Spatial expression of transcription factors in Drosophila embryonic organ development

Genome Biology
Ann S HammondsSusan Celniker

Abstract

Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in developme...Continue Reading

References

Oct 30, 1980·Nature·C Nüsslein-Volhard, E Wieschaus
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SchultzC P Ponting
Dec 11, 1999·Nature·C Niehrs, N Pollet
Dec 19, 2003·Nucleic Acids Research·Axel ViselGregor Eichele
Mar 3, 2004·Developmental Dynamics : an Official Publication of the American Association of Anatomists·George W BellParker B Antin
May 27, 2004·Gene Expression Patterns : GEP·Raul HerranzRoberto Marco
Feb 1, 2005·Journal of Anatomy·Jonathan B L Bard
Mar 15, 2005·Mechanisms of Development·Nicolas PolletChristof Niehrs
Dec 31, 2005·Nucleic Acids Research·Nicolas HuloChristian J A Sigrist
Dec 31, 2005·Nucleic Acids Research·Sarah K Kummerfeld, Sarah A Teichmann
Dec 8, 2006·Nature·Ed S LeinAllan R Jones
Jul 25, 2007·Genome Biology·Pavel TomancakGerald M Rubin
Sep 26, 2007·Molecular and Cellular Biology·Fawzia A AtchaMarian L Waterman
Oct 6, 2007·Nucleic Acids Research·Yannick HaudryThorsten Henrich
Jan 22, 2008·Bioinformatics·Saraswathi AbhimanL Aravind
Apr 15, 2008·Developmental Biology·Ming-Ching WongMary K Baylies
Jul 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Barret D PfeifferGerald M Rubin
Mar 17, 2009·Genome Biology·Debra L FultonRob Sladek
Nov 26, 2009·Nucleic Acids Research·Jun ZhaoDavid Shotton
Jan 21, 2010·Molecular Systems Biology·Erwin FriseSusan E Celniker
Apr 14, 2010·Genome Biology·Boris Adryan, Sarah A Teichmann
Dec 24, 2010·Science·UNKNOWN modENCODE ConsortiumManolis Kellis
Dec 24, 2010·Nature·Brenton R GraveleySusan E Celniker
Mar 25, 2011·Nature·Nicolas NègreKevin P White
Apr 29, 2011·PLoS Biology·UNKNOWN ENCODE Project Consortium
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
Nov 1, 2011·Nature Methods·Korneel HensBart Deplancke
Dec 1, 2011·Nucleic Acids Research·Peter McQuiltonUNKNOWN FlyBase Consortium
Aug 15, 2012·Genome Biology·UNKNOWN Mouse ENCODE ConsortiumLeslie B Adams

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Citations

Sep 23, 2014·Cell Reports·David Y RheeSpyros Artavanis-Tsakonas
Apr 14, 2015·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Julien RouxMarc Robinson-Rechavi
Jul 19, 2015·Developmental Biology·Irepan Salvador-Martínez, Isaac Salazar-Ciudad
Apr 14, 2016·Proceedings of the National Academy of Sciences of the United States of America·Siqi WuErwin Frise
Mar 31, 2015·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Naureen JaveedKevin A Edwards
Apr 10, 2015·Wiley Interdisciplinary Reviews. Developmental Biology·Douglas W Allan, Stefan Thor
Aug 16, 2016·Journal of Theoretical Biology·M Mocarlo ZhengQi Ouyang
Mar 15, 2018·Nature·Darren A CusanovichEileen E M Furlong
Apr 17, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chelsea M LawhornOlav Rueppell
Dec 2, 2017·Epigenetics & Chromatin·Olga V PosukhStepan N Belyakin
Nov 4, 2016·G3 : Genes - Genomes - Genetics·Porfirio Quintero-Cadena, Paul W Sternberg
Nov 4, 2016·EMBO Reports·Tomoko AsaokaFumiyo Ikeda
Dec 20, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·A K M Firoj MahmudSoumyadeep Nandi
Mar 13, 2020·The EMBO Journal·Pierre B CattenozAngela Giangrande
Aug 23, 2018·PLoS Genetics·Ignacio Monedero CobetaJonathan Benito-Sipos
Sep 19, 2017·PLoS Computational Biology·Paul VilloutreixStanislav Y Shvartsman
Aug 15, 2014·PloS One·Phan Nguyen Thuy AnEiichiro Fukusaki
Nov 25, 2016·Journal of Biomedical Science·P Githure M'Angale, Brian E Staveley
Jul 16, 2019·Frontiers in Zoology·Virginia PanaraRalf Janssen
Sep 7, 2014·G3 : Genes - Genomes - Genetics·Thomas W R HarropPhilip Batterham
Sep 4, 2020·Genetics·Stephen Small, David N Arnosti
Jul 12, 2017·G3 : Genes - Genomes - Genetics·Alexander J CarrilloKatherine A Borkovich
Nov 25, 2018·International Journal of Molecular Sciences·Zhaojiang GuoYoujun Zhang
Jan 17, 2016·G3 : Genes - Genomes - Genetics·Marcus StoiberPeter Cherbas
Jun 8, 2017·Frontiers in Genetics·Lily Li, Zeba Wunderlich
Aug 8, 2018·Genetics·Arzu Öztürk-ÇolakSofia J Araújo

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Methods Mentioned

BETA
RNA-seq
PCA

Software Mentioned

InterProScan
SOM
4DXpress
Matlab somtoolbox
modENCODE
Prosite
SalGl
Ectoderm
Muscle
VisualPr

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