Structural Insight into the Recognition of the H3K4me3 Mark by the TFIID Subunit TAF3

Ingen, Hugo van; Schaik, F.M.A. van; Wienk, Hans; Ballering, Joost; Rehmann, Holger; Dechesne, Annemarie; Kruijzer, John A.W.; Liskamp, Rob M. J.; Timmers, H. Th. Marc; Boelens, Rolf

doi:10.1016/j.str.2008.04.015

Cited by 126 publications

(131 citation statements)

References 56 publications

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“…It is interesting to note that the methylation of H3K4 has been related with the transcriptional activation of genes and is a strong predictor for RNA pol II promoters. In particular, the trimethylated form of H3K4 has been found primarily around the transcription start sites of active genes (van Ingen et al, 2008) as in our case.…”

Section: Post Translational Modifications (Ptms) and Pltalpha2 Gene Asupporting

confidence: 69%

Chromatin dynamics of the developmentally regulatedP. lividus neural alpha tubulin gene

Emanuele¹,

Costa²,

Ragusa³

et al. 2011

Int. J. Dev. Biol.

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Over 40 years ago, Allfrey and colleagues (1964) suggested that two histone modifications, namely acetylation and methylation, might regulate RNA synthesis. Nowadays it is universally accepted that activation of gene expression strictly depends on enzymatic mechanisms able to dynamically modify chromatin structure. Here, using techniques including DNaseI hypersensitive site analysis, chomatin immunoprecipitation and quantitative PCR analysis, we have analyzed the dynamics of histone post-translation modifications involved in developmentally/spatially controlled activation of the sea urchin PlTalpha2 tubulin gene. We have demonstrated that only when the PlTalpha2 core promoter chromatin is acetylated on H3K9, tri-methylated on H3K4 and not di-methylated on H3K27, RNA pol II can be enrolled. In contrast, we have shown that when chromatin is methylated both on H3K9 (me2/3) and H3K27 (me2) and mono methylated on H3K4 the promoter is not accessible to RNA pol II. Our results suggest that, during P. lividus embryogenesis, both HAT/HDAC and HMT/HDM activities, which are able to regulate accessibility of the PlTalpha2 basal promoter to RNA polymerase II, are coordinately switched-on.

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Section: Post Translational Modifications (Ptms) and Pltalpha2 Gene Asupporting

confidence: 69%

Chromatin dynamics of the developmentally regulatedP. lividus neural alpha tubulin gene

Emanuele¹,

Costa²,

Ragusa³

et al. 2011

Int. J. Dev. Biol.

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“…Based on our findings and studies published to date regarding the role of TAF7 and TAF1 in transient transcriptional repression required for effective PIC assembly (28), we suggest that the TAF1/7 complex could read the repressive H3K27me3 mark to help induce this temporary transcriptional arrest and that subsequent H3S28 phosphorylation could reverse this effect to induce transcription initiation. It will also be interesting to see if TAF1/7 plays a role in recognition of bivalent chromatin in embryonic stem cells, which contains both the repressive H3K27me3 mark and an active H3K4me3 mark, and in cross-talk with the TAF3-PHD domain that recognizes the H3K4me3 mark on genes that are marked with bivalent chromatin (6,(29)(30)(31). Further experiments would be required to test these, and other, possibilities, but our findings will provide a strong structural basis for future studies of the possible regulatory interplay between the TAF1/7 complex and H3K27me3/H3S28ph switch in transcription initiation.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, TFIID can behave as an epigenetic effector, capable of recognizing posttranslational histone modifications associated with activated transcription. Eukaryotic TAF1 contains a double bromodomain that recognizes acetylated histones, and TAF3 contains a plant homeo domain (PHD) that binds to histone H3 methylated at lysine 4 (5,6). In addition to roles in basal transcription, TFIID is also associated with diseases.…”

mentioning

confidence: 99%

Structural and functional insight into TAF1–TAF7, a subcomplex of transcription factor II D

Bhattacharya

Lou

Hwang

et al. 2014

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

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Transcription factor II D (TFIID) is a multiprotein complex that nucleates formation of the basal transcription machinery. TATA binding protein-associated factors 1 and 7 (TAF1 and TAF7), two subunits of TFIID, are integral to the regulation of eukaryotic transcription initiation and play key roles in preinitiation complex (PIC) assembly. Current models suggest that TAF7 acts as a dissociable inhibitor of TAF1 histone acetyltransferase activity and that this event ensures appropriate assembly of the RNA polymerase IImediated PIC before transcriptional initiation. Here, we report the 3D structure of a complex of yeast TAF1 with TAF7 at 2.9 Å resolution. The structure displays novel architecture and is characterized by a large predominantly hydrophobic heterodimer interface and extensive cofolding of TAF subunits. There are no obvious similarities between TAF1 and known histone acetyltransferases. Instead, the surface of the TAF1-TAF7 complex contains two prominent conserved surface pockets, one of which binds selectively to an inhibitory trimethylated histone H3 mark on Lys27 in a manner that is also regulated by phosphorylation at the neighboring H3 serine. Our findings could point toward novel roles for the TAF1-TAF7 complex in regulation of PIC assembly via reading epigenetic histone marks.initiation complex | protein structure | protein-protein interaction | X-ray crystallography T he general transcription factor II D (TFIID) plays a central role in recognition of the core promoter element and mediates accurate transcription initiation by RNA Polymerase (Pol) II for a large class of genes. TFIID nucleates the formation of the preinitiation complex (PIC) at the transcriptional start site by recruiting other general transcription factors (TFII-A, -B, -E, -F, and -H), along with RNA Pol II. TFIID is assembled in a stepwise manner, with a symmetric TFIID core complex recruited first, followed by further recruitment of additional TATA binding protein (TBP)-associated factors (TAFs) to form the complete asymmetric holo-TFIID complex (1). This megadalton-sized multiprotein assembly, comprised of TBP and 13 evolutionary conserved TAFs (2), is organized into a trilobed structure (3) and undergoes striking rearrangements upon binding to TFIIA and DNA (4). TAF subunits serve multiple functions within the TFIID holocomplex. In addition to TBP, TAF1, TAF2, TAF6, and TAF9 are also involved in recognition of DNA initiator and promoter elements. Moreover, TFIID can behave as an epigenetic effector, capable of recognizing posttranslational histone modifications associated with activated transcription. Eukaryotic TAF1 contains a double bromodomain that recognizes acetylated histones, and TAF3 contains a plant homeo domain (PHD) that binds to histone H3 methylated at lysine 4 (5, 6). In addition to roles in basal transcription, TFIID is also associated with diseases. Overexpression of TAF1, which acts as a specific coactivator of androgen receptor, is related to the progression of human prostate cancer (7). Additionally, altera...

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“…This modification counteracts the active transcriptional state by blocking the function of the H3K4 methyltransferase complexes COMPASS in yeast and ASH2/MLL in humans (39). Previously, H3R2me2a was shown to strongly reduce the binding affinity of AIRE-PHD1 to H3K4me0 (26) and of the TAF3-PHD finger to H3K4me3 (40), whereas only a limited effect was observed for the ING2-or BPTF-PHD fingers (30). This suggested that H3R2me2a plays distinct cross-talk roles for different proteins.…”

Section: Volume 286 • Number 42 • October 21 2011mentioning

confidence: 99%

Recognition of Unmodified Histone H3 by the First PHD Finger of Bromodomain-PHD Finger Protein 2 Provides Insights into the Regulation of Histone Acetyltransferases Monocytic Leukemic Zinc-finger Protein (MOZ) and MOZ-related factor (MORF)

Jin

Zhang

et al. 2011

Journal of Biological Chemistry

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MOZ (monocytic leukemic zinc-finger protein) and MORF (MOZ-related factor) are histone acetyltransferases important for HOX gene expression as well as embryo and postnatal development. They form complexes with other regulatory subunits through the scaffold proteins BRPF1/2/3 (bromodomain-PHD (plant homeodomain) finger proteins 1, 2, or 3). BRPF proteins have multiple domains, including two PHD fingers, for potential interactions with histones. Here we show that the first PHD finger of BRPF2 specifically recognizes the N-terminal tail of unmodified histone H3 (unH3) and report the solution structures of this PHD finger both free and in complex with the unH3 peptide. Structural analysis revealed that the unH3 peptide forms a third antiparallel ␤-strand that pairs with the PHD1 two-stranded antiparallel ␤-sheet. The binding specificity was determined primarily through the recognition of arginine 2 and lysine 4 of the unH3 by conserved aspartic acids of PHD1 and of threonine 6 of the unH3 by a conserved asparagine. Isothermal titration calorimetry and NMR assays showed that post-translational modifications such as H3R2me2as, H3T3ph, H3K4me, H3K4ac, and H3T6ph antagonized the interaction between histone H3 and PHD1. Furthermore, histone binding by PHD1 was important for BRPF2 to localize to the HOXA9 locus in vivo. PHD1 is highly conserved in yeast NuA3 and other histone acetyltransferase complexes, so the results reported here also shed light on the function and regulation of these complexes.Histone acetyltransferases (HATs) 3 are enzymes that catalyze the transfer of an acetyl group from acetyl-CoA to the ⑀-amino groups of lysine on histones, which results in important regulatory effects in chromatin structure and assembly as well as gene expression. HATs are highly diverse and generally form multiprotein complexes. Different HAT complexes are composed of various unique subunits, and the combination of these subunits contributes to the unique features of each HAT complex (1).MOZ (monocytic leukemic zinc-finger protein) and MORF (MOZ-related factor), a pair of large HATs of the MYST (Moz, Ybf2/Sas3, Sas2, Tip60) family, are important for hematopoiesis, skeletogenesis, neurogenesis, and other developmental processes, and they also have been implicated in leukemogenic and other tumorigenic progressions (2). A recent study in mice embryos reported that MOZ is required for normal levels of spatially correct Hox gene expression and for correct body segment identity. MOZ is specifically required for the H3K9 acetylation of active Hox gene loci (3). MOZ is also required for the maintenance of hematopoietic stem cells and plays a role in the differentiation of erythroid and myeloid cells (4). By contrast, MORF is required for the maintenance of undifferentiated neuronal progenitors and for adult neural stem cell self-renewal and neuronal differentiation (5). MOZ and MORF genes are often translocated in acute myeloid leukemia cells, producing either fusion proteins with CBP (cAMP-response elementbinding protein (CREB)-bind...

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Structural Insight into the Recognition of the H3K4me3 Mark by the TFIID Subunit TAF3

Cited by 126 publications

References 56 publications

Chromatin dynamics of the developmentally regulatedP. lividus neural alpha tubulin gene

Chromatin dynamics of the developmentally regulatedP. lividus neural alpha tubulin gene

Structural and functional insight into TAF1–TAF7, a subcomplex of transcription factor II D

Recognition of Unmodified Histone H3 by the First PHD Finger of Bromodomain-PHD Finger Protein 2 Provides Insights into the Regulation of Histone Acetyltransferases Monocytic Leukemic Zinc-finger Protein (MOZ) and MOZ-related factor (MORF)

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