H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

Guillemette, Benoît; Drogaris, Paul; Lin, H.; Armstrong, Harry; Hiragami-Hamada, Kyoko; Imhof, Axel; Bonneil, Éric; Thibault, Pierre; Verreault, Alain; Festenstein, Richard

doi:10.1371/journal.pgen.1001354

Cited by 173 publications

(164 citation statements)

References 106 publications

Supporting

Mentioning

148

Contrasting

Unclassified

Order By: Relevance

“…In addition, we speculate that the HU sensitivities of tH2A:H3T3A and tH2A:H3Q5A mutant cells could be due to the defects either in Set1-mediated methylation on H3K4 and/or in binding of effector proteins to methylated H3K4, given the fact that these residues are right next to H3K4. We note a recent report showing that H3K4 can be acetylated in yeast (39). Therefore, it is still possible that H3K4ac may also play a role in HU sensitivity.…”

Section: Double Deletion Of the Histone N-tails Uncovers Unidentifiedmentioning

confidence: 71%

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

Kim

Hsu

Smith

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

A large body of literature provides compelling evidence for the role of evolutionarily conserved core histone residues in various biological processes. However, site-directed mutagenesis of individual residues that are known to be sites of posttranslational modifications often does not result in clear phenotypic defects. In some cases, the combination of multiple mutations can give rise to stronger phenotypes, implying functional redundancy between distinct residues on histones. Here, we examined the “histone redundancy hypothesis” by characterizing double deletion of all pairwise combinations of amino-terminal tails (N-tails) from the four core histones encoded in budding yeast. First, we found that multiple lysine residues on the N-tails of both H2A and H4 are redundantly involved in cell viability. Second, simultaneous deletion of N-tails from H2A and H3 leads to a severe growth defect, which is correlated with perturbed gross chromatin structure in the mutant cells. Finally, by combining point mutations on H3 with deletion of the H2A N-tail, we revealed a redundant role for lysine 4 on H3 and the H2A N-tail in hydroxyurea-mediated response. Altogether, these data suggest that the N-tails of core histones share previously unrecognized, potentially redundant functions that, in some cases are different from those of the widely accepted H2A/H2B and H3/H4 dimer pairs.

show abstract

Section: Double Deletion Of the Histone N-tails Uncovers Unidentifiedmentioning

confidence: 71%

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

Kim

Hsu

Smith

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…5D, Lower). H3K4ac has been reported to enrich at active gene promoters just upstream of H3K4me3 (26). Presumably, the observed "TAF3-H3K4ac" interaction might facilitate TAF3 searching for H3K4me3 at the transcription start site by priming the association of TAF3 with promoter chromatin.…”

Section: Resultsmentioning

confidence: 99%

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Zhao

Yang

Zhou

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chipbased surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant. The mechanisms leading to differential transcriptional and developmental outcomes under the same genetic background are known as epigenetics. Posttranslational modification (PTM) on histones is a major epigenetic regulatory mechanism such that more than 30 types of PTMs occur on histones, with new ones still being discovered (1). The well-studied histone PTMs include methylation, acetylation, phosphorylation, and most recently discovered nonacetyl acylations (2). Histone PTMs regulate transcription either by directly affecting the structure/stability of single nucleosome and the high-order folding of chromatin, or by recruiting specific effector proteins (also called histone readers) recognizing them (3, 4).The ever-expanding repertoire of histone readers are diverse in sequence and structure, and how they engage diversely modified chromatin is complicated, hard to predict, yet important for their functions. Often one type of reader domains can recognize different types of PTMs. For example, PHD finger proteins can recognize unmodified, methylated, or acylated lysine residue on histones (5, 6). Several YEATS domain proteins, originally identified as readers of lysine acetylation (Kac), in fact accommodate a wide range of lysine acylations with lysine crotonylation (Kcr) most preferred (7). These "mark-reader" interactions vary greatly in binding affinity, ranging from submicromolar to millimolar levels. To complicate the matter further, the recognition of marks by reader proteins is often either synergized or antagonized by other marks in close proximity (8). For instance, Spindlin1 recognizes histone H3 trimethylation of Lys-4 (H3K4me3) and asymmetrically dimethylation of Arg-8 (H3R8me2a) in concert, while phosphorylation of Ser-10 on H3 (H3S10ph) completely abrogates the binding of H3 Lys-9 trimethylation (H3K9me3) by HP1 protein (9, 10). BRDT protein binds neither histone H4 Lys-5 acetylation (H4K5ac) nor Lys-8 acetylation (H4K8ac) but engages H4 peptide bearing both marks with decent affinity (K...

show abstract

“…H3K4me3 is a marker associated with active transcription, and it has a close relationship with histone acetylation and deacetylation (Eissenberg and Shilatifard, 2010;Guillemette et al, 2011). A previous study has shown that histone H3 is deacetylated globally in the MII oocytes of 3-week-old mice, and the acetylation at all of the lysine residues of histone H3 was undetectable or negligible in the oocytes during meiosis (Kim et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Differences in H3K4 trimethylation in in vivo and in vitro fertilization mouse preimplantation embryos

Wu¹,

Liu²,

Shang³

et al. 2012

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Trimethylation of lysine 4 at histone 3 (H3K4me3) is considered a marker of active transcription; it plays an important role in transcription reprogramming efficiency. We compared the levels of H3K4me3 in mouse preimplantation embryos from MII stage oocytes produced by in vivo and in vitro fertilization (IVF) using immunofluorescence histochemistry. IVF embryos were further treated with trichostatin A (a histione deacetylase inhibitor) to investigate the effect of histone acetylation on H3K4me3. We found higher levels of H3K4me3 in MII stage oocytes in metaphase chromosomes. The pattern of H3K4 trimethylation of in vivo embryos from zygote to blastocyst stages was similar to that of IVF embryos; however, the concentration of H3K4me3 was significantly higher in the in vivo fertilization embryos. The levels of H3K4me3 in the trichostatin A-treated groups were also significantly increased. We conclude that culture condition and environmental changes can cause histone modification and that the effect of these environmental conditions on epigenetic changes should be taken into consideration.

show abstract

H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

Cited by 173 publications

References 106 publications

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Differences in H3K4 trimethylation in in vivo and in vitro fertilization mouse preimplantation embryos

Contact Info

Product

Resources

About