In eukaryotes, the SET1 family of methyltransferases carry out the methylation of Lysine 4 on Histone H3. Alone, these enzymes exhibit low enzymatic activity and require the presence of additional regulatory proteins, which include RbBP5, Ash2L, WDR5 and DPY-30, to stimulate their catalytic activity. While previous structural studies established the structural basis underlying the interaction between RbBP5, Ash2L and WDR5, the formation of the Ash2L/DPY-30 complex remains elusive. Here we report the crystal structure of the Ash2L/DPY-30 complex solved at 2.2Å. Our results show that a Cterminal amphipathic α-helix on Ash2L makes several hydrophobic interactions with the DPY-30 homodimer. Moreover, the structure reveals that a tryptophan residue on Ash2L, which directly precedes its C-terminal amphipathic α-helix, makes key interactions with one of DPY-30 α-helix. Finally, biochemical studies of Ash2L revealed a hitherto unknown ability of this protein to bind anionic lipids.

The MAPK pathway is important in various biological functions. It is also important in regulating processes associated with gene transcription via different mechanisms such as by phosphorylation of transcription factors, coactivators/corepressors and histone modifier complexes. H3K4 methylation is highly associated with active transcription. Deposition of this mark is catalysed by SET-domain methyltransferases which consists of a WAR complex (WDR5, ASH2L and RBBP5), a catalytic SET-domain protein and other subunits. However, potential links between ERK MAPK signaling and H3K4 methylation in gene expression are not well understood. Thus, the aim of this study was to probe the potential links between these two pathways towards gene-regulatory networks. This study attempted to elucidate their direct functional interaction by studying whether components of the SETD1A complex could be phosphorylated upon ERK activation. Our results showed that the core components of SETD1A complex were not phosphorylated in vivo and in vitro by ERK. Importantly, we reported that at least two splicing variants of RBBP5 exist. ERK-dependent stabilization of exogenous RBBP5 was observed but the mechanism underlying this is unknown. Surprisingly, we found that WAR complex depletion increased the pre-mRNA expression of immediate-early (IE) genes which did not necessarily reflect changes in their mRNA levels. In addition, this occurred in an H3K4me3-independent manner. This regulation is likely to be posttranscriptional that involves pre-mRNA processing events. First, we noticed a decrease of transcription initiation in WAR complex-depleted cells upon ERK activation. Second, depletion of the WAR complex affects the splicing efficiency of FOS and EGR1. Third, RBBP5 occupancy was observed and was significantly reduced upon siRNA-mediated RBBP5 depletion at the coding region and the 3' end of FOS gene. Therefore, we propose that the WAR complex regulates the pre-mRNA processing of IE genes through an interaction between RBBP5 and a splicing factor that has yet to be identified.

Methylation of lysine residues in histone tails is an intensively studied epigenetic signal that regulates transcription throughout development. Methylation of histone 3 lysine 4 (H3K4) is usually associated with promoters of actively transcribed genes whereas H3K27 or H3K9 methylation silences genes. Yeast possess only one H3K4 methyltransferase, Set1. In contrast, there are six enzymes capable of catalyzing this modification in mammals implying a certain specialization or division of labor. The present study examined the functions of the mouse H3K4 methyltransferase paralogs, Mixed Lineage Leukemia 1 (Mll1) and Mll2, during neural differentiation and reprogramming of neural stem (NS) cells to induced pluripotency. We could show that Mll2 is required for differentiation of embryonic stem (ES) cells to neural progenitors and identified Nuclear transport factor 2-like export factor 2 (Nxt2) as essential target gene. Mll2 trimethylated the Nxt2 promoter in ES cells in order to allow for transcriptional upregulation during subsequent neural differentiation. Additionally, Mll2 prevented apoptosis of differentiating cells by regulating B cell leukemia/lymphoma 2 (Bcl2) levels. Mll1 could replace Mll2 after the first steps of cell commitment towards epiblast stem (EpiS) cells. While Mll2 activity was only required briefly when ES cells started to differentiate, the influence of Mll1 seemed to increase with developmental progression. It stabilized the NS cell state by regulating expression of the neural transcription factor Orthodenticle homolog 2 (Otx2). Thereby, Mll1 impeded early steps of reprogramming to induced pluripotency and its inactivation increased the efficiency. Besides their specificity for certain target genes, both enzymes also differed in their activity. The major function of Mll1 was to prevent silencing by H3K27 methylation and possibly recruitment of transcription factors. In contrast, Mll2 conducted H3K4 trimethylation of its target genes. Importantly, once established in NS cells, the expression of Nxt2 became independent of promoter H3K4 methylation. Thus, Mll2 and its target gene Nxt2 represent an example for H3K4 methylation functioning as priming mechanism rather than for fine-tuning or maintenance of transcription levels.

Methylation of lysine residues in histone tails is an intensively studied epigenetic signal that regulates transcription throughout development. Methylation of histone 3 lysine 4 (H3K4) is usually associated with promoters of actively transcribed genes whereas H3K27 or H3K9 methylation silences genes. Yeast possess only one H3K4 methyltransferase, Set1. In contrast, there are six enzymes capable of catalyzing this modification in mammals implying a certain specialization or division of labor. The present study examined the functions of the mouse H3K4 methyltransferase paralogs, Mixed Lineage Leukemia 1 (Mll1) and Mll2, during neural differentiation and reprogramming of neural stem (NS) cells to induced pluripotency. We could show that Mll2 is required for differentiation of embryonic stem (ES) cells to neural progenitors and identified Nuclear transport factor 2-like export factor 2 (Nxt2) as essential target gene. Mll2 trimethylated the Nxt2 promoter in ES cells in order to allow for transcriptional upregulation during subsequent neural differentiation. Additionally, Mll2 prevented apoptosis of differentiating cells by regulating B cell leukemia/lymphoma 2 (Bcl2) levels. Mll1 could replace Mll2 after the first steps of cell commitment towards epiblast stem (EpiS) cells. While Mll2 activity was only required briefly when ES cells started to differentiate, the influence of Mll1 seemed to increase with developmental progression. It stabilized the NS cell state by regulating expression of the neural transcription factor Orthodenticle homolog 2 (Otx2). Thereby, Mll1 impeded early steps of reprogramming to induced pluripotency and its inactivation increased the efficiency. Besides their specificity for certain target genes, both enzymes also differed in their activity. The major function of Mll1 was to prevent silencing by H3K27 methylation and possibly recruitment of transcription factors. In contrast, Mll2 conducted H3K4 trimethylation of its target genes. Importantly, once established in NS cells, the expression of Nxt2 became independent of promoter H3K4 methylation. Thus, Mll2 and its target gene Nxt2 represent an example for H3K4 methylation functioning as priming mechanism rather than for fine-tuning or maintenance of transcription levels.

In higher eukaryotes, the DNA base Cytosine can exist in a variety of modified forms when in the dinucleotide CpG. Although a methylated form tends to dominate within the genome, approximately 1% of all CpG dinucleotides are found unmodified at high densities spanning around 1Kb and tend to co-localise to the 5’ ends of around 60% of annotated gene promoters. These unique DNA sequences are known as CpG islands (CGIs) and their role within the genome to date is largely unknown. Methylation of CGIs in cancers however has been linked to silencing of associated genes implying a role in gene regulation. Furthermore these sites are also interesting as they remain specifically nonmodified within a genome rich in methylated CpG. We set out to better understand the roles for CGIs through the characterisation of any specific CGI binding proteins. Digestion of nuclei with methyl sensitive restriction enzymes facilitates the purification of CGI fragments. Subsequent immunohistochemistry on the CGI chromatin fragments along with ChIP-PCR over several CGIs revealed an enrichment of the “active” histone modifications including H3K4me3, a depletion of the “silencing” marks such as H3K27me3, as well as a group of CGI specific binding factors. These latter proteins contained a domain previously shown to bind to non-methylated CpG dinucleotides (the CXXC domain) and as such were ideal candidates for CGI specific factors, in particular a protein called Cfp1. Genome wide sequencing revealed a striking correlation between Cfp1 and H3K4me3 which were both seen at around 80% of islands. Furthermore, the presence of Cfp1/H3K4me3 at islands tended to have a negative correlation with the presence of chromatin rich in the silencing histone modification H3K27me3. Closer investigation of the Cfp1 protein reveals it to be a true non-methyl CGI binding factor in vivo and shRNA reduction of Cfp1 levels to around 10% of wild type resulted in a precipitous drop in H3K4me3 levels over CGIs without a dramatic reduction in global H3K4me3 levels. As Cfp1 has been shown to be part of the Set1 histone H3K4 methyltransferase complex responsible for this modification, this CXXC protein may be attracting this histone modifying complex and as such represents a method whereby the underlying DNA sequence (CpG) can drive the overlying epigenetic state. This study may go some way to understanding the functional significance of CGIs within the genome.

Indiana University-Purdue University Indianapolis (IUPUI) / Setd1 histone 3 lysine 4 methyltransferases are critical for epigenetic regulation and gene expression. Setd1a is multiprotein complex comprised of several critical subunits including wdr82, which is essential for embryonic development, and cfp1, critical for regulation of both activation and repression of transcriptional programs required in basic and developmental cellular processes.

No description available.

Covalent modification of histones is an important factor in the regulation of the chromatin structure implicated in DNA replication, repair, recombination, and transcription, as well as in RNA processing. In recent years, histone methylation has emerged as one of the key modifications regulating chromatin function. However, the mechanisms involved are complex and not well understood. Histone 3 lysine 4 (H3K4) methylation is deposited by a family of histone H3K4 methyltransferases (HMTs) that share a conserved SET domain. In mammalian cells, six family members have been characterized: Setd1a and Setd1b (the mammalian orthologs of yeast Set1) and four Mixed lineage leukemia (Mll) family HMTs, which share limited similarity with yeast Set1 beyond the SET domain. Several studies demonstrated that the H3K4 methyltransferases exist as multiprotein complexes. To functionally dissect H3K4 methyltransferase complexes, GFP tagging of the core subunit Ash2l and the complex-specific subunits Cxxc1 and Wdr82 (Setd1a/b complexes) Men1 (Mll1/2 complexes), and Ptip (Mll3/Mll4 complexes), was used. The fusion proteins were successfully expressed in mouse embryonic stem cells (ES cells), analyzed by confocal microscopy, Mass Spectrometry (MS) and ChIP-seq. Ptip was the only subunit able to bind mitotic chromatin. Additionally, both Ptip and Wdr82 were found to associate with cell cycle regulators, suggesting a possible role of the two proteins or respective complexes in cell cycle regulation. Mass Spectrometry revealed that Wdr82 and Ptip interact with members of he PAF complex, and ChIP-seq showed that Wdr82, Cxxc1 and Ptip positively modulate pluripotency genes. Thus, Setd1a/b and Mll3/4 complexes might act together in the regulation of embryonic stem cells identity. Protein pull downs identified at least one new Setd1a/b interactor, Bod1l that is orthologous to the yeast protein Sgh1, a component of the Set1C complex. Furthermore, our MS and ChIP-seq data suggested that only Mll2 complex binds to bivalent promoters, wheras Mll2 and Setd1a complexes might function together in a set of promoters.

Covalent modification of histones is an important factor in the regulation of the chromatin structure implicated in DNA replication, repair, recombination, and transcription, as well as in RNA processing. In recent years, histone methylation has emerged as one of the key modifications regulating chromatin function. However, the mechanisms involved are complex and not well understood. Histone 3 lysine 4 (H3K4) methylation is deposited by a family of histone H3K4 methyltransferases (HMTs) that share a conserved SET domain. In mammalian cells, six family members have been characterized: Setd1a and Setd1b (the mammalian orthologs of yeast Set1) and four Mixed lineage leukemia (Mll) family HMTs, which share limited similarity with yeast Set1 beyond the SET domain. Several studies demonstrated that the H3K4 methyltransferases exist as multiprotein complexes. To functionally dissect H3K4 methyltransferase complexes, GFP tagging of the core subunit Ash2l and the complex-specific subunits Cxxc1 and Wdr82 (Setd1a/b complexes) Men1 (Mll1/2 complexes), and Ptip (Mll3/Mll4 complexes), was used. The fusion proteins were successfully expressed in mouse embryonic stem cells (ES cells), analyzed by confocal microscopy, Mass Spectrometry (MS) and ChIP-seq. Ptip was the only subunit able to bind mitotic chromatin. Additionally, both Ptip and Wdr82 were found to associate with cell cycle regulators, suggesting a possible role of the two proteins or respective complexes in cell cycle regulation. Mass Spectrometry revealed that Wdr82 and Ptip interact with members of he PAF complex, and ChIP-seq showed that Wdr82, Cxxc1 and Ptip positively modulate pluripotency genes. Thus, Setd1a/b and Mll3/4 complexes might act together in the regulation of embryonic stem cells identity. Protein pull downs identified at least one new Setd1a/b interactor, Bod1l that is orthologous to the yeast protein Sgh1, a component of the Set1C complex. Furthermore, our MS and ChIP-seq data suggested that only Mll2 complex binds to bivalent promoters, wheras Mll2 and Setd1a complexes might function together in a set of promoters.

La chromatine est essentielle au maintien de l’intégrité du génome, mais, ironiquement, constitue l’obstacle principal à la transcription des gènes. Plusieurs mécanismes ont été développés par la cellule pour pallier ce problème, dont l’acétylation des histones composant les nucléosomes. Cette acétylation, catalysée par des histones acétyl transférases (HATs), permet de réduire la force de l’interaction entre les nucléosomes et l’ADN, ce qui permet à la machinerie transcriptionnelle de faire son travail. Toutefois, on ne peut laisser la chromatine dans cet état permissif sans conséquence néfaste. Les histone déacétylases (HDACs) catalysent le clivage du groupement acétyle pour permettre à la chromatine de retrouver une conformation compacte. Cette thèse se penche sur la caractérisation de la fonction et du mécanisme de recrutement des complexes HDACs Rpd3S et Set3C. Le complexe Rpd3S est recruté aux régions transcrites par une interaction avec le domaine C-terminal hyperphosphorylé de Rpb1, une sous-unité de l’ARN polymérase II. Toutefois, le facteur d’élongation DSIF joue un rôle dans la régulation de cette association en limitant le recrutement de Rpd3S aux régions transcrites. L’activité HDAC de Rpd3S, quant à elle, dépend de la méthylation du résidu H3K36 par l’histone méthyltransférase Set2. La fonction du complexe Set3C n’est pas clairement définie. Ce complexe est recruté à la plupart de ses cibles par l’interaction entre le domaine PHD de Set3 et le résidu H3K4 di- ou triméthylé. Un mécanisme indépendant de cette méthylation, possiblement le même que pour Rpd3S, régit toutefois l’association de Set3C aux régions codantes des gènes les plus transcrits. La majorité de ces résultats ont été obtenus par la technique d’immunoprécipitation de la chromatine couplée aux biopuces (ChIP-chip). Le protocole technique et le design expérimental de ce type d’expérience fera aussi l’objet d’une discussion approfondie. / Chromatin is essential for the maintenance of genomic integrity but, ironically, is also the main barrier to gene transcription. Many mechanisms, such as histone acetylation, have evolved to overcome this problem. Histone acetylation, catalyzed by histone acetyltransferases (HATs), weakens the internucleosomal and nucleosome-DNA interactions, thus permitting the transcriptional machinery access to its template. However, this permissive chromatin state also allows for opportunistic DNA binding events. Histone deacetylases (HDACs) help restore a compact chromatin structure by catalyzing the removal of acetyl moieties from histones. This thesis focuses on the characterization of the function and of the recruitment mechanism of HDAC complexes Rpd3S and Set3C. The Rpd3S complex is recruited to actively transcribed coding regions through interactions with the hyperphosphorylated C-terminal domain of Rpb1, a subunit of RNA polymerase II, with the DSIF elongation factor playing a role in limiting this recruitment. However, the HDAC activity of Rpd3S depends on H3K36 methylation, which is catalyzed by the Set2 histone methyltransferase. The Set3C complex’ function is still not clearly defined. It is recruited to most of its targets through the interaction between the Set3 PHD domain and di- or trimethylated H3K4. However, Set3C recruitment to genes displaying high RNA polymerase II occupancy is independent of H3K4 methylation. The mechanism by which Set3C is recruited to this gene subset is under investigation. These results have mostly been obtained through chromatin immunoprecipitation coupled to tiling microarrays (ChIP-chip). The protocol and experimental design challenges inherent to this technique will also be discussed in depth.