Chromatin modifications comprise an essential layer of gene regulation. We previously showed that one particular chromatin modification, tri-methylation of lysine 36 on histone H3 (H3K36me3), is enriched on exonic regions of transcribed genes relative to intronic regions (Kolasinska-Zwierz et al., 2009). This observation suggests a link between chromatin modification and splicing. We are using a number of approaches to test the function of exon marking and to elucidate how it works. First we are searching for enzymes involved in H3K36me3 exon marking. We are studying both histone methyltransferases and histone demethylases, as both could contribute to exon marking. Histone lysine methyltransferases are usually characterized by possession of a SET domain whereas histone lysine demethylases are characterized by JmjC domains. Previous work showed that mutants of the SET domain gene met-1 have reduced overall levels of H3K36me3 whereas mutants of the JmjC domain gene jmjd-2 have increased H3K36me3 levels (Andersen and Horvitz, 2007; Whetstine et al, 2006). By ChIP-chip analysis, we find that exon marking is reduced but not eliminated in met-1 mutants. We are currently screening for additional enzymes that contribute to tri-methylation of H3K36 and testing roles for C. elegans JmjC domain proteins in H3K36me3 exon marking. Using ChIP-seq, we are also mapping the genome-wide locations of SET and JmjC domain proteins implicated in trimethylation of H3K36. Concurrently, we are using RNA-seq to test whether changes in exon marking result in altered splicing patterns. ANDERSEN, E.C. and HORVITZ, H.R., 2007. Two C. elegans histone methyltransferases repress lin-3 EGF transcription to inhibit vulval development. Development, 134(16), pp. 2991-2999. KOLASINSKA-ZWIERZ, P., DOWN, T., LATORRE, I., LIU, T., LIU, X.S. and AHRINGER, J., 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature genetics, 41(3), pp. 376-381. WHETSTINE, J.R., NOTTKE, A., LAN, F., HUARTE, M., SMOLIKOV, S., CHEN, Z., SPOONER, E., LI, E., ZHANG, G., COLAIACOVO, M. and SHI, Y., 2006. Reversal of Histone Lysine Trimethylation by the JMJD2 Family of Histone Demethylases. Cell, 125(3), pp. 467-481.

Affiliation:
- The Gurdon Institute, Department of Genetics, University of Cambridge, United Kingdom