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

Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X, Artieri, Carlo, Khezri, Navid, Singh, Rama S. and Gupta, Bhagwati P. (2008) Comparative analysis of function and interaction of transcription factors in nematodes:Extensive conservation of orthology coupled to rapid sequence evolution. BMC Genomics, 9. ISSN 1471-2164

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Abstract

Background: 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. Results: 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 species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion: Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription factors even across distant evolutionary lineages and form the basis for future experiments to examine TF gene function in nematodes and other divergent phyla.

Item Type: Article
Additional Information: Funding Information: We thank Phil Cumbo, Eric Schwartz, Jack Chen, and anonymous reviewers for constructive comments and advice. This work was supported by Natural Sciences and Engineering Research Council of Canada (NSERC) funds to BPG and RSS. CA is supported by an NSERC Post-Graduate Doctoral Scholarship and NK was an NSERC undergraduate summer trainee.
Uncontrolled Keywords: biotechnology,genetics,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 15 Sep 2022 15:31
Last Modified: 23 Sep 2022 02:59
URI: https://ueaeprints.uea.ac.uk/id/eprint/88340
DOI: 10.1186/1471-2164-9-399

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