Literature DB >> 31383947

Ancient animal genome architecture reflects cell type identities.

Bob Zimmermann1, Nicolas S M Robert1,2, Ulrich Technau1, Oleg Simakov3.   

Abstract

The level of conservation of ancient metazoan gene order (synteny) is remarkable. Despite this, the functionality of the vast majority of such regions in metazoan genomes remains elusive. Utilizing recently published single-cell expression data from several anciently diverging metazoan species, we reveal the level of correspondence between cell types and genomic synteny, identifying genomic regions conferring ancient cell type identity.

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Year:  2019        PMID： 31383947     DOI： 10.1038/s41559-019-0946-7

Source DB:  PubMed          Journal:  Nat Ecol Evol        ISSN： 2397-334X            Impact factor:   19.100


  19 in total

1.  Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq.

Authors:  Arnau Sebé-Pedrós; Baptiste Saudemont; Elad Chomsky; Flora Plessier; Marie-Pierre Mailhé; Justine Renno; Yann Loe-Mie; Aviezer Lifshitz; Zohar Mukamel; Sandrine Schmutz; Sophie Novault; Patrick R H Steinmetz; François Spitz; Amos Tanay; Heather Marlow
Journal:  Cell       Date:  2018-05-31       Impact factor: 41.582

2.  Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.

Authors:  Mireya Plass; Jordi Solana; F Alexander Wolf; Salah Ayoub; Aristotelis Misios; Petar Glažar; Benedikt Obermayer; Fabian J Theis; Christine Kocks; Nikolaus Rajewsky
Journal:  Science       Date:  2018-04-19       Impact factor: 47.728

3.  Genomic regulatory blocks underlie extensive microsynteny conservation in insects.

Authors:  Pär G Engström; Shannan J Ho Sui; Oyvind Drivenes; Thomas S Becker; Boris Lenhard
Journal:  Genome Res       Date:  2007-11-07       Impact factor: 9.043

4.  Early metazoan cell type diversity and the evolution of multicellular gene regulation.

Authors:  Arnau Sebé-Pedrós; Elad Chomsky; Kevin Pang; David Lara-Astiaso; Federico Gaiti; Zohar Mukamel; Ido Amit; Andreas Hejnol; Bernard M Degnan; Amos Tanay
Journal:  Nat Ecol Evol       Date:  2018-06-25       Impact factor: 15.460

5.  Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.

Authors:  Manuel Irimia; Juan J Tena; Maria S Alexis; Ana Fernandez-Miñan; Ignacio Maeso; Ozren Bogdanovic; Elisa de la Calle-Mustienes; Scott W Roy; José L Gómez-Skarmeta; Hunter B Fraser
Journal:  Genome Res       Date:  2012-06-21       Impact factor: 9.043

6.  Bayesian approach to single-cell differential expression analysis.

Authors:  Peter V Kharchenko; Lev Silberstein; David T Scadden
Journal:  Nat Methods       Date:  2014-05-18       Impact factor: 28.547

7.  Integrated single cell data analysis reveals cell specific networks and novel coactivation markers.

Authors:  Shila Ghazanfar; Adam J Bisogni; John T Ormerod; David M Lin; Jean Y H Yang
Journal:  BMC Syst Biol       Date:  2016-12-05

8.  JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Authors:  Aziz Khan; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime A Castro-Mondragon; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R Kulkarni; Ge Tan; Damir Baranasic; David J Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoît Ballester; Wyeth W Wasserman; François Parcy; Anthony Mathelier
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

9.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.

Authors:  David M Emms; Steven Kelly
Journal:  Genome Biol       Date:  2015-08-06       Impact factor: 13.583

10.  Insights into bilaterian evolution from three spiralian genomes.

Authors:  Oleg Simakov; Ferdinand Marletaz; Sung-Jin Cho; Eric Edsinger-Gonzales; Paul Havlak; Uffe Hellsten; Dian-Han Kuo; Tomas Larsson; Jie Lv; Detlev Arendt; Robert Savage; Kazutoyo Osoegawa; Pieter de Jong; Jane Grimwood; Jarrod A Chapman; Harris Shapiro; Andrea Aerts; Robert P Otillar; Astrid Y Terry; Jeffrey L Boore; Igor V Grigoriev; David R Lindberg; Elaine C Seaver; David A Weisblat; Nicholas H Putnam; Daniel S Rokhsar
Journal:  Nature       Date:  2012-12-19       Impact factor: 49.962
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  5 in total

1.  CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes.

Authors:  Heiner Kuhl; Ling Li; Sven Wuertz; Matthias Stöck; Xu-Fang Liang; Christophe Klopp
Journal:  Gigascience       Date:  2020-05-01       Impact factor: 6.524

2.  Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?

Authors:  Lukáš Kratochvíl; Tony Gamble; Michail Rovatsos
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2021-07-26       Impact factor: 6.671

3.  Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions.

Authors:  Nicolas S M Robert; Fatih Sarigol; Bob Zimmermann; Axel Meyer; Christian R Voolstra; Oleg Simakov
Journal:  BMC Genomics       Date:  2022-02-17       Impact factor: 3.969

4.  Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization.

Authors:  Hannah Schmidbaur; Akane Kawaguchi; Tereza Clarence; Xiao Fu; Oi Pui Hoang; Bob Zimmermann; Elena A Ritschard; Anton Weissenbacher; Jamie S Foster; Spencer V Nyholm; Paul A Bates; Caroline B Albertin; Elly Tanaka; Oleg Simakov
Journal:  Nat Commun       Date:  2022-04-21       Impact factor: 17.694

5.  Deeply conserved synteny and the evolution of metazoan chromosomes.

Authors:  Oleg Simakov; Jessen Bredeson; Kodiak Berkoff; Ferdinand Marletaz; Therese Mitros; Darrin T Schultz; Brendan L O'Connell; Paul Dear; Daniel E Martinez; Robert E Steele; Richard E Green; Charles N David; Daniel S Rokhsar
Journal:  Sci Adv       Date:  2022-02-02       Impact factor: 14.136
  5 in total

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