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Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis.
McDonald OG, Li X, Saunders T, Tryggvadottir R, Mentch SJ, Warmoes MO, Word AE, Carrer A, Salz TH, Natsume S, Stauffer KM, Makohon-Moore A, Zhong Y, Wu H, Wellen KE, Locasale JW, Iacobuzio-Donahue CA, Feinberg AP
(2017) Nat Genet 49: 367-376
MeSH Terms: Carcinogenesis, Carcinoma, Pancreatic Ductal, Chromatin, Epigenesis, Genetic, Epigenomics, Gene Expression, Glucose, Heterochromatin, Histones, Humans, Neoplasm Metastasis, Pancreatic Neoplasms
Show Abstract · Added July 20, 2018
During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis. Changes were targeted to thousands of large chromatin domains across the genome that collectively specified malignant traits, including euchromatin and large organized chromatin histone H3 lysine 9 (H3K9)-modified (LOCK) heterochromatin. Remarkably, distant metastases co-evolved a dependence on the oxidative branch of the pentose phosphate pathway (oxPPP), and oxPPP inhibition selectively reversed reprogrammed chromatin, malignant gene expression programs, and tumorigenesis. These findings suggest a model whereby linked metabolic-epigenetic programs are selected for enhanced tumorigenic fitness during the evolution of distant metastasis.
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MeSH Terms
RNAi-mediated gene silencing in zebrafish triggered by convergent transcription.
Andrews OE, Cha DJ, Wei C, Patton JG
(2014) Sci Rep 4: 5222
MeSH Terms: Animals, Gene Expression, Gene Silencing, Heterochromatin, Promoter Regions, Genetic, RNA Interference, RNA, Double-Stranded, Transcription, Genetic, Transgenes, Zebrafish
Show Abstract · Added January 20, 2015
RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable transcriptional gene silencing (TGS) in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Convergent transcription enabled detection of both sense and antisense transcripts and silencing was suppressed upon Dicer knockdown, indicating processing of double stranded RNA. By ChIP analyses, increased silencing was accompanied by enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.
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10 MeSH Terms
Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat.
Leung A, Cajigas I, Jia P, Ezhkova E, Brickner JH, Zhao Z, Geng F, Tansey WP
(2011) Mol Biol Cell 22: 2741-53
MeSH Terms: Cell Wall, Euchromatin, Gene Expression Regulation, Fungal, Gene Silencing, Genetic Loci, Genome, Fungal, Heterochromatin, Histones, Hot Temperature, Lysine, Methylation, Plasmids, Protein Processing, Post-Translational, RNA, Messenger, Saccharomyces cerevisiae, Sequence Analysis, DNA, Silent Information Regulator Proteins, Saccharomyces cerevisiae, Site-Specific DNA-Methyltransferase (Adenine-Specific), Transcription, Genetic, Transfection, Ubiquitination
Show Abstract · Added March 10, 2014
In Saccharomyces cerevisiae, ubiquitylation of histone H2B signals methylation of histone H3 at lysine residues 4 (K4) and 79. These modifications occur at active genes but are believed to stabilize silent chromatin by limiting movement of silencing proteins away from heterochromatin domains. In the course of studying atypical phenotypes associated with loss of H2B ubiquitylation/H3K4 methylation, we discovered that these modifications are also required for cell wall integrity at high temperatures. We identified the silencing protein Sir4 as a dosage suppressor of loss of H2B ubiquitylation, and we showed that elevated Sir4 expression suppresses cell wall integrity defects by inhibiting the function of the Sir silencing complex. Using comparative transcriptome analysis, we identified a set of euchromatic genes-enriched in those required for the cellular response to heat-whose expression is attenuated by loss of H2B ubiquitylation but restored by disruption of Sir function. Finally, using DNA adenine methyltransferase identification, we found that Sir3 and Sir4 associate with genes that are silenced in the absence of H3K4 methylation. Our data reveal that H2B ubiquitylation/H3K4 methylation play an important role in limiting ectopic association of silencing proteins with euchromatic genes important for cell wall integrity and the response to heat.
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21 MeSH Terms
Analysis of chromatin structure of genes silenced by heterochromatin in trans.
Nisha P, Plank JL, Csink AK
(2008) Genetics 179: 359-73
MeSH Terms: ATP-Binding Cassette Transporters, Animals, Chromatin Immunoprecipitation, Chromosomal Proteins, Non-Histone, DNA Primers, Drosophila Proteins, Drosophila melanogaster, Gene Silencing, Heterochromatin, Nucleosomes, Restriction Mapping
Show Abstract · Added April 7, 2010
While heterochromatic gene silencing in cis is often accompanied by nucleosomal compaction, characteristic histone modifications, and recruitment of heterochromatin proteins, little is known concerning genes silenced by heterochromatin in trans. An insertion of heterochromatic satellite DNA in the euchromatic brown (bw) gene of Drosophila melanogaster results in bwDominant (bwD), which can inactivate loci on the homolog by relocation near the centric heterochromatin (trans-inactivation). Nucleosomal compaction was found to accompany trans-inactivation, but stereotypical heterochromatic histone modifications were mostly absent on silenced reporter genes. HP1 was enriched on trans-inactivated reporter constructs and this enrichment was more pronounced on adult chromatin than on larval chromatin. Interestingly, this HP1 enrichment in trans was unaccompanied by an increase in the 2MeH3K9 mark, which is generally thought to be the docking site for HP1 in heterochromatin. However, a substantial increase in the 2MeH3K9 mark was found on or near the bwD satellite insertion in cis, but did not spread further. These observations suggest that the interaction of HP1 with chromatin in cis is fundamentally different from that in trans. Our molecular data agree well with the differential phenotypic effect on bwD trans-inactivation of various genes known to be involved in histone modification and cis gene silencing.
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11 MeSH Terms
Control of SRF binding to CArG box chromatin regulates smooth muscle gene expression in vivo.
McDonald OG, Wamhoff BR, Hoofnagle MH, Owens GK
(2006) J Clin Invest 116: 36-48
MeSH Terms: Animals, Aorta, Binding Sites, Cell Culture Techniques, Chromatin, Gene Expression Regulation, Heterochromatin, Histones, Muscle, Smooth, Vascular, Protein Binding, Rats, Serum Response Element, Serum Response Factor, Transfection
Show Abstract · Added May 5, 2016
Precise control of SMC transcription plays a major role in vascular development and pathophysiology. Serum response factor (SRF) controls SMC gene transcription via binding to CArG box DNA sequences found within genes that exhibit SMC-restricted expression. However, the mechanisms that regulate SRF association with CArG box DNA within native chromatin of these genes are unknown. Here we report that SMC-restricted binding of SRF to murine SMC gene CArG box chromatin is associated with patterns of posttranslational histone modifications within this chromatin that are specific to the SMC lineage in culture and in vivo, including methylation and acetylation to histone H3 and H4 residues. We found that the promyogenic SRF coactivator myocardin increased SRF association with methylated histones and CArG box chromatin during activation of SMC gene expression. In contrast, the myogenic repressor Kruppel-like factor 4 recruited histone H4 deacetylase activity to SMC genes and blocked SRF association with methylated histones and CArG box chromatin during repression of SMC gene expression. Finally, we observed deacetylation of histone H4 coupled with loss of SRF binding during suppression of SMC differentiation in response to vascular injury. Taken together, these findings provide novel evidence that SMC-selective epigenetic control of SRF binding to chromatin plays a key role in regulation of SMC gene expression in response to pathophysiological stimuli in vivo.
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14 MeSH Terms
Tal1/SCL binding to pericentromeric DNA represses transcription.
Wen J, Huang S, Pack SD, Yu X, Brandt SJ, Noguchi CT
(2005) J Biol Chem 280: 12956-66
MeSH Terms: Amino Acid Motifs, Base Sequence, Basic Helix-Loop-Helix Transcription Factors, Binding Sites, Cell Nucleus, Chromatin, Chromatin Immunoprecipitation, Chromosomes, DNA, DNA Methylation, DNA Primers, DNA-Binding Proteins, Genes, Reporter, HeLa Cells, Heterochromatin, Histones, Humans, Hydroxamic Acids, Image Processing, Computer-Assisted, In Situ Hybridization, Fluorescence, K562 Cells, Leukocytes, Male, Models, Genetic, Molecular Sequence Data, Plasmids, Protein Binding, Proto-Oncogene Proteins, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Nucleic Acid, T-Cell Acute Lymphocytic Leukemia Protein 1, Transcription Factors, Transcription, Genetic
Show Abstract · Added March 5, 2014
Tal1/SCL is a basic helix-loop-helix transcription factor critical for normal hematopoiesis. To understand the mechanisms underlying transcriptional regulation by Tal1/SCL, we combined an in vitro DNA binding strategy and an in vivo chromatin immunoprecipitation analysis to search for Tal1/SCL target regions in K562 erythroleukemia cells. A 0.4-kb genomic DNA clone containing two Tal1/SCL binding E-boxes and GATA- and SATB1-binding motifs (EEGS) was identified that localized to the pericentromeric region with high homology to satellite 2 DNA. Pericentric DNA is related to heterochromatin and gene inactivation. We found that Tal1/SCL could complex with the histone H3 lysine 9 (H3K9)-specific methyltransferase Suv39H1. Binding of Tal1/SCL to EEGS chromatin correlated with hypermethylation of H3K9 and the association of heterochromatin protein HP1 to this region. In Rep4 reporter gene assays, EEGS affected repression in a manner dependent on the expression level of Tal1/SCL that was accompanied by increased H3K9 methylation in chromatin associated with EEGS and a linked promoter. A specific histone deacetylase inhibitor, trichostatin A, relieved Tal1/SCL-mediated repression by EEGS. In addition, SATB1 bound EEGS chromatin and promoted Tal1/SCL EEGS-dependent repression. We expand the list of potential interacting partners for Tal1/SCL by demonstrating direct associations of Tal1/SCL with SATB1 and with Suv39H1. These results reveal a novel mechanism of action for Tal1/SCL and implicate heterochromatin-like silencing via a cis-acting binding motif for transcriptional repression.
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33 MeSH Terms
A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin.
Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J
(2004) PLoS Biol 2: E131
MeSH Terms: Adenosine Triphosphatases, Adenosine Triphosphate, Animals, Binding Sites, Cell Nucleus, Cell Survival, Chromatin, Chromatin Immunoprecipitation, DNA-Binding Proteins, Drosophila, Epigenesis, Genetic, Euchromatin, Fungal Proteins, Gene Expression Regulation, Fungal, Genome, Fungal, Heterochromatin, Histones, Humans, Molecular Sequence Data, Nucleosomes, Oligonucleotide Array Sequence Analysis, Oligonucleotides, Peptides, Protein Binding, Protein Structure, Tertiary, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic
Show Abstract · Added February 20, 2015
The conserved histone variant H2A.Z functions in euchromatin to antagonize the spread of heterochromatin. The mechanism by which histone H2A is replaced by H2A.Z in the nucleosome is unknown. We identified a complex containing 13 different polypeptides associated with a soluble pool of H2A.Z in Saccharomyces cerevisiae. This complex was designated SWR1-Com in reference to the Swr1p subunit, a Swi2/Snf2-paralog. Swr1p and six other subunits were found only in SWR1-Com, whereas six other subunits were also found in the NuA4 histone acetyltransferase and/or the Ino80 chromatin remodeling complex. H2A.Z and SWR1 were essential for viability of cells lacking the EAF1 component of NuA4, pointing to a close functional connection between these two complexes. Strikingly, chromatin immunoprecipitation analysis of cells lacking Swr1p, the presumed ATPase of the complex, revealed a profound defect in the deposition of H2A.Z at euchromatic regions that flank the silent mating type cassette HMR and at 12 other chromosomal sites tested. Consistent with a specialized role for Swr1p in H2A.Z deposition, the majority of the genome-wide transcriptional defects seen in swr1Delta cells were also found in htz1Delta cells. These studies revealed a novel role for a member of the ATP-dependent chromatin remodeling enzyme family in determining the region-specific histone subunit composition of chromatin in vivo and controlling the epigenetic state of chromatin. Metazoan orthologs of Swr1p (Drosophila Domino; human SRCAP and p400) may have analogous functions.
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29 MeSH Terms
From silencing to gene expression: real-time analysis in single cells.
Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV, Ried T, Shav-Tal Y, Bertrand E, Singer RH, Spector DL
(2004) Cell 116: 683-98
MeSH Terms: Animals, Carrier Proteins, Cell Line, Chromatin, Chromosomal Proteins, Non-Histone, DNA, Gene Expression Regulation, Gene Silencing, Heterochromatin, Histones, Humans, Immunohistochemistry, In Situ Hybridization, Fluorescence, Protein Isoforms, RNA, Recombinant Fusion Proteins, Transcription, Genetic, Transgenes
Show Abstract · Added March 10, 2014
We have developed an inducible system to visualize gene expression at the levels of DNA, RNA and protein in living cells. The system is composed of a 200 copy transgene array integrated into a euchromatic region of chromosome 1 in human U2OS cells. The condensed array is heterochromatic as it is associated with HP1, histone H3 methylated at lysine 9, and several histone methyltransferases. Upon transcriptional induction, HP1alpha is depleted from the locus and the histone variant H3.3 is deposited suggesting that histone exchange is a mechanism through which heterochromatin is transformed into a transcriptionally active state. RNA levels at the transcription site increase immediately after the induction of transcription and the rate of synthesis slows over time. Using this system, we are able to correlate changes in chromatin structure with the progression of transcriptional activation allowing us to obtain a real-time integrative view of gene expression.
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18 MeSH Terms