Literature DB >> 18176564

Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

Axel Visel1, Shyam Prabhakar, Jennifer A Akiyama, Malak Shoukry, Keith D Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward M Rubin, Len A Pennacchio.   

Abstract

Extended perfect human-rodent sequence identity of at least 200 base pairs (ultraconservation) is potentially indicative of evolutionary or functional uniqueness. We used a transgenic mouse assay to compare the embryonic enhancer activity of 231 noncoding ultraconserved human genome regions with that of 206 extremely conserved regions lacking ultraconservation. Developmental enhancers were equally prevalent in both populations, suggesting instead that ultraconservation identifies a small, functionally indistinct subset of similarly constrained cis-regulatory elements.

Entities:  

Mesh：

Year:  2008        PMID： 18176564      PMCID： PMC2647775          DOI： 10.1038/ng.2007.55

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


  15 in total

1.  Initial sequencing and comparative analysis of the mouse genome.

Authors:  Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

2.  A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.

Authors:  Elisa de la Calle-Mustienes; Cármen Gloria Feijóo; Miguel Manzanares; Juan J Tena; Elisa Rodríguez-Seguel; Annalisa Letizia; Miguel L Allende; José Luis Gómez-Skarmeta
Journal:  Genome Res       Date:  2005-07-15       Impact factor: 9.043

3.  Distribution and intensity of constraint in mammalian genomic sequence.

Authors:  Gregory M Cooper; Eric A Stone; George Asimenos; Eric D Green; Serafim Batzoglou; Arend Sidow
Journal:  Genome Res       Date:  2005-06-17       Impact factor: 9.043

4.  Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.

Authors:  R C Hardison; J Oeltjen; W Miller
Journal:  Genome Res       Date:  1997-10       Impact factor: 9.043

5.  Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.

Authors:  Adnan Derti; Frederick P Roth; George M Church; C-ting Wu
Journal:  Nat Genet       Date:  2006-09-24       Impact factor: 38.330

6.  In vivo characterization of a vertebrate ultraconserved enhancer.

Authors:  Francis Poulin; Marcelo A Nobrega; Ingrid Plajzer-Frick; Amy Holt; Veena Afzal; Edward M Rubin; Len A Pennacchio
Journal:  Genomics       Date:  2005-04-15       Impact factor: 5.736

7.  Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Authors:  Shyam Prabhakar; Francis Poulin; Malak Shoukry; Veena Afzal; Edward M Rubin; Olivier Couronne; Len A Pennacchio
Journal:  Genome Res       Date:  2006-06-12       Impact factor: 9.043

8.  Conserved noncoding sequences are selectively constrained and not mutation cold spots.

Authors:  Jared A Drake; Christine Bird; James Nemesh; Daryl J Thomas; Christopher Newton-Cheh; Alexandre Reymond; Laurent Excoffier; Homa Attar; Stylianos E Antonarakis; Emmanouil T Dermitzakis; Joel N Hirschhorn
Journal:  Nat Genet       Date:  2005-12-25       Impact factor: 38.330

9.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Authors:  Adam Siepel; Gill Bejerano; Jakob S Pedersen; Angie S Hinrichs; Minmei Hou; Kate Rosenbloom; Hiram Clawson; John Spieth; Ladeana W Hillier; Stephen Richards; George M Weinstock; Richard K Wilson; Richard A Gibbs; W James Kent; Webb Miller; David Haussler
Journal:  Genome Res       Date:  2005-07-15       Impact factor: 9.043

10.  In vivo enhancer analysis of human conserved non-coding sequences.

Authors:  Len A Pennacchio; Nadav Ahituv; Alan M Moses; Shyam Prabhakar; Marcelo A Nobrega; Malak Shoukry; Simon Minovitsky; Inna Dubchak; Amy Holt; Keith D Lewis; Ingrid Plajzer-Frick; Jennifer Akiyama; Sarah De Val; Veena Afzal; Brian L Black; Olivier Couronne; Michael B Eisen; Axel Visel; Edward M Rubin
Journal:  Nature       Date:  2006-11-05       Impact factor: 49.962
View more
  168 in total

1.  Transcriptional analysis of Gli3 mutants identifies Wnt target genes in the developing hippocampus.

Authors:  Kerstin Hasenpusch-Theil; Dario Magnani; Eleni-Maria Amaniti; Lin Han; Douglas Armstrong; Thomas Theil
Journal:  Cereb Cortex       Date:  2012-01-10       Impact factor: 5.357

Review 2.  The complex transcription regulatory landscape of our genome: control in three dimensions.

Authors:  Erik Splinter; Wouter de Laat
Journal:  EMBO J       Date:  2011-09-27       Impact factor: 11.598

3.  Enhancers of GnRH transcription embedded in an upstream gene use homeodomain proteins to specify hypothalamic expression.

Authors:  Anita K Iyer; Nichol L G Miller; Kathleen Yip; Brian H Tran; Pamela L Mellon
Journal:  Mol Endocrinol       Date:  2010-07-28

4.  Discover regulatory DNA elements using chromatin signatures and artificial neural network.

Authors:  Hiram A Firpi; Duygu Ucar; Kai Tan
Journal:  Bioinformatics       Date:  2010-05-07       Impact factor: 6.937

5.  Changes in selective effects over time facilitate turnover of enhancer sequences.

Authors:  Kevin Bullaughey
Journal:  Genetics       Date:  2010-11-23       Impact factor: 4.562

6.  ChIP-Seq identification of weakly conserved heart enhancers.

Authors:  Matthew J Blow; David J McCulley; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; James Bristow; Bing Ren; Brian L Black; Edward M Rubin; Axel Visel; Len A Pennacchio
Journal:  Nat Genet       Date:  2010-08-22       Impact factor: 38.330

7.  Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies.

Authors:  Jacob M Daane; Nicolas Rohner; Peter Konstantinidis; Sergej Djuranovic; Matthew P Harris
Journal:  Mol Biol Evol       Date:  2015-10-08       Impact factor: 16.240

8.  Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries.

Authors:  Charleston W K Chiang; Adnan Derti; Daniel Schwartz; Michael F Chou; Joel N Hirschhorn; C-Ting Wu
Journal:  Genetics       Date:  2008-10-28       Impact factor: 4.562

9.  A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers.

Authors:  Jemmie Cheng; Roy Blum; Christopher Bowman; Deqing Hu; Ali Shilatifard; Steven Shen; Brian D Dynlacht
Journal:  Mol Cell       Date:  2014-03-20       Impact factor: 17.970

10.  Microarray transfection analysis of conserved genomic sequences from three immediate early genes.

Authors:  Xiaomei Ren; Michael D Uhler
Journal:  Genomics       Date:  2008-11-08       Impact factor: 5.736
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.