Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription

Nucleic Acids Res. 2013 Mar 1;41(5):2881-93. doi: 10.1093/nar/gks1472. Epub 2013 Jan 15.

Abstract

Histone H3 of nucleosomes positioned on active genes is trimethylated at Lys36 (H3K36me3) by the SETD2 (also termed KMT3A/SET2 or HYPB) methyltransferase. Previous studies in yeast indicated that H3K36me3 prevents spurious intragenic transcription initiation through recruitment of a histone deacetylase complex, a mechanism that is not conserved in mammals. Here, we report that downregulation of SETD2 in human cells leads to intragenic transcription initiation in at least 11% of active genes. Reduction of SETD2 prevents normal loading of the FACT (FAcilitates Chromatin Transcription) complex subunits SPT16 and SSRP1, and decreases nucleosome occupancy in active genes. Moreover, co-immunoprecipitation experiments suggest that SPT16 is recruited to active chromatin templates, which contain H3K36me3-modified nucleosomes. Our results further show that within minutes after transcriptional activation, there is a SETD2-dependent reduction in gene body occupancy of histone H2B, but not of histone H3, suggesting that SETD2 coordinates FACT-mediated exchange of histone H2B during transcription-coupled nucleosome displacement. After inhibition of transcription, we observe a SETD2-dependent recruitment of FACT and increased histone H2B occupancy. These data suggest that SETD2 activity modulates FACT recruitment and nucleosome dynamics, thereby repressing cryptic transcription initiation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • DNA-Binding Proteins / metabolism*
  • Gene Knockdown Techniques
  • HEK293 Cells
  • HeLa Cells
  • High Mobility Group Proteins / metabolism*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism
  • Histone-Lysine N-Methyltransferase / physiology*
  • Humans
  • Kinetics
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Nucleosomes / metabolism*
  • Protein Binding
  • RNA Polymerase II / metabolism
  • RNA, Small Interfering / genetics
  • Transcription Factor CHOP / genetics
  • Transcription Factor CHOP / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription Initiation Site
  • Transcription Initiation, Genetic*
  • Transcription, Genetic
  • Transcriptional Activation
  • Transcriptional Elongation Factors / metabolism*
  • Transcriptome

Substances

  • Cell Cycle Proteins
  • DDIT3 protein, human
  • DNA-Binding Proteins
  • HERPUD1 protein, human
  • High Mobility Group Proteins
  • Membrane Proteins
  • Nucleosomes
  • RNA, Small Interfering
  • SSRP1 protein, human
  • SUPT16H protein, human
  • Transcription Factors
  • Transcriptional Elongation Factors
  • Transcription Factor CHOP
  • Histone-Lysine N-Methyltransferase
  • Set2 protein, human
  • RNA Polymerase II