Global and Specific Responses of the Histone Acetylome to Systematic Perturbation

Abstract

Regulation of histone acetylation is fundamental to the utilization of eukaryotic genomes in chromatin. Aberrant acetylation contributes to disease and can be clinically combated by inhibiting the responsible enzymes. Our knowledge of the histone acetylation system is patchy because we so far lacked the methodology to describe acetylation patterns and their genesis by integrated enzyme activities. We devised a generally applicable, mass spectrometry-based strategy to precisely and accurately quantify combinatorial modification motifs. This was applied to generate a comprehensive inventory of acetylation motifs on histones H3 and H4 in Drosophila cells. Systematic depletion of known or suspected acetyltransferases and deacetylases revealed specific alterations of histone acetylation signatures, established enzyme-substrate relationships, and unveiled an extensive crosstalk between neighboring modifications. Unexpectedly, overall histone acetylation levels remained remarkably constant upon depletion of individual acetyltransferases. Conceivably, the acetylation level is adjusted to maintain the global charge neutralization of chromatin and the stability of nuclei.

Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids

“…Taf1 encodes a TAF (TATA-box-binding associated factor) constituting one subunit of transcription factor TFIID broadly required for transcription by RNA polymerase II (46,47). The product of Taf1 serves as a multifunctional transcriptional regulator operating in the normal cell cycle, the assembly of other TAFs and TBPs (TATA-binding proteins), promoter activities, histone acetylation, and other chromatin modifications that can modulate chromatin structure enabling it to access transcriptionally repressed chromatin (48).…”

Regulation of KAT6 Acetyltransferases and Their Roles in Cell Cycle Progression, Stem Cell Maintenance, and Human Disease

“…Similarly, the loss of Sas3 does not affect global H3K9ac and -K14ac levels, but disrupting the HAT activity of Sas3 led to decreased levels of H3K9ac and -K14ac in the absence of a HAT in the GNAT family, Gcn5 (3). In striking contrast to the subtle effects of the loss of MOZ or Sas3 alone on the bulk levels of H3K9ac and -K14ac, the global H3K23ac levels are highly dependent on the HAT activity of Enok in flies (43,46). In addition, since H3K23ac is abundant in fly cells (47% of H3), the depletion of Enok resulted in an ϳ35% reduction in global histone H3 and H4 (H3ϩH4) acetylation levels (46).…”

“…In striking contrast to the subtle effects of the loss of MOZ or Sas3 alone on the bulk levels of H3K9ac and -K14ac, the global H3K23ac levels are highly dependent on the HAT activity of Enok in flies (43,46). In addition, since H3K23ac is abundant in fly cells (47% of H3), the depletion of Enok resulted in an ϳ35% reduction in global histone H3 and H4 (H3ϩH4) acetylation levels (46). This significant effect of Enok depletion on global H3ϩH4 acetylation levels is unique, as individually depleting any of the other 22 lysine acetyltransferases (including Gcn5/ KAT2, Nej/KAT3, Tip60/KAT5, and Chm/KAT7) has much weaker effects that are all less than 10% (46).…”

“…In addition, since H3K23ac is abundant in fly cells (47% of H3), the depletion of Enok resulted in an ϳ35% reduction in global histone H3 and H4 (H3ϩH4) acetylation levels (46). This significant effect of Enok depletion on global H3ϩH4 acetylation levels is unique, as individually depleting any of the other 22 lysine acetyltransferases (including Gcn5/ KAT2, Nej/KAT3, Tip60/KAT5, and Chm/KAT7) has much weaker effects that are all less than 10% (46). Therefore, Enok may have a role in regulating the bulk charges of histones in specific chromatin regions.…”

Drosophila O-GlcNAcase Deletion Globally Perturbs Chromatin O-GlcNAcylation

“…Mammalian OGA (MGEA5) is suggested to play an O-GlcNAc independent role in activation of gene expression in that the pseudo-histone acetyltransferase domain of MGEA5 may play a role in gene activation (56). The deletion in oga del.1 mutants spans the O-GlcNAcase catalytic domain but leaves the C-terminal pseudo-histone acetyltransferase domain intact.…”