RNA Binding by Histone Methyltransferases Set1 and Set2

Abstract

Histone methylation at H3K4 and H3K36 is commonly associated with genes actively transcribed by RNA polymerase II (RNAPII) and is catalyzed by Saccharomyces cerevisiae Set1 and Set2, respectively. Here we report that both methyltransferases can be UV cross-linked to RNA in vivo. High-throughput sequencing of the bound RNAs revealed strong Set1 enrichment near the transcription start site, whereas Set2 was distributed along pre-mRNAs. A subset of transcripts showed notably high enrichment for Set1 or Set2 binding relative to RNAPII, suggesting functional posttranscriptional interactions. In particular, Set1 was strongly bound to the SET1 mRNA, Ty1 retrotransposons, and noncoding RNAs from the ribosomal DNA (rDNA) intergenic spacers, consistent with its previously reported silencing roles. Set1 lacking RNA recognition motif 2 (RRM2) showed reduced in vivo cross-linking to RNA and reduced chromatin occupancy. In addition, levels of H3K4 trimethylation were decreased, whereas levels of dimethylation were increased. We conclude that RNA binding by Set1 contributes to both chromatin association and methyltransferase activity.

Tri-methylation of histone H3 lysine 4 facilitates gene expression in ageing cells

“…Activation of Rad6/Bre1 and COMPASS recruitment also require interactions with the Ser-5 phosphorylated CTD of RNA polymerase II, providing a tight transcriptional connection ( Krogan et al, 2003 ; Ng et al, 2003 ; Xiao et al, 2005 ). COMPASS recruitment then occurs through interactions of Swd2 with active H2B-associated Rad6/Bre1, and of Set1/Spp1 with nascent mRNA ( Battaglia et al, 2017 ; Luciano et al, 2017 ; Sayou et al, 2017 ; Thornton et al, 2014 ). In mammals, additional CxxC domains in Cfp1 (the orthologue of yeast Spp1) and some SET-domain proteins further specify and diversify COMPASS activity, allowing DNA methylation-dependent activity and selective recruitment of COMPASS to promoter and enhancer sequences ( Brown et al, 2017 ; Clouaire et al, 2012 ; Hu et al, 2017 ; Thomson et al, 2010 ).…”

Tri-methylation of Histone H3 Lysine 4 Facilitates Gene Expression in Ageing Cells

“…Activation of Rad6/Bre1 and COMPASS recruitment also require interactions with the Ser-5 phosphorylated CTD of RNA polymerase II, providing a tight transcriptional connection (Krogan et al, 2003;Ng et al, 2003;Xiao et al, 2005). COMPASS recruitment occurs through interactions of Swd2 with active H2B-associated Rad6/Bre1, and of Set1/Spp1 with nascent mRNA (Battaglia et al, 2017;Luciano et al, 2017;Sayou et al, 2017;Thornton et al, 2014). In mammals, additional CxxC domains in Cfp1 (the orthologue of yeast Spp1) and some SETdomain proteins further specify and diversify COMPASS activity, allowing DNA methylationdependent activity and selective recruitment of COMPASS to promoter and enhancer sequences (Brown et al, 2017;Clouaire et al, 2012;Hu et al, 2017;Thomson et al, 2010).…”

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

“…As a positive control, CRAC data for the RNA-binding protein Nab3 ( Bresson et al, 2017 ) were similarly analyzed and identified the previously reported UUCU-binding site. Analysis of negative control data from the BY control strain, Rpo21 (the large subunit of RNAPII) or the histone methyl-transferases Set1 and Set2 ( Sayou et al, 2017 ), identified no clearly enriched motifs.…”

“…PCR duplicates that were not collapsed during preprocessing due to sequencing errors or differential trimming at the 3’ end were collapsed ( Tuck and Tollervey, 2013 ). After the exclusion of reads mapping to RNAPI and RNAPIII transcripts or originating from the mitochondrial genome ( Sayou et al, 2017 ), reads mapping to protein-coding genes and containing single nucleotide deletions (indicating the precise nucleotide crosslinked to the bait protein) were selected using pyReadCounters from pyCRAC ( Webb et al, 2014 ). To remove biases in sequence representation caused by abundantly expressed genes, overlapping reads were assembled into a single sequence using pyClusterReads from pyCRAC ( Webb et al, 2014 ).…”

“…Nab3 CRAC sequences were analyzed using the same pipeline and recovered the Nab3 motif ( Bresson et al, 2017 ). CRAC sequences from Rpo21 (this study), the untagged BY4741 strain (this study), Set1 and Set2 ( Sayou et al, 2017 ) were also analyzed as negative control and no motifs were found. CRAC sequences generated during this work have been deposited with GEO; accession number GSE94944, subseries GSE94941.…”