Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

BMC Genomics
Wilfried HaertyBhagwati P Gupta


Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human) we sought to identify orthologous TFs and characterized their patterns of evolution. We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set), approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types) and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two sp...Continue Reading


Jun 1, 1992·Computer Applications in the Biosciences : CABIOS·D T JonesJ M Thornton
Jan 1, 1996·Nucleic Acids Research·UNKNOWN Flybase Consortium
Jan 27, 1999·Bioinformatics·S R Eddy
Apr 10, 1999·Journal of Molecular Evolution·C Semple, K H Wolfe
Sep 30, 1999·Human Mutation·D R Lohmann
Dec 29, 1999·Human Mutation·A HamoshV A McKusick
Mar 29, 2001·Trends in Genetics : TIG·A E Sluder, C V Maina
Mar 30, 2001·Nature Genetics·P J WangD C Page
May 5, 2001·Cell·P W Sternberg
Jun 28, 2001·Physiological Reviews·A Aranda, A Pascual
Dec 18, 2001·Journal of Molecular Biology·M RemmE L Sonnhammer
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Apr 27, 2002·Science·Hunter B FraserMarcus W Feldman
May 7, 2002·Nature Genetics·Martin J LercherLaurence D Hurst
May 29, 2002·Molecular Biology and Evolution·Ziheng Yang, Rasmus Nielsen
Jul 27, 2002·Annual Review of Genomics and Human Genetics·Valerie Reinke, Kevin P White
Jul 30, 2002·Journal of Biology·Paul T Spellman, Gerald M Rubin
Dec 3, 2002·Nature Reviews. Genetics·Pat Simpson
Dec 13, 2002·Nature·Alexander M BoutanaevDmitry I Nurminsky
May 29, 2003·BMC Evolutionary Biology·Hunter B FraserAaron E Hirsh
Jun 5, 2003·Molecular Biology and Evolution·Gregory A WrayLaura A Romano
Jun 26, 2003·Nucleic Acids Research·Rasmus Wernersson, Anders Gorm Pedersen
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Nov 19, 2003·PLoS Biology·Lincoln D SteinRobert H Waterston
Nov 26, 2003·Journal of Evolutionary Biology·A D Cutter, B A Payseur
Jan 6, 2004·Science·Siming LiMarc Vidal
Feb 6, 2004·Nature Genetics·Xiaodong Wang, Helen M Chamberlin
Jun 25, 2004·Nucleic Acids Research·Burkhard Morgenstern
Jul 23, 2004·Current Biology : CB·Michael A MillerDavid Greenstein
Dec 3, 2004·Genes & Development·Joseph S Lipsick
Dec 21, 2004·Nucleic Acids Research·Kevin P O'BrienErik L L Sonnhammer
Dec 24, 2004·Molecular Biology and Evolution·Matthew W Hahn, Andrew D Kern
Jun 29, 2005·Journal of Molecular Evolution·Marc Robinson-RechaviAnn Sluder
Jul 8, 2005·PLoS Biology·Sean B Carroll

❮ Previous
Next ❯


Mar 18, 2009·Molecular Biology and Evolution·Asher D CutterRosalind L Murray
Jan 20, 2009·Nucleic Acids Research·Monica C SleumerSteven J M Jones
Feb 6, 2013·PloS One·Carmie Puckett RobinsonPaul W Sternberg
Jun 27, 2013·WormBook : the Online Review of C. Elegans Biology·Valerie ReinkePeter Okkema
May 13, 2010·Gene Expression Patterns : GEP·Jaroslav VohankaMarta Kostrouchová
Jan 20, 2010·Trends in Genetics : TIG·Matthew T Weirauch, Timothy R Hughes
Jul 2, 2014·Biochimica Et Biophysica Acta·Marta Kostrouchova, Zdenek Kostrouch
Apr 10, 2015·Wiley Interdisciplinary Reviews. Developmental Biology·Douglas W Allan, Stefan Thor
Jan 28, 2014·Cell Reports·Dominic GrünNikolaus Rajewsky
Mar 3, 2009·Biotechnology Journal·Rakesh TuliPravendra Nath
Aug 30, 2017·Proceedings of the National Academy of Sciences of the United States of America·Thomas J LampertPeter N Devreotes
Sep 10, 2020·ELife·Asher D Cutter, Joanna D Bundus
Nov 11, 2017·G3 : Genes - Genomes - Genetics·Virginia S MuirPhilip Anderson
Dec 7, 2019·Development·Taylor N Medwig-KinneyDavid Q Matus

❮ Previous
Next ❯

Software Mentioned

Wormbase genome browser

Related Concepts

Trending Feeds


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 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.


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.

Related Papers

WormBook : the Online Review of C. Elegans Biology
Adam Antebi
Nature Reviews. Genetics
Kirst King-Jones, Carl S Thummel
G3 : Genes - Genomes - Genetics
C. elegans Deletion Mutant Consortium
Critical Reviews in Eukaryotic Gene Expression
Marc R Van GilstAnn Sluder
© 2021 Meta ULC. All rights reserved