Methylation of histone H3 Lys 4 in coding regions of active genes

By Bradley E. Bernstein, Emily L. Humphrey, R. Erlich, Robert Schneider, P. Bouman, J. Liu, Tony Kouzarides, Stefan Schreiber. Proceedings of the National Academy of Sciences of the United States of America, 2002

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Posttranslational modifications of histone tails regulate chromatin structure and transcription. Here we present global analyses of histone acetylation and histone H3 Lys 4 methylation patterns in yeast. We observe a significant correlation between acetylation of histones H3 and H4 in promoter regions and transcriptional activity. In contrast, we find that dimethylation of histone H3 Lys 4 in coding regions correlates with transcriptional activity. The histone methyltransferase Set1 is required to maintain expression of these active, promoter-acetylated, and coding region-methylated genes. Global comparisons reveal that genomic regions deacetylated by the yeast enzymes Rpd3 and Hda1 overlap extensively with Lys 4 hypo- but not hypermethylated regions. In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, we conclude that Set1 facilitates transcription, in part, by protecting active coding regions from deacetylation.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d3a0432529fcb32e4342c178fa815a269533067a

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Citations in the corpus

Genomic maps and comparative analysis of histone modifications in human and mouse. (2005, methodology): “For example, chromatin im-Harvard Medical School munoprecipitation (ChIP) has been combined with DNABoston, Massachusetts 02115 microarrays to map the locations of modified histones4 Affymetrix genome-wide in yeast and flies (Bernstein et al., 2002;3380 Central Expressway Schubeler et al., 2004).”
Identification and distinct regulation of yeast TATA box-containing genes. (2004, neutral): “…and tup1 (DeRisi et al., 1997); (F) rsc30 (Angus-Hill et al., 2001), swi2(K798A) (Holstege et al., 1998), hos3 (Bernstein et al., 2000), and hda1 (Bernstein et al., 2002); (G) mot1-14 (Dasgupta et al., 2002), bur6-1 (Cang and Prelich, 2002), TBP(F182V) (Chitikila et al., 2002), spt3…”
The diverse functions of histone lysine methylation (2005, background): “Analyses of the different H3-K4 methylation states and their distribution in various organisms indicate that both the dimethyl-and trimethyl-H3-K4 modifications are enriched at actively transcribed genes 27,83,96,97 .”
Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. (2003, background): “In addition, the finding that ubiquitylation and methylation effects occur even in glucose may reflect their role in marking euchromatin and transcribed regions relative to heterochromatin (Bernstein et al. 2002; van Leeuwen et al. 2002).”
Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. (2003, background): “…can be recruited by specific activa- 1997) and transcriptional profiling (Miller et al., 2001; tors or repressors, depending on the promoter (Cosma Bernstein et al., 2002) experiments have identified genes et al., 1999; Agalioti et al., 2000; Goldmark et al., 2000; whose expression appears to be…”
Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. (2005, methodology): “This is in contrast to modifications such as trimethylation of lysine 4 of histone H3 in yeast, which does correlate with transcription rate and typically occurs on the first nucleosomes downstream of the transcription initiation site (Bernstein et al., 2002; Krogan et al., 2003a; Ng et al., 2003b).”
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. (2004, background): “cerevisiae for H3-dimeK4 (Bernstein et al. 2002).”
Genome-wide map of nucleosome acetylation and methylation in yeast. (2005, neutral): “level of individual genes (Bannister et al., 2005; Bernstein et al., 2002; Krogan et al., 2003b; Ng et al., 2003a; Xiao et al., 2003), we sought to systematically profile mono-, di-, and trimethylated residues at K4, K36, and K79 of histone H3 in nucleosomes associated with genomic DNA.”
High-resolution profiling of histone methylations in the human genome. (2007, background): “The general picture emerging from these studies is that promoter regions of active genes have reduced nucleosome occupancy and elevated histone acetylation (Bernstein et al., 2002, 2004; Lee et al., 2004; Liu et al., 2005; Pokholok et al., 2005; Sekinger et al., 2005; Yuan et al., 2005).”
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. (2004, background): “For example, several factors lead to low enrichment rates in wholegenome ChIPs designed to map the location of specific histone modifications [24].”