SET2

SET2 (PF3D7_1322100) is the histone-lysine N-methyltransferase that writes H3K36 trimethylation across var gene loci in Plasmodium falciparum and thereby enforces mutually exclusive silencing of this virulence-associated gene family (PMID:23823717). H3K36me3 spans the entire var gene body, and knockout of SET2 abolishes this mark and derepresses virtually all var genes simultaneously, driving their expression as surface proteins on infected erythrocytes (PMID:23823717). SET2 is recruited to var loci through direct binding to the unphosphorylated C-terminal domain of RNA polymerase II — an interaction linked to non-coding rather than mRNA transcription — such that dominant-negative disruption of this contact triggers rapid var gene switching (PMID:24391504). The mark is deposited at both active and silent var loci, and an internal PHD-like domain that reads the H3K36me2 intermediate allosterically stimulates the SET2 catalytic domain on nucleosomes, providing a mechanism for spreading H3K36me3 across the family (PMID:24391504, PMID:34389510). At the genome-organization level, SET2-dependent H3K36me3 sustains high-interacting chromatin regions at telomeres and var clusters, and its deletion collapses these intra- and interchromosomal interactions in concert with var activation (PMID:36602337).

1. 2013 High

   Establishing which enzyme controls var gene silencing addressed how the parasite achieves mutually exclusive expression of its virulence gene family; SET2 was identified as the H3K36me3 writer whose loss derepresses nearly all var genes.

   Evidence Gene knockout with ChIP, RNA-seq and surface protein flow cytometry in P. falciparum

   PMID:23823717

   Open questions at the time

   • Does not resolve how a single active var gene escapes silencing
   • Mechanism of mark deposition timing across the cell cycle not addressed
2. 2013 High

   Mapping the H3K36me3 distribution clarified where SET2 acts, showing the mark covers the full var gene body and that reduced occupancy near the transcription start site and intronic promoter coincides with antisense lncRNA and var activation.

   Evidence Genome-wide ChIP-seq and RNA-seq with knockout in P. falciparum

   PMID:23823717

   Open questions at the time

   • Causal direction between antisense lncRNA and loss of SET2 occupancy unresolved
3. 2014 Medium

   How SET2 is targeted to var loci was addressed by showing it binds the unphosphorylated RNA Pol II CTD, linking recruitment to non-coding transcription and demonstrating functional relevance via dominant-negative-induced switching.

   Evidence Co-IP, dominant-negative overexpression with var switching assay, and ChIP in P. falciparum

   PMID:24391504

   Open questions at the time

   • Single lab; reciprocal validation of the Pol II interaction limited
   • Nature of the non-coding transcript directing recruitment not defined
4. 2014 Medium

   Determining that H3K36me3 is present at both active and silent var loci showed SET2 recruitment and mark deposition are not gated by transcriptional state, refining the silencing model.

   Evidence Genome-wide ChIP-seq in P. falciparum

   PMID:24391504

   Open questions at the time

   • Does not explain how identical mark levels yield different transcriptional outcomes at active versus silent loci
5. 2021 Medium

   The biochemical basis for spreading H3K36me3 was addressed by showing a SET2 PHD-like domain reads the H3K36me2 intermediate and allosterically boosts catalytic activity on nucleosomes.

   Evidence In vitro binding and histone methyltransferase assays with domain mutagenesis/truncation on nucleosome substrates in P. falciparum

   PMID:34389510

   Open questions at the time

   • Single in vitro study; allosteric propagation not demonstrated in vivo
   • Structural basis of PHD–H3K36me2 recognition not resolved
6. 2023 High

   Whether SET2 shapes 3D genome architecture was addressed by showing its deletion collapses intra- and interchromosomal interactions at telomeric and var high-interacting regions, coupling chromatin reorganization to var activation.

   Evidence Hi-C, ChIP-seq, RNA-seq and CRISPR/Cas9 deletion in P. falciparum

   PMID:36602337

   Open questions at the time

   • Does not establish whether architectural change is cause or consequence of transcriptional activation
   • Basis for distinct activation potential among var clusters unexplained

• How the single active var gene evades SET2-mediated silencing while the mark blankets the rest of the family remains unresolved.
• No mechanism linking non-coding transcript identity to selective SET2 exclusion at the active locus
• In vivo confirmation of PHD-driven mark propagation lacking