Set2 mediated H3 lysine 36 methylation: regulation of transcription elongation and implications in organismal development

Abstract

Set2 is a RNA polymerase II (RNAPII) associated histone methyltransferase involved in the cotranscriptional methylation of the H3 K36 residue (H3K36me). It is responsible for multiple degrees of methylation (mono-, di-, and trimethylation), each of which has a distinct functional consequence. The extent of methylation and its genomic distribution is determined by different factors that coordinate to achieve a functional outcome. In yeast, the Set2-mediated H3K36me is involved in suppressing histone exchange, preventing hyperacetylation and promoting maintenance of well-spaced chromatin structure over the coding regions. In metazoans, separation of this enzymatic activity affords greater functional diversity extending beyond the control of transcription elongation to developmental gene regulation. This review focuses on the molecular aspects of the Set2 distribution and function, and discusses the role played by H3 K36 methyl mark in organismal development.

Figure 1. RNAPII CTD phosphorylation cycle across the coding region

Distribution of the RNAPII CTD phosphorylation marks across the coding region of genes. Differential phosphorylation of the S5 or S2 residues in the heptad repeat contributes to the stage-specific association of transcription regulatory proteins. The font size of the CTD phosphorylation at the top of the figure corresponds to the relative abundance of that post-translational CTD modification at a particular stage. The distribution of the Set2-dependent H3K36 methyl marks (me1, me2, me3) across the coding region is denoted as a heat map at the bottom.

Figure 2. Set2 domain architecture and its effect on H3 K36 methylation

Domain architecture and interactions of the yeast Set2 protein and their effect on H3K36me. The green arrows indicate the necessity of the domain for the methyltransferase activity of the SET domain. AWS: Associated with SET; SET: Su(var), E(z) and Trithorax; PS: Post-SET; WW: Typtophan-rich domain; CC: coiled coil domain; SRI: Set2-Rpb1 interaction domain.

Figure 3. Role of Set2-mediated H3K36 methylation in nucleosomal dynamics

Set2-mediated K36 methylation regulates nucleosome dynamics through different mechanisms. It suppresses histone exchange over the coding regions by preventing binding of the Asf1 protein to the methylated histones, and promotes the retention of the original nucleosome. This prevents the enrichment of pre-acetylated histones on the coding regions. H3K36me also recruits the Isw1b protein complex to maintain regular nucleosomal spacing after the passage of the elongating polymerase. H3K36me also activates the deacetylase activity of the RNAPII-associated Rpd3S complex, to remove the acetyl marks that have been added by histone acetyltransferase complexes.

Figure 4. Cryptic transcription upon loss of Set2/Rpd3S pathway

Total RNA was prepared from the wild type, set2Δ and rco1Δ strains and subjected to Northern blot analysis. The probes used in these assays were from the 5′ and 3′ ends of the STE11 gene (top). An SCR1 probe was used as a loading control. The full-length transcript and the short cryptic transcripts are indicated. The approximate start sites for the cryptic transcripts from within the coding regions are indicated.

Figure 5. H3 K36 methylation in transcription regulation

H3K36me regulates transcription rates by a number of methods. (a) In dosage compensation in flies, it recruits the MSL/DCC to the coding regions of the X-chromosome, stimulating the H4 K16 acetylation by the MOF subunit. This increases the rate of transcription over the X-chromosome to equal that of the autosomes. (b) H3K36me prevents the binding and subsequent methylation of the H3K27 residue by the repressive polycomb PRC2 complexes. (c) H3K36me regulates alternate splicing of the transcript in a co-transcriptional manner. The MRG15 (yeast Eaf3) protein binds the H3K36me mark through its chromodomain. PTB binds MRG15 and facilitates exon skipping.