Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo

PLoS One. 2008;3(11):e3621. doi: 10.1371/journal.pone.0003621. Epub 2008 Nov 3.


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 fog(sk8) zebrafish mutant, which disrupts the foggy/spt5 gene. We identified that fog(sk8) 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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Cell Cycle / genetics
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • Chromosomal Proteins, Non-Histone / physiology*
  • Cluster Analysis
  • Embryo, Nonmammalian
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Genes, Developmental
  • Models, Biological
  • Mutant Proteins / genetics
  • Mutant Proteins / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • Protein Binding
  • RNA Polymerase II / metabolism
  • Transcriptional Elongation Factors / genetics
  • Transcriptional Elongation Factors / metabolism
  • Transcriptional Elongation Factors / physiology*
  • Zebrafish / embryology*
  • Zebrafish / genetics*
  • Zebrafish Proteins / genetics*


  • Chromosomal Proteins, Non-Histone
  • Mutant Proteins
  • Transcriptional Elongation Factors
  • Zebrafish Proteins
  • SPT5 transcriptional elongation factor
  • RNA Polymerase II