Identification of Spt5 Target Genes in Zebrafish Development Reveals Its Dual Activity In Vivo

Krishnan, K., Salomonis, N., Guo, S. (2008) Identification of Spt5 Target Genes in Zebrafish Development Reveals Its Dual Activity In Vivo. PLoS ONE, 3 (11). e3621.

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URL: http://www.ncbi.nlm.nih.gov/pubmed/18978947
DOI: 10.1371/journal.pone.0003621

Abstract

Spt5 is a conserved essential protein that represses or stimulates transcription elongation in vitro. Immunolocalization studies on Drosophila polytene chromosomes suggest that Spt5 is associated with many loci throughout the genome. However, little is known about the prevalence and identity of Spt5 target genes in vivo during development. Here, we identify direct target genes of Spt5 using fogsk8 zebrafish mutant, which disrupts the foggy/spt5 gene. We identified that fogsk8 and their wildtype siblings differentially express less than 5% of genes examined. These genes participate in diverse biological processes from stress response to cell fate specification. Up-regulated genes exhibit shorter overall gene length compared to all genes examined. Through chromatin immunoprecipitation in zebrafish embryos, we identified a subset of developmentally critical genes that are bound by both Spt5 and RNA polymerase II. The protein occupancy patterns on these genes are characteristic of both repressive and stimulatory elongation regulation. Together our findings establish Spt5 as a dual regulator of transcription elongation in vivo and identify a small but diverse set of target genes critically dependent on Spt5 during development.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > animal
organism description > animal > fish
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
organism description > animal > fish > zebrafish
CSHL Authors:
Communities: CSHL labs > Huang lab
CSHL Post Doctoral Fellows
Depositing User: Matt Covey
Date Deposited: 26 Feb 2013 19:42
Last Modified: 02 May 2013 19:46
PMCID: PMC2575381
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27546

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