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Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation.

Edmunds JW, Mahadevan LC, Clayton AL - EMBO J. (2007)

Bottom Line: Upon stimulation, transcription-dependent increases in H3K4 and H3K36 trimethylation are seen across coding regions, peaking at 5' and 3' ends, respectively.Addressing molecular mechanisms involved, we find that Huntingtin-interacting protein HYPB/Setd2 is responsible for virtually all global and transcription-dependent H3K36 trimethylation, but not H3K36-mono- or dimethylation, in these cells.These studies reveal four distinct layers of histone modification across inducible mammalian genes and show that HYPB/Setd2 is responsible for H3K36 trimethylation throughout the mouse nucleus.

View Article: PubMed Central - PubMed

Affiliation: Nuclear Signalling Laboratory, Department of Biochemistry, Oxford University, Oxford, UK.

ABSTRACT
Understanding the function of histone modifications across inducible genes in mammalian cells requires quantitative, comparative analysis of their fate during gene activation and identification of enzymes responsible. We produced high-resolution comparative maps of the distribution and dynamics of H3K4me3, H3K36me3, H3K79me2 and H3K9ac across c-fos and c-jun upon gene induction in murine fibroblasts. In unstimulated cells, continuous turnover of H3K9 acetylation occurs on all K4-trimethylated histone H3 tails; distribution of both modifications coincides across promoter and 5' part of the coding region. In contrast, K36- and K79-methylated H3 tails, which are not dynamically acetylated, are restricted to the coding regions of these genes. Upon stimulation, transcription-dependent increases in H3K4 and H3K36 trimethylation are seen across coding regions, peaking at 5' and 3' ends, respectively. Addressing molecular mechanisms involved, we find that Huntingtin-interacting protein HYPB/Setd2 is responsible for virtually all global and transcription-dependent H3K36 trimethylation, but not H3K36-mono- or dimethylation, in these cells. These studies reveal four distinct layers of histone modification across inducible mammalian genes and show that HYPB/Setd2 is responsible for H3K36 trimethylation throughout the mouse nucleus.

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(C) Aliquots of formaldehyde crosslinked mononucleosomes prepared as in (B) were used in ChIP assays with H3K36me3- (i), H3K36me2- (ii) and H3K36me1- (iii) specific antibodies. Recovery of c-fos, c-jun and hbb coding region sequences were quantified by real-time PCR. Average % input recoveries and s.d. from two independent experiments are plotted. Regions analysed are indicated to the left of the panels.
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f5b: (C) Aliquots of formaldehyde crosslinked mononucleosomes prepared as in (B) were used in ChIP assays with H3K36me3- (i), H3K36me2- (ii) and H3K36me1- (iii) specific antibodies. Recovery of c-fos, c-jun and hbb coding region sequences were quantified by real-time PCR. Average % input recoveries and s.d. from two independent experiments are plotted. Regions analysed are indicated to the left of the panels.

Mentions: Setd2 knockdown produced almost complete loss of total cellular K36me3 in these cells (Figure 5B) and a marked reduction of K36me3 at c-fos- and c-jun coding regions (Figure 5C, panel i). Stimulation with EGF for 60 min resulted in a 2.7- to 3.4-fold increase in the K36me3 observed at these regions (black bars panel i), whereas in the Setd2 knockdown, induced levels of K36me3 were much smaller—1.3- to 1.8-fold (middle bars panel i). K36me3 was also decreased by >50% within the coding regions of gapdh, cycb, polr3b and glnrs after Setd2 knockdown (Figure 5D, panel i). Setd2 therefore appears to be responsible for both basal and inducible K36me3 at IE gene coding regions, and K36me3 levels at constitutively active genes.


Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation.

Edmunds JW, Mahadevan LC, Clayton AL - EMBO J. (2007)

(C) Aliquots of formaldehyde crosslinked mononucleosomes prepared as in (B) were used in ChIP assays with H3K36me3- (i), H3K36me2- (ii) and H3K36me1- (iii) specific antibodies. Recovery of c-fos, c-jun and hbb coding region sequences were quantified by real-time PCR. Average % input recoveries and s.d. from two independent experiments are plotted. Regions analysed are indicated to the left of the panels.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2168397&req=5

f5b: (C) Aliquots of formaldehyde crosslinked mononucleosomes prepared as in (B) were used in ChIP assays with H3K36me3- (i), H3K36me2- (ii) and H3K36me1- (iii) specific antibodies. Recovery of c-fos, c-jun and hbb coding region sequences were quantified by real-time PCR. Average % input recoveries and s.d. from two independent experiments are plotted. Regions analysed are indicated to the left of the panels.
Mentions: Setd2 knockdown produced almost complete loss of total cellular K36me3 in these cells (Figure 5B) and a marked reduction of K36me3 at c-fos- and c-jun coding regions (Figure 5C, panel i). Stimulation with EGF for 60 min resulted in a 2.7- to 3.4-fold increase in the K36me3 observed at these regions (black bars panel i), whereas in the Setd2 knockdown, induced levels of K36me3 were much smaller—1.3- to 1.8-fold (middle bars panel i). K36me3 was also decreased by >50% within the coding regions of gapdh, cycb, polr3b and glnrs after Setd2 knockdown (Figure 5D, panel i). Setd2 therefore appears to be responsible for both basal and inducible K36me3 at IE gene coding regions, and K36me3 levels at constitutively active genes.

Bottom Line: Upon stimulation, transcription-dependent increases in H3K4 and H3K36 trimethylation are seen across coding regions, peaking at 5' and 3' ends, respectively.Addressing molecular mechanisms involved, we find that Huntingtin-interacting protein HYPB/Setd2 is responsible for virtually all global and transcription-dependent H3K36 trimethylation, but not H3K36-mono- or dimethylation, in these cells.These studies reveal four distinct layers of histone modification across inducible mammalian genes and show that HYPB/Setd2 is responsible for H3K36 trimethylation throughout the mouse nucleus.

View Article: PubMed Central - PubMed

Affiliation: Nuclear Signalling Laboratory, Department of Biochemistry, Oxford University, Oxford, UK.

ABSTRACT
Understanding the function of histone modifications across inducible genes in mammalian cells requires quantitative, comparative analysis of their fate during gene activation and identification of enzymes responsible. We produced high-resolution comparative maps of the distribution and dynamics of H3K4me3, H3K36me3, H3K79me2 and H3K9ac across c-fos and c-jun upon gene induction in murine fibroblasts. In unstimulated cells, continuous turnover of H3K9 acetylation occurs on all K4-trimethylated histone H3 tails; distribution of both modifications coincides across promoter and 5' part of the coding region. In contrast, K36- and K79-methylated H3 tails, which are not dynamically acetylated, are restricted to the coding regions of these genes. Upon stimulation, transcription-dependent increases in H3K4 and H3K36 trimethylation are seen across coding regions, peaking at 5' and 3' ends, respectively. Addressing molecular mechanisms involved, we find that Huntingtin-interacting protein HYPB/Setd2 is responsible for virtually all global and transcription-dependent H3K36 trimethylation, but not H3K36-mono- or dimethylation, in these cells. These studies reveal four distinct layers of histone modification across inducible mammalian genes and show that HYPB/Setd2 is responsible for H3K36 trimethylation throughout the mouse nucleus.

Show MeSH