H3K27me3 Binding Research Articles

Low expression of endothelin receptor B (EDNRB) is related to H3K9me3 binding with the EDNRB promoter region and is associated with the clinical T tumor stage in salivary adenoid cystic carcinoma

To investigate the endothelin receptor B (EDNRB) expression in salivary adenoid cystic carcinoma (ACC) and the mechanism of the regulation of EDNRB expression. After screening, EDNRB was selected, and the expression was detected using immunohistochemistry in 33 ACC samples (including 6 clinical tumor stage 1 [T1] patients, 13 T2 patients, 9 T3 patients, and 5 T4 patients) and 20 adjacent glands. Interaction between the EDNRB promoter region and histone H3 lysine 9 trimethylation (H3K9me3) was examined using chromatin immunoprecipitation (ChIP) in combination with ChIP-polymerase chain reaction (ChIP-PCR). EDNRB expression in ACC cells treated with chaetocin was detected using quantitative real-time PCR (qRT-PCR) and Western blot tests. EDNRB expression was lower in ACC than that in adjacent glands (P = .006). The expression of EDNRB in patients with advanced T stage was lower than that in patients with early T stage (P = .024). The low EDNRB gene expression group had more H3K9me3 binding regions in the gene promoter (P = .003). EDNRB gene expression significantly increased in the ACC cell lines after treatment with chaetocin. Chaetocin could reduce the interaction between the EDNRB promoter and H3K9me3. H3K9me3 binding to the EDNRB promoter region could reduce the EDNRB expression. Low EDNRB expression played a role in the progression of ACC tumors.

Abstract P6-07-02: Amplified DERE-mediated epigenetic repression in ERα-mediated breast tumorigenesis

Abstract Epidemiological studies reveal that maternal exposure to estrogenic chemicals during pregnancy results in higher risk of breast cancer in offspring. One of possible causal mechanisms is epigenetic reprogramming, but how estrogen/ERα signaling contributes to tumorigenesis through epigenetic machinery remains unclear. In this study, we demonstrate that the epigenetic modulation mediated by estrogen-driven amplification of distant-acting regulatory elements, or enhancers, may be an explanation addressing to this question. Enhancers contain transcription factor binding sites known to remotely regulate transcription through chromatin looping or transvection. Using our in vitro model to mimic maternal estrogen exposure and a "Seq-to-Seek" strategy integrating three next-generation sequencing approaches, we comprehensively mapped distant estrogen response elements (DEREs) that remotely control transcription of target genes through chromatin proximity. Surprisingly, a densely mapped DERE region located on chromosome 20q13 frequently amplifies in ERα-positive breast cancer with poor prognosis. Progressive accumulation of DERE copies was observed in normal breast progenitor and cancer cells chronically exposed to estrogen. Upon estrogen stimulation, these aberrantly amplified DEREs are clustered as a potential transcriptional depot for suppressing target gene expression through altering chromatin interactions, leading to accumulation of repressive histone marks (e.g. trimethylated H3K27 and H3K9), polycomb repressive complex 2, the presence of heterochromatin protein 1 (HP1) and DNA methylation, following prevention of RNA polymerase II and active histone mark- H3K4me3 binding. Furthermore, neutralization of HP1 function can significantly attenuate estrogen-driven DERE clustering and DERE-mediated repressive chromatin interactions, resulting in inhibition of cell proliferation. Deletion of the interested DERE regions using CRISPR/Cas9 genomic editing system further demonstrated that DERE-driven remote transcriptional control play a crucial role in tumor cell growth. Our data support a model in which amplified DEREs preferentially induce repressive epigenetic modulation of target genes. These findings indicate that 20q13 DERE region is a potential transcriptionally repressive domain whose aberrant amplification can result in suppressing expression of tumor suppressor genes, leading to tumorigenesis. In summary, our findings suggest that amplification of DNA regulatory elements can profoundly alter target transcriptome during tumorigenesis and amplified DEREs can be used as potential prognostic markers for endocrine resistance and predicative for progeny at risk of breast cancer. Citation Format: Pei-Yin Hsu, Hang-Kai Hsu, Yi-dong Chen, Victor X Jin, Zelton D Sharp, Tim H-M Huang. Amplified DERE-mediated epigenetic repression in ERα-mediated breast tumorigenesis [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-07-02.

The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output

Phosphoinositides (PI) are important signalling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly impacts on the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates nuclear PI5P and the expression of myogenic genes during myoblast differentiation. A targeted screen for PI interactors identified the PHD finger of TAF3, a TATA box binding protein associated factor with important roles in transcription regulation, pluripotency and differentiation. We show that the PI interaction site is distinct from the known H3K4me3 binding region of TAF3 and that PI binding modulates association of TAF3 with H3K4me3 in vitro and with chromatin in vivo. Analysis of TAF3 mutants indicates that TAF3 transduces PIP4K2B-mediated alterations in PI into changes in specific gene transcription. Our study reveals TAF3 as a direct target of nuclear PI and further illustrates the importance of basal transcription components as signal transducers.

H3K9me3 Binding to the DNA Promoter Causes the Inactivation of EDNRB Gene in ACC Tumors

H3K9me3 Binding to the DNA Promoter Causes the Inactivation of EDNRB Gene in ACC Tumors

Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain

Chromobox homolog 7 (CBX7) plays an important role in gene transcription in a wide array of cellular processes, ranging from stem cell self-renewal and differentiation to tumor progression. CBX7 functions through its N-terminal chromodomain (ChD), which recognizes trimethylated lysine 27 of histone 3 (H3K27me3), a conserved epigenetic mark that signifies gene transcriptional repression. In this study, we report the discovery of small molecules that inhibit CBX7ChD binding to H3K27me3. Our crystal structures reveal the binding modes of these molecules that compete against H3K27me3 binding through interactions with key residues in the methyl-lysine binding pocket of CBX7ChD. We further show that a lead compound, MS37452, derepresses transcription of Polycomb repressive complex target gene p16/CDKN2A by displacing CBX7 binding to the INK4A/ARF locus in prostate cancer cells. These small molecules have the potential to be developed into high-potency chemical modulators that target CBX7 functions in gene transcription in different disease pathways.

Chromatin State Shaping the Gene Expression Profiling in the Inducible Differentiation of Promyelocytic Leukemia Cells

Background Epigenetic changes in DNA and chromatin are regarded as emerging major players for hematopoietic stem cells development and lineage differentiation. Epigenetic deregulation of gene expression leads to leukemia and reversibility of epigenetic modifications makes DNA and chromatin changes attractive targets for therapeutic intervention. The promyelocytic leukemia HL-60 cell can differentiate into microphage, granulocyte and monocyte with stimulation of phorbol myristic acid (PMA), dimethylsulfoxide (DMSO), and Vitamin D3, respectively, by affecting the gene expression on cell cycle and cell differentiation. However, how epigenetic regulation on gene expression in the inducible differentiation is still undetermined.Methods and Results We did the microarray analysis to identify the genome-wide gene expression profile of HL-60 cells in various time points(0h, 6h, 1d,2d,4d and 6d) under the treatment of PMA, DMSO and D3 and found that around 3000 genes are significantly altered commonly in the cells upon the 3 treatments. The percentage of down-regulated genes in the all commonly altered genes is significantly higher than that of up-regulated genes, and the significantly altered genes showed significantly physical clustering on chromosome loci, indicating the epigenetic regulation involved in the regulation of the gene expression. We did observed the expression changes of epigenetic enzymes in the process and further did the ChIP-on-ChIP analysis by using the customer array tiling the selected changed genes and 5 genomic loci hybridizing with ChIP’d DNA of histone markers (H3K4me3, H3K9me3 and H3K27me3). We found that the obvious decrease of H3K4me3 binding and increase of H3K9me3 and H3K27me3 are observed in the promoter of the commonly down-regulated genes. These data indicated histone H3K4, H3K9 and H3K27 marker play important roles in shaping the chromatin state and regulating gene expression.Conclusion We identified the signature genes controlling the inducible differentiation of promyelocytic leukemiacells and found the epigenetic mechanism regulating the gene expression in the process. DisclosuresNo relevant conflicts of interest to declare.

Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat.

Long non-coding RNAs (lncRNAs) are potentially important mediators of genomic regulation. lncRNAs, however, remain poorly characterized in the rat model organism widely used in biomedical research. Using poly(A)-independent and strand-specific RNA-seq, we identified 1,500 to 1,800 lncRNAs expressed in each of the following tissues of Brown Norway rats: the renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, and hypothalamus. Expression and the binding of histone H3K4me3 to promoter regions were confirmed for several lncRNAs. Rat lncRNA expression appeared to be more tissue-specific than mRNA. Rat lncRNAs had 4.5 times fewer exons and 29% shorter transcripts than mRNA. The median cumulative abundance of rat lncRNAs was 53% of that of mRNA. Approximately 28% of the lncRNAs identified in the renal outer medulla appeared to lack a poly(A) tail. Differential expression of 74 lncRNAs was detected in the renal outer medulla between Dahl SS rats, a model of salt-sensitive hypertension, and salt-insensitive, congenic SS.13BN26 rats fed a high-salt diet. Two of the differentially expressed lncRNAs, which were confirmed, were located within the congenic region and contained several sequence variants. The study identified genome-wide characteristics of lncRNAs in the rat model and suggested a role of lncRNAs in hypertension.

Abstract 570: Characteristics of Long Non-coding RNAs in the Brown Norway Rat and Alterations in the Dahl Salt-Sensitive Rat

Long non-coding RNAs (lncRNAs) are emerging as important mediators of genomic regulation. lncRNAs, however, remain poorly characterized in the rat model organism, which is widely used in hypertension research. Using poly(A)-independent and strand-specific RNA-seq, we identified approximately 1,500 to 1,800 lncRNAs expressed in each of the following tissues of Brown Norway rats: the renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, and hypothalamus. Expression patterns and the binding of histone H3K4me3 to promoter regions were confirmed for several of the identified lncRNAs. Patterns of rat lncRNA expression appeared to be more tissue-specific than mRNA. Rat lncRNAs, on average, had similar lengths to mRNA but substantially fewer exons. The median abundance of rat lncRNAs was approximately 40% of that of mRNA. Approximately 28% of the lncRNAs identified in the renal outer medulla appeared to lack a poly(A) tail. Differential expression of 74 lncRNAs was detected in the renal outer medulla between Dahl salt-sensitive SS rats and salt-insensitive, congenic SS.13BN26 rats fed a high-salt diet. Two of the differentially expressed lncRNAs, which were confirmed, were located within the substituted congenic region. The study identified genome-wide characteristics of lncRNAs in the rat model and suggested a role of lncRNAs in hypertension.

Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq

Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI.

Leukemia Driven By a NUP98-Phd Domain Fusion Is Highly Sensitive To Disruption Of H3K4me3-Phd Domain Binding By a Small Molecule Inhibitor

NUP98 gene fusions, created by non-random chromosomal translocations, are associated with a wide spectrum of high risk hematologic malignancies, and typically lead to overexpression of abdominal-b HOXA genes, a common theme shared by ∼50% of AML patients. We have generated a transgenic mouse model of the NUP98-PHF23 (NP23) gene fusion, initially identified in patients with AML, which develop AML, erythroleukemia, pre-T lymphoblastic leukemia (pre-T LBL), and a novel pre-B1 B cell acute lymphoblastic leukemia (pre-B1 ALL). A common theme in the leukemias and the premalignant hematopoietic tissues, is the overexpression of a Hoxa/b +Meis1 stem cell-like gene expression signature. GSEA analysis reveals this signature to be enriched in both human AML and ALL malignancies, and in human HSPC profiles. In addition, we found Bahcc1, a gene not previously associated with malignancy, to consistently segregate with the Hoxa/b+Meis1 signature in the NP23 leukemias and the premalignant tissues, independent of hematopoietic cell lineage. Furthermore, data-mining revealed BAHCC1 to be markedly overexpressed in AML patients with HOXA9/MEIS1 overexpression, and in a subset of MLL rearranged pre-B-ALL patients, suggesting BAHCC1 may be a previously unsuspected marker of leukemic transformation.NUP98-PHF23 belongs to a subset of fusion oncoproteins (including some MLL- and NUP98-fusions) that are potently tumorigenic and act by abrogating the normal reading, writing and erasure of histone methylation. Wild type PHF23 binds H3K4me3 residues via a PHD domain, therefore we used ChIP-seq to characterize global chromatin H3K4me3 and NP23 enrichment in NP23 leukemia derived cell lines. The vast majority (88%) of NP23 binding sites were enriched for H3K4me3 binding. Conversely, the NP23 protein co-localized at only 1.6% of all H3K4me3 enriched sites (including Hoxa, Hoxb and Meis1 loci) identifying these sites as direct targets of the NP23 fusion protein. Given that the NP23 fusion appears to function, at least in part, via binding to H3K4me3 sites at specific loci, we hypothesized that NP23 cells would be sensitive to disruption of the H3K4me4 binding by the NP23 PHD domain. Treatment of leukemic NP23 cells with Tetraethylthiuram disulfide (Disulfiram), a small molecule shown to inhibit PHD domain binding of H3K4me3 marks in vitro, rapidly and selectively killed NP23 myeloblasts but not control myeloblast cell lines (188G3, 189E6 and 32D) at 2 µM. Cell death was rapid, being 100% complete within 24 hours. Cell death was preceded by decreased levels of NP23 protein bound at target loci and decreased expression of these loci (e.g., Hoxa7/9/10, Hoxb5 and Meis1). We conclude that inhibitors of H3K4me3 PHD domain readers are promising therapeutic compounds that can kill leukemic cells driven by proteins that aberrantly read or write the histone code. The NP23 model provides a robust platform on which to identify and improve such compounds. Disclosures:Denu:Sirtris-GSK: Consultancy.

An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer

BackgroundPancreatic cancer is a highly lethal cancer with limited diagnostic and therapeutic modalities.MethodsTo begin to explore the genomic landscape of pancreatic cancer, we used massively parallel sequencing to catalog and compare transcribed regions and potential regulatory elements in two human cell lines derived from normal and cancerous pancreas.ResultsBy RNA-sequencing, we identified 2,146 differentially expressed genes in these cell lines that were enriched in cancer related pathways and biological processes that include cell adhesion, growth factor and receptor activity, signaling, transcription and differentiation. Our high throughput Chromatin immunoprecipitation (ChIP) sequence analysis furthermore identified over 100,000 regions enriched in epigenetic marks, showing either positive (H3K4me1, H3K4me3, RNA Pol II) or negative (H3K27me3) correlation with gene expression. Notably, an overall enrichment of RNA Pol II binding and depletion of H3K27me3 binding were seen in the cancer derived cell line as compared to the normal derived cell line. By selecting genes for further assessment based on this difference, we confirmed enhanced expression of aldehyde dehydrogenase 1A3 (ALDH1A3) in two larger sets of pancreatic cancer cell lines and in tumor tissues as compared to normal derived tissues.ConclusionsAs aldehyde dehydrogenase (ALDH) activity is a key feature of cancer stem cells, our results indicate that a member of the ALDH superfamily, ALDH1A3, may be upregulated in pancreatic cancer, where it could mark pancreatic cancer stem cells.

Epigenetic control of hematopoietic stem

The balance between self-renewal and differentiation of adult stem cells is essential for tissue homeostasis. Here we show that in the haematopoietic system this process is governed by polycomb chromobox (Cb×) proteins. Cb×7 is specifically expressed in haematopoietic stem cells (HSCs), and its overexpression enhances self-renewal and induces leukaemia. This effect is dependent on integration into polycomb repressive complex-1 (PRC1) and requires H3K27me3 binding. In contrast, overexpression of Cb×2, Cb×4 or Cb×8 results in differentiation and exhaustion of HSCs.

Role of Macrophage Receptor with Collagenous Structure in Innate Immune Tolerance

Macrophages play a key role in host defense against microbes, in part, through phagocytosis. Macrophage receptor with collagenous structure (MARCO) is a scavenger receptor on the cell surface of macrophages that mediates opsonin-independent phagocytosis. The goal of our study is to investigate the role of MARCO in LPS or lipotechoic acid-induced macrophage tolerance. Although it has been established that expression of MARCO and phagocytosis is increased in tolerant macrophages, the transcriptional regulation and biological role of MARCO in tolerant macrophages have not been investigated. In this study, we confirm that tolerized mouse bone marrow-derived macrophages (BMDM) selectively increase expression of MARCO (both transcript and cell surface receptor) and increase phagocytosis. We found that H3K4me3 dynamic modification of a promoter site of MARCO was increased in tolerized BMDM. Blocking methylation by treatment with 5-aza-2'-deoxycytidine resulted in reduced H3K4me3 binding in the promoter of MARCO, decreased expression of MARCO, and impaired phagocytosis in tolerized BMDM. However, 5-aza-2'-deoxycytidine had no effect on the inflammatory component of innate immune tolerance. In aggregate, we found that histone methylation was critical to MARCO expression and phagocytosis in tolerized macrophages, but did not affect the inflammatory component of innate immune tolerance.

The Scaffold attachment factor b1 (Safb1) regulates myogenic differentiation by facilitating the transition of myogenic gene chromatin from a repressed to an activated state

The regulation of skeletal muscle gene expression during myogenesis is mediated by lineage-specific transcription factors in combination with numerous cofactors, many of which modify chromatin structure. However, the involvement of scaffolding proteins that organize chromatin and chromatin-associated regulatory proteins has not extensively been explored in myogenic differentiation. Here, we report that Scaffold attachment factor b1 (Safb1), primarily associated with transcriptional repression, functions as a positive regulator of myogenic differentiation. Knockdown of Safb1 inhibited skeletal muscle marker gene expression and differentiation in cultured C2C12 myoblasts. In contrast, over-expression resulted in the premature expression of critical muscle structural proteins and formation of enlarged thickened myotubes. Safb1 co-immunoprecipitated with MyoD and was co-localized on myogenic promoters. Upon Safb1 knockdown, the repressive H3K27me3 histone mark and binding of the Polycomb histone methyltransferase Ezh2 persisted at differentiation-dependent gene promoters. In contrast, the appearance of histone marks and regulators associated with myogenic gene activation, such as myogenin and the SWI/SNF chromatin remodelling enzyme ATPase, Brg1, was blocked. These results indicate that the scaffold protein Safb1 contributes to the activation of skeletal muscle gene expression during myogenic differentiation by facilitating the transition of promoter sequences from a repressive chromatin structure to one that is transcriptionally permissive.

Interactions of all‐trans retinoic acid and interleukin‐4 in the development of alternatively activated lung macrophages

Previously, we showed that all‐trans retinoic acid (ATRA), the most active vitamin A (VA) metabolite, increased in vitro polarization of pig alveolar macrophages (AM) toward an AAM phenotype after interleukin‐4 (IL‐4) treatment and increased the expression of IL‐4 in the lungs of pigs infected with the parasite, Ascaris suum. Others have shown that VA may reduce the susceptibility to additional parasitic infections in animals and humans. The mechanism(s) underlying these effects of VA remain undetermined. Herein, we demonstrate that AM, treated in vitro with IL‐4 or isolated from the lungs of A. suum infected pigs, had 2–8‐fold increases in mRNA expression of alcohol and aldehyde dehydrogenases involved in ATRA generation. At the epigenetic level, ATRA increased mRNA expression of cytochrome P450, family 26, subfamily A, polypeptide 1 (CYP26A1), an enzyme involved in ATRA catabolism, through a 7‐fold increase in methylated activator histone H3K4me3 binding to the CYP26A1 promoter. In contrast, IL‐4 pre‐treatment reduced ATRA‐induced CYP26A1 mRNA expression 4‐fold through a 4 fold increase, above control, in the binding of methylated repressor histone H3K27me3 to the promoter. In conclusion, VA, via metabolism to ATRA, and IL‐4, by favoring conditions that lead to increased ATRA, may synergistically sustain an AAM response to Th2‐dependent responses.Grant Funding Source: USDA/ARS Project Plan 1235–51000‐055–00D.

Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation

The balance between self-renewal and differentiation of adult stem cells is essential for tissue homeostasis. Here we show that in the haematopoietic system this process is governed by polycomb chromobox (Cbx) proteins. Cbx7 is specifically expressed in haematopoietic stem cells (HSCs), and its overexpression enhances self-renewal and induces leukaemia. This effect is dependent on integration into polycomb repressive complex-1 (PRC1) and requires H3K27me3 binding. In contrast, overexpression of Cbx2, Cbx4 or Cbx8 results in differentiation and exhaustion of HSCs. ChIP-sequencing analysis shows that Cbx7 and Cbx8 share most of their targets; we identified approximately 200 differential targets. Whereas genes targeted by Cbx8 are highly expressed in HSCs and become repressed in progenitors, Cbx7 targets show the opposite expression pattern. Thus, Cbx7 preserves HSC self-renewal by repressing progenitor-specific genes. Taken together, the presence of distinct Cbx proteins confers target selectivity to PRC1 and provides a molecular balance between self-renewal and differentiation of HSCs.

Histone Alterations Are Associated with Hematopoietic Stem Cell (HSC) Differentiation and Aging

AbstractAbstract 1188Chromatin regulators, including both Trithorax-group (trxG) and Polycomb-group (PcG) families, have been reported to maintain hematopoietic stem cells (HSC) self-renewal and differentiation. However, their primary targets in HSC remain to be fully identified. Moreover, those histone modifiers have been recently found to control longevity in C.elegans, which leads us to further investigate their roles in HSC aging. HSCs increase in number, decrease in regeneration capacity, and exhibit a myeloid biased differentiation with age. In this study, we profiled global mRNA (RNA-seq) and chromatin changes (ChIP-seq) in highly purified young (4 month) and old (24 month) murine bone marrow-derived HSCs (SP-KSL-CD150+). One key challenge in this study is that mouse HSCs represent less than 0.01% of all bone marrow cells. Thus, we first developed and optimized a method for successful application of ChIP-seq to a limited number of cells (<20,000 cells). This method allowed us to generate the binding profiles for H3K4me3, H3K27me3 and H3K36me3 in young and old HSCs, differentiated granulocytes (Gr1+) and B (B220+) cells.In young HSCs, we determined ∼18,000 peaks for the active gene mark H3K4me3. For the repressive mark H3K27me3, we identified ∼6000 peaks across the genome, 2591 of which were present in the promoter region defined as the transcriptional start site (TSS) ± 100 bp. Strikingly, 70.2% (1820 out of 2591) of H3K27me3-enriched genes were also bound by H3K4me3. These so-called “Bivalent genes”, with both H3K4me3 and H3K27me3, are also found in embryonic stem cell (ESC) where they represent master regulators for lineage development. Here we found that these 1820 genes in HSC are prevalent in development, transcriptional regulation and RNA metabolism. They include many lineage-specific transcription factors, such as Cebpa, Ebf-1, Pax5, Gata3, Tbx21, Runx3 and Eomes. During HSC differentiation to granulocytes or B cells, HSC pluripotency regulators acquired the H3K27me3 repressive mark, while lineage regulators lost it in differentiated lineages. In addition, we observed with HSC differentiation alternative promoter usage on many epigenetic modifiers or transcription factors, such as Dnmt3a, Dnmt3b and Kdm6b (Jmjd3) and Runx3. The different isoforms may have different functions in hematopoiesis.Compared to HSC differentiation, HSC aging showed less extensive chromatin changes. Increased H3K4me3 binding at the TSS was identified for ∼300 genes, including Selp, Nupr1, Sdpr, Plscr2, Slamf1 (CD150) and Mt1. Interestingly, several genes in the Hoxb cluster showed increased H3K4me3 binding and higher expression with age. For H3K27me3, although PcG family member EZh2 expression decreases with HSC aging, we did not detect a global H3K27me3 decrease. On the contrary, H3K27me3 binding increased at ∼500 genes and decreased at ∼100 genes. Among them, the lymphoid transcription factors Pax5 and Ebf1 exhibited increased H3K27me3 binding. The enhanced repression of these lymphoid regulators may explain the myeloid-skewed differentiation that occurs with age. We also observed increased H3K27me3 on several Wnt ligands, including Wnt2a, Wnt8a and Wnt8b. As Wnt signaling is required for active HSC cycling, the increased H3K27me3 binding on these ligands may reinforce HSC quiescence. One well known target of the PcG family in aging is Cdkn2a (p16), which showed progressive loss of H3K27me3 repression with aging in neural stem cell (NSC). In contrast, our results revealed that p16 is repressed by H3K27me3 in both 4M and 24M HSC, and we did not observe its expression increase with aging. However, another cell cycle regulator p21 expression increases with aging, accompanied by a decrease of H3K27me3.In summary, we mapped chromatin state alterations with HSC differentiation and aging in this study. These findings will advance our fundamental understanding of HSC biology. Furthermore, chromatin regulators, such as Bmi1 and EZh2, have been implicated in leukemia transformation. This study provides a mechanistic link into how deregulation of these factors correlates with cancer progression. Disclosures:No relevant conflicts of interest to declare.

Comparative Epigenomic Annotation of Regulatory DNA

Despite the explosive growth of genomic data, functional annotation of regulatory sequences remains difficult. Here, we introduce "comparative epigenomics"-interspecies comparison of DNA and histone modifications-as an approach for annotation of the regulatory genome. We measured in human, mouse, and pig pluripotent stem cells the genomic distributions of cytosine methylation, H2A.Z, H3K4me1/2/3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, transcribed RNAs, and P300, TAF1, OCT4, and NANOG binding. We observed that epigenomic conservation was strong in both rapidly evolving and slowly evolving DNA sequences, but not in neutrally evolving sequences. In contrast, evolutionary changes of the epigenome and the transcriptome exhibited a linear correlation. We suggest that the conserved colocalization of different epigenomic marks can be used to discover regulatory sequences. Indeed, seven pairs of epigenomic marks identified exhibited regulatory functions during differentiation of embryonic stem cells into mesendoderm cells. Thus, comparative epigenomics reveals regulatory features of the genome that cannot be discerned from sequence comparisons alone.

Abstract 993: A high-throughput peptide array screen of H3K9 methyl effectors identifies UHRF1 as an exception to the “phospho/methyl switch.”

Abstract Increasing evidence suggests that histone post-translational modifications (PTMs) function in combination to regulate the diverse activities associated with chromatin. However, the mechanisms through which multiple histone PTMs influence the association of effector proteins with chromatin is poorly understood. To address this problem, we recently developed a histone peptide array platform containing singly- and multiply-modified histone peptides to examine the binding of chromatin-associated proteins. Using these arrays, we surveyed protein domains that bound methylated H3K9, and uncovered a number of PTM “patterns” that influenced the association with this mark. Interestingly, while most H3K9 methyl binders were ejected by neighboring H3S10 phosphorylation (a PTM enriched in G2/M-phase chromatin), the tandem Tudor domain (TTD) of UHRF1 was insensitive to this known “phospho/methyl switch”. In agreement, structural and biophysical studies confirmed the insensitivity of the UHRF1 TTD to H3S10 phosphorylation. Furthermore, we found that UHRF1 remains bound to chromatin throughout the cell cycle in contrast to HP1, which is ejected from chromatin during mitosis. These results suggest an important role for this ubiquitin ligase during mitosis. Significantly, we further find that the TTD of UHRF1 regulates global DNA methylation, thus definitively linking H3K9me3 binding by UHRF1 to the maintenance of DNA methylation. Taken together, our data suggest that the regulation of DNA methylation by UHRF1 extends beyond S-phase and requires H3K9me3 recognition during mitosis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 993. doi:1538-7445.AM2012-993

The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis

Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and SET1b, MLL1-MLL4) whose specific functions are largely unknown. By using a genomic approach, we found that in macrophages, MLL4 (also known as Wbp7) was required for the expression of Pigp, an essential component of the GPI-GlcNAc transferase, the enzyme catalyzing the first step of glycosylphosphatidylinositol (GPI) anchor synthesis. Impaired Pigp expression in Wbp7(-/-) macrophages abolished GPI anchor-dependent loading of proteins on the cell membrane. Consistently, loss of GPI-anchored CD14, the coreceptor for lipopolysaccharide (LPS) and other bacterial molecules, markedly attenuated LPS-triggered intracellular signals and gene expression changes. These data link a histone-modifying enzyme to a biosynthetic pathway and indicate a specialized biological role for Wbp7 in macrophage function and antimicrobial response.