Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription

• Published in: Nucleic acids research 2013-03, Vol.41 (5), p.2881-2893
• Main Authors: Carvalho, Sílvia, Raposo, Ana Cláudia, Martins, Filipa Batalha, Grosso, Ana Rita, Sridhara, Sreerama Chaitanya, Rino, José, Carmo-Fonseca, Maria, de Almeida, Sérgio Fernandes
• Format: Article
• Language: English
• Subjects: Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; DNA-Binding Proteins - metabolism; Gene Knockdown Techniques; Gene Regulation, Chromatin and Epigenetics; 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
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gks1472

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.