RNA binding by the histone methyltransferases Set1 and Set2

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 post-transcriptional 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.H3K4与H3K36位点的组蛋白甲基化通常与RNA聚合酶II（RNAPII）主动转录的基因相关，且分别由酿酒酵母Set1和Set2催化。本研究表明，这两种甲基转移酶均可在体内与RNA发生紫外交联。对结合RNA的高通量测序结果显示，Set1在转录起始位点附近富集显著，而Set2则沿前体mRNA分布。相较于RNAPII，部分转录本对Set1或Set2的结合富集度显著偏高，提示二者存在功能性转录后相互作用。特别值得注意的是，Set1可强力结合SET1 mRNA、Ty1逆转录转座子以及核糖体DNA（rDNA）基因间隔区来源的非编码RNA，这与其此前报道的基因沉默功能相符。缺失RNA识别基序2（RRM2）的Set1突变体，其体内与RNA的交联水平以及染色质结合能力均出现下降。此外，该突变体的H3K4三甲基化水平降低，而H3K4二甲基化水平则有所升高。综上，Set1的RNA结合能力既参与其染色质结合过程，也对其甲基转移酶活性具有调控作用。