejeranoDavid Haussler

Abstract

Hundreds of highly conserved distal cis-regulatory elements have been characterized so far in vertebrate genomes. Many thousands more are predicted on the basis of comparative genomics. However, in stark contrast to the genes that they regulate, in invertebrates virtually none of these regions can be traced by using sequence similarity, leaving their evolutionary origins obscure. Here we show that a class of conserved, primarily non-coding regions in tetrapods originated from a previously unknown short interspersed repetitive element (SINE) retroposon family that was active in the Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in the Silurian period at least 410 million years ago (ref. 4), and seems to be recently active in the 'living fossil' Indonesian coelacanth, Latimeria menadoensis. Using a mouse enhancer assay we show that one copy, 0.5 million bases from the neuro-developmental gene ISL1, is an enhancer that recapitulates multiple aspects of Isl1 expression patterns. Several other copies represent new, possibly regulatory, alternatively spliced exons in the middle of pre-existing Sarcopterygian genes. One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identi...Continue Reading

References

Jun 1, 1971·The Quarterly Review of Biology·R J Britten, E H Davidson
Jan 12, 1999·Neuron·D A FeldheimJ G Flanagan
Apr 25, 2000·Journal of Molecular Biology·J H KimS K Jang
May 11, 2002·RNA·Aleksandr V Makeyev, Stephen A Liebhaber
Jun 18, 2002·Current Opinion in Cell Biology·Alan M Weiner
Oct 9, 2002·Genome Research·Prescott L Deininger, Mark A Batzer
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Dec 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P LewisSteven E Brenner
May 24, 2003·Science·Wojciech Makalowski
Sep 16, 2003·Molecular and Cellular Biology·Shelly A Waggoner, Stephen A Liebhaber
Nov 13, 2003·Molecular and Cellular Biology·Alexander N Chkheidze, Stephen A Liebhaber
Feb 26, 2004·Journal of Experimental Zoology. Part A, Comparative Experimental Biology·Joshua DankeChris T Amemiya
Mar 16, 2004·Science·Haig H Kazazian
May 8, 2004·Science·Gill BejeranoDavid Haussler
Jul 21, 2004·Bioinformatics·Gill BejeranoMathieu Blanchette
Jun 1, 1950·Proceedings of the National Academy of Sciences of the United States of America·B McCLINTOCK
May 12, 2005·Genomics·Francis PoulinLen A Pennacchio
Jun 21, 2005·Biochemical and Biophysical Research Communications·Yonghe LiGuojun Bu
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler

❮ Previous
Next ❯

Citations

Oct 8, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Paulo P Amaral, John S Mattick
Nov 19, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Yoshiyuki SakurabaYoichi Gondo
Oct 1, 2008·Molecular Genetics and Genomics : MGG·Xianran LiChuanqing Sun
Feb 23, 2008·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Astrid BöhneJean-Nicolas Volff
Dec 24, 2010·Nature·Brenton R GraveleySusan E Celniker
Apr 20, 2013·Nature·Chris T AmemiyaKerstin Lindblad-Toh
May 4, 2010·Nature Biotechnology·Cory Y McLeanGill Bejerano
Nov 3, 2011·Nature Communications·Shai CarmiErez Y Levanon
Jun 27, 2013·Nature Genetics·Zohar Mukamel, Amos Tanay
Jun 29, 2010·Nature Genetics·Len A Pennacchio, Axel Visel
Mar 28, 2008·Nature Reviews. Genetics·Cédric Feschotte
Sep 19, 2009·Nature Reviews. Genetics·Richard Cordaux, Mark A Batzer
Apr 21, 2009·Nature Structural & Molecular Biology·Ming C HammondRonald R Breaker
Sep 19, 2009·Molecular BioSystems·Jianrong WangI King Jordan
Mar 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·Takeshi SasakiNorihiro Okada
Feb 9, 2010·Proceedings of the National Academy of Sciences of the United States of America·Chris T AmemiyaPeter F Stadler
Dec 29, 2010·Proceedings of the National Academy of Sciences of the United States of America·Chiara BraconiTushar Patel
Apr 30, 2011·Proceedings of the National Academy of Sciences of the United States of America·Alejandro P Rooney
Aug 31, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lucía F FranchiniMarcelo Rubinstein
Apr 13, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jeff RenekerDmitry Korkin
Jun 7, 2008·Journal of Biomolecular Structure & Dynamics·W-X Zheng, C-T Zhang
Aug 5, 2009·Briefings in Functional Genomics & Proteomics·Senda Jiménez-DelgadoJordi Garcia-Fernàndez
Mar 10, 2012·Briefings in Functional Genomics·Laura Beaster-Jones
Mar 25, 2010·The Journal of Heredity·Craig B LoweDavid Haussler
Jan 18, 2008·Molecular Biology and Evolution·J Michael MacphersonDmitri A Petrov
Apr 9, 2008·Molecular Biology and Evolution·Kenji K Kojima, Minoru Kanehisa
May 22, 2008·Molecular Biology and Evolution·Ivan Ovcharenko
Nov 6, 2008·Molecular Biology and Evolution·Chongjian ChenDaniel Gautheret
Mar 25, 2010·Molecular Biology and Evolution·Maria WarneforsAdam Eyre-Walker
Jan 29, 2011·Molecular Biology and Evolution·Vladimir PaarInes Vlahović
Apr 23, 2011·Molecular Biology and Evolution·Oliver Piskurek, Daniel J Jackson
Nov 3, 2011·Molecular Biology and Evolution·Jeramiah J SmithChris T Amemiya
Mar 15, 2013·Molecular Biology and Evolution·Flávio S J de SouzaMarcelo Rubinstein
Oct 24, 2008·Nucleic Acids Research·Cristian TaccioliCarlo Maria Croce
Dec 4, 2012·Nucleic Acids Research·Nikita S Vassetzky, Dmitri A Kramerov
Nov 13, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gretel B KammLucía F Franchini
Nov 13, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Nathan HarmstonBoris Lenhard

❮ Previous
Next ❯

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Michael KamalEric S Lander
Proceedings of the National Academy of Sciences of the United States of America
Takeshi SasakiNorihiro Okada
© 2022 Meta ULC. All rights reserved