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Results for “Targeting chromatin regulators”

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At least 55 records · Page 3Linked to original sources

PubMed1995

Drosophila Polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA.

The genes of the Polycomb-group (Pc-G) are responsible for maintaining the inactive expression state of homeotic genes. They act through specific cis-regulatory DNA elements termed PREs (Pc-G Response Elements). Multimeric complexes containing the Pc-G proteins are thought to induce heterochromatin-like structures, which stably and heritably inactivate transcription. We have tested the functional role of the FAB fragment, a PRE of the bithorax complex. We find that this element behaves as an orientation dependent silencer, capable of inducing mosaic gene expression on neighboring genes. Transgenic fly lines were constructed containing a PRE adjacent to a reporter gene inducible by the yeast GAL4 trans-activator. The competition between the activator and Pc-G-containing chromatin was visualized on polytene chromosomes using immunocytochemistry. The Pc-G protein Polycomb and GAL4 have mutually exclusive binding patterns, supporting the notion that Pc-G-induced chromatin structures can prevent activators from binding to their target sequences. However, this antagonistic function can be overcome by high doses of GAL4, even in the absence of DNA replication.

Animals↗

PubMed2005

Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation.

DAF-16, a forkhead transcription factor, is a key regulator of longevity, metabolism and dauer diapause in Caenorhabditis elegans. The precise mechanism by which DAF-16 regulates multiple functions, however, is poorly understood. Here, we used chromatin immunoprecipitation (ChIP) to identify direct targets of DAF-16. We cloned 103 target sequences containing consensus DAF-16 binding sites and selected 33 targets for further analysis. Expression of most of these genes is regulated in a DAF-16-dependent manner, and inactivation of more than half of these genes significantly altered DAF-16-dependent functions, including life span, fat storage and dauer formation. Our results show that the ChIP-based cloning strategy leads to greater enrichment for DAF-16 target genes than previous screening strategies. We also demonstrate that DAF-16 is recruited to multiple promoters to coordinate regulation of its downstream targets. The large number of target genes discovered provides insight into how DAF-16 controls diverse biological functions.

Alleles↗

PubMed2005

Transcriptional regulation by the acetylation of nonhistone proteins in humans -- a new target for therapeutics.

Gene expression from the dynamic chromatin template is regulated by certain key cellular players that cause post-translational modifications of both histones and nonhistone proteins. The acetyltransferases and deacetylases are two such key groups of enzymes that play crucial roles in maintaining the reversible acetylation status of histones and nonhistone proteins. Emerging evidence suggests that acetylation of nonhistone protein is equally important in the transcription regulation as the histone acetylation. Since dysfunction of HATs and HDACs leads to several diseases, aberrant acetylation of nonhistone protein is also associated with diseases. Small molecule modulators of these enzymes, which may help in maintaining the normal cellular acetylation status of these proteins, have important therapeutic implications.

Acetylation↗

PubMed1999

Structural requirements and dynamics of mitosin-kinetochore interaction in M phase.

Mitosin is a 350-kDa human nuclear protein which transiently associates with centromeres and spindle poles in M phase. Ultrastructure studies reveal that it is located at the outer kinetochore plate. In this work, we explored the detailed structural basis and dynamics of the mitosin-kinetochore interaction. Two major regions important for targeting to centromeres were identified by analyzing different deletion mutants expressed in CHO cells: (i) the "core region" between amino acids 2792 and 2887, which was essential for the centromere localization of mitosin; and (ii) the internal repeats between residues 2094 and 2487, which cooperated with the core region to achieve strong mitosin-kinetochore interaction. The core region is characteristic of two leucine zipper motifs. Deletion of either motif abolished the centromere localization activity. In addition, Cys2864, adjacent to the second motif, was also essential for the activity of the core region. In contrast, the internal repeats alone were insufficient for centromere localization. We propose that this region may serve as a regulatory domain to facilitate interaction of the core region with the kinetochore. We showed that mitosin molecules entering nuclei after nuclear envelope breakdown (NEBD) were not assembled onto kinetochores efficiently, suggesting that the mitosin-kinetochore interaction is stabilized prior to NEBD. This result supports the idea of an ordered process for kinetochore assembly. Our data also suggest that mitosin might interact with chromatin in interphase. Evidence for coordinated regulation between the centromere-targeting and the putative chromatin-binding activities is also provided.

Amino Acid Sequence↗

PubMed2006

A chromatin-mediated mechanism for specification of conditional transcription factor targets.

Organisms respond to changes in their environment, and many such responses are initiated at the level of gene transcription. Here, we provide evidence for a previously undiscovered mechanism for directing transcriptional regulators to new binding targets in response to an environmental change. We show that repressor-activator protein 1 (Rap1), a master regulator of yeast metabolism, binds to an expanded target set after glucose depletion despite decreasing protein levels and no evidence of posttranslational modification. Computational analysis predicts that proteins capable of recruiting the chromatin regulator Tup1 act to restrict the binding distribution of Rap1 in the presence of glucose. Deletion of the gene(s) encoding Tup1, recruiters of Tup1 or chromatin regulators recruited by Tup1 cause Rap1 to bind specifically and inappropriately to low-glucose targets. These data, combined with whole-genome measurements of nucleosome occupancy and Tup1 distribution, provide evidence for a mechanism of dynamic target specification that coordinates the genome-wide distribution of intermediate-affinity DNA sequence motifs with chromatin-mediated regulation of accessibility to those sites.

Base Sequence↗

PubMed2003

Transcription-coupled events associating with immunoglobulin switch region chromatin.

Class switch recombination (CSR) at the antibody immunoglobulin locus is regulated by germline transcription (GLT)-coupled modifications in the accessibility of the switch region, where CSR takes place. Here we show that histone acetylation of switch regions is linked to CSR but that histone acetylation cannot alone promote CSR or GLT. Activation-induced cytidine deaminase (AID) specifically associates with the CSR target chromatin in a GLT-coupled manner, which may occur potentially by means of physical interaction between AID and the transcription machinery. These data indicate an important role of GLT in the regulation of chromatin accessibility, strongly suggesting that the target of AID is chromatin DNA. Our results give insights on the role of AID and the regulatory mechanism of CSR.

Acetylation↗

PubMed2006

HSP70 induction by ING proteins sensitizes cells to tumor necrosis factor alpha receptor-mediated apoptosis.

ING proteins affect apoptosis, growth, and DNA repair by transducing stress signals such as DNA damage, binding histones, and subsequently regulating chromatin structure and p53 activity. p53 target genes, including the p21 cyclin-dependent kinase inhibitor and Bax, an inducer of apoptosis, are regulated by ING proteins. To identify additional targets downstream of p33ING1 and p32ING2, cDNA microarrays were performed on phenotypically normal human primary fibroblasts. The 0.36% of genes affected by ING proteins in primary fibroblasts were distinct from targets seen in established cells and included the HSP70 heat shock gene, whose promoter was specifically induced >10-fold. ING1-induced expression of HSP70 shifted cells from survival to a death pathway in response to tumor necrosis factor alpha (TNF-alpha), and p33ING1b protein showed synergy with TNF-alpha in inducing apoptosis, which correlated with reduced NF-kappaB-dependent transcription. These findings are consistent with previous reports that HSP70 promotes TNF-alpha-mediated apoptosis by binding I-kappaBeta kinase gamma and impairing NF-kappaB survival signaling. Induction of HSP70 required the amino terminus of ING1b but not the plant homeodomain region that was recently identified as a histone binding domain. Regulation of HSP70 gene expression by the ING tumor suppressors provides a novel link between the INGs and the stress-regulated NF-kappaB survival pathway important in hypoxia and angiogenesis.

Apoptosis↗

PubMed2002

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis.

Previously, identification of promoters regulated by mammalian transcription factors has relied upon overexpression studies. Here we present the identification of a large set of promoters that are bound by E2F in physiological conditions. Probing a human CpG microarray with chromatin immunoprecipitated using an antibody to E2F4, we have identified 68 unique target loci; 15% are bidirectional promoters and 25% recruit E2F via a mechanism distinct from the defined consensus site. Interestingly, although E2F has been shown previously to regulate genes involved in cell cycle progression, many of the new E2F target genes encode proteins involved in DNA repair or recombination. We suggest that human CpG microarrays, in combination with chromatin immunoprecipitation, will allow rapid identification of target promoters for many mammalian transcription factors.

Base Sequence↗

PubMed2004

p55, the Drosophila ortholog of RbAp46/RbAp48, is required for the repression of dE2F2/RBF-regulated genes.

Many proteins have been proposed to be involved in retinoblastoma protein (pRB)-mediated repression, but it is largely uncertain which cofactors are essential for pRB to repress endogenous E2F-regulated promoters. Here we have taken advantage of the stream-lined Drosophila dE2F/RBF pathway, which has only two E2Fs (dE2F1 and dE2F2), and two pRB family members (RBF1 and RBF2). With RNA interference (RNAi), we depleted potential corepressors and looked for the elevated expression of groups of E2F target genes that are known to be directly regulated by RBF1 and RBF2. Previous studies have implicated histone deacetylase (HDAC) and SWI/SNF chromatin-modifying complexes in pRB-mediated repression. However, our results fail to support the idea that the SWI/SNF proteins are required for RBF-mediated repression and suggest that a requirement for HDAC activities is likely to be limited to a subset of targets. We found that the chromatin assembly factor p55/dCAF-1 is essential for the repression of dE2F2-regulated targets. The removal of p55 deregulated the expression of E2F targets that are normally repressed by dE2F2/RBF1 and dE2F2/RBF2 complexes in a cell cycle-independent manner but had no effect on the expression of E2F targets that are normally coupled with cell proliferation. The results indicate that the mechanisms of RBF regulation at these two types of E2F targets are different and suggest that p55, and perhaps p55's mammalian orthologs RbAp46 and RbAp48, have a conserved function in repression by pRB-related proteins.

Animals↗

PubMed2004

A 210-kb segment of tandem repeats and retroelements located between imprinted subdomains of mouse distal chromosome 7.

Mammalian genes subject to genomic imprinting often form clusters and are regulated by long-range mechanisms. The distal imprinted domain of mouse chromosome 7 is orthologous to the Beckwith-Wiedemann syndrome domain in human chromosome 11p15.5 and contains at least 13 imprinted genes. This domain consists of two subdomains, which are respectively regulated by an imprinting center. We here report the finished-quality sequence of a 0.6-Mb region encompassing the more centromeric subdomain. The sequence contains four imprinted genes (Ascl2/Mash2, Ins2, Igf2 and H19) and reveals previously unidentified CpG islands and tandem repeats, which may be features of imprinted genes. Most interestingly, a unique 210-kb segment consisting almost exclusively of tandem repeats and retroelements is identified. This segment, located between Th and Ins2, has features of heterochromatin-forming DNA and is highly methylated at CpG sites. The segment exhibits asynchronous replication on the parental chromosomes, a feature of the imprinted domains. We propose that this repeat segment could serve either as a boundary between the two subdomains or as a target for epigenetic chromatin modifications that regulate imprinting.

Animals↗

PubMed2004

Atf1-Pcr1-M26 complex links stress-activated MAPK and cAMP-dependent protein kinase pathways via chromatin remodeling of cgs2+.

Although co-ordinate interaction between different signal transduction pathways is essential for developmental decisions, interpathway connections are often obscured and difficult to identify due to cross-talk. Here signals from the fission yeast stress-activated MAPK Spc1 are shown to regulate Cgs2, a negative regulator of the cAMP-dependent protein kinase (protein kinase A) pathway. Pathway integration is achieved via Spc1-dependent binding of Atf1-Pcr1 heterodimer to an M26 DNA site in the cgs2+ promoter, which remodels chromatin to regulate expression of cgs2+ and targets downstream of protein kinase A. This direct interpathway connection co-ordinates signals of nitrogen and carbon source depletion to affect a G0 cell-cycle checkpoint and sexual differentiation. The Atf1-Pcr1-M26 complex-dependent chromatin remodeling provides a molecular mechanism whereby Atf1-Pcr1 heterodimer can function differentially as either a transcriptional activator, or as a transcriptional repressor, or as an inducer of meiotic recombination. We also show that the Atf1-Pcr1-M26 complex functions as both an inducer and repressor of chromatin remodeling, which provides a way for various chromatin remodeling-dependent effector functions to be regulated.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2003

TIP49 regulates beta-catenin-mediated neoplastic transformation and T-cell factor target gene induction via effects on chromatin remodeling.

Beta-catenin has a key role in Wnt signaling via effects on T-cell factor (TCF)-mediated transcription. Mutational defects in beta-catenin regulation are seen in many cancers, leading to elevated beta-catenin levels, enhanced binding of beta-catenin to TCFs, and increased expression of TCF-regulated genes. Factors cooperating with beta-catenin in transcription of TCF-regulated genes are not well defined. TIP49, an ATPase previously implicated as a cofactor for oncogenic transformation by c-Myc, has been shown to bind to beta-catenin. We found that expression of an ATPase-deficient mutant form of TIP49 (TIP49D302N) substantially inhibited beta-catenin-mediated neoplastic transformation of immortalized rat epithelial cells and anchorage-independent growth of human colon cancer cells with deregulated beta-catenin. The TIP49D302N mutant inhibited beta-catenin-mediated activation of TCF-dependent cellular genes. Similar inhibition of the expression of beta-catenin/TCF-dependent genes was seen with small interfering RNA approaches against endogenous TIP49. TIP49 was found in complexes with chromatin remodeling and histone-modifying factors and cofactors, including the TIP60 histone acetylase-associated proteins transactivation/transformation-domain associated protein (TRRAP) and BAF53. Using chromatin immunoprecipitation methods, the TIP49, TIP60, and TRRAP proteins were found to interact with sequences in the regulatory region of the gene for ITF-2, a TCF-dependent cellular gene. The ability of TIP49D302N to inhibit ITF-2 gene expression was linked to decreased acetylation of histones in the vicinity of the TCF-binding sites in the ITF-2 promoter region. We suggest that TIP49 is an important cofactor in beta-catenin/TCF gene regulation in normal and neoplastic cells, likely functioning in chromatin remodeling.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2003

Regulation of T-cell receptor D beta 1 promoter by KLF5 through reiterated GC-rich motifs.

Rearrangement of T-cell receptor (TCR) and immunoglobulin genes by a common V(D)J recombination machinery is regulated by developmentally specific chromatin changes at the target locus, a process associated with transcription. At the TCRbeta locus, the Ebeta enhancer and the Dbeta1 promoter regulate germline transcription originating near the TCR Dbeta1 gene segment. The Dbeta1 promoter contains 3 GC-rich motifs that bind a common set of nuclear proteins from pro-T-cell lines. Mutations that diminish the binding of nuclear proteins also diminish the activity of the Dbeta1 promoter in transcriptional reporter assays. Using a yeast one-hybrid approach, 3 Krüppel-like factors-KLF3, KLF5, and KLF6-and a novel zinc finger protein were identified in a thymus library, all of which bound the GC-rich motif in a sequence-specific manner. Of these genes, KLF5 mRNA was expressed in a restricted manner in lymphoid cells and tissues, with highest expression in pro-T-cell lines and Rag-deficient thymocytes. Antibody supershift studies and chromatin immunoprecipitation assay confirmed that KLF5 bound the Dbeta1 promoter. In reporter gene assays, KLF5 but not KLF6 efficiently transactivated the Dbeta1 promoter, whereas a dominant-negative KLF5 construct inhibited reporter expression. These data suggest that reiterated GC motifs contribute to germline TCRbeta transcription through binding of KLF5 and other Krüppel family members and that restricted expression of KLF5 may contribute to lineage-specific regulation of germline TCRbeta transcription.

Animals↗

PubMed1998

A NIMA homologue promotes chromatin condensation in fission yeast.

Entry into mitosis requires p34(cdc2), which activates downstream mitotic events through phosphorylation of key target proteins. In Aspergillus nidulans, the NIMA protein kinase has been identified as a potential downstream target and plays a role in regulating chromatin condensation at mitosis. nimA- mutants arrest in a state that physically resembles interphase even though p34(cdc2) is fully active. Despite evidence for the existence of NIMA-like activities in a variety of cell types, the only bona fide NIMA homologue that has been identified is the nim-1 gene of Neurospora crassa. We report here the isolation of a fission yeast NIMA homologue, and have designated this gene fin1 and the 83 kDa predicted protein p83(fin1). Overexpression of fin1 promotes premature chromatin condensation from any point in the cell cycle independently of p34(cdc2) function. Like NIMA, p83(fin1) levels fluctuate through the cell cycle, peaking in mitosis and levels are greatly elevated by removal of C-terminal PEST sequences. Deletion of fin1 results in viable but elongated cells, indicative of a cell cycle delay. Genetic analysis has placed this delay in G2 but, unlike in nimA mutants of Aspergillus, p34(cdc2) activation appears to be delayed. Interaction of fin1 mutants with other strains defective in chromatin organisation also support the hypothesis of p83(fin1) playing a role in this process at the onset of mitosis. These data indicate that NIMA-related kinases may be a general feature of the cell cycle and chromatin organisation at mitosis.

Amino Acid Sequence↗

PubMed2006

RNAi components are required for nuclear clustering of Polycomb group response elements.

Drosophila Polycomb group (PcG) proteins silence homeotic genes through binding to Polycomb group response elements (PREs). Fab-7 is a PRE-containing regulatory element from the homeotic gene Abdominal-B. When present in multiple copies in the genome, Fab-7 can induce long-distance gene contacts that enhance PcG-dependent silencing. We show here that components of the RNA interference (RNAi) machinery are involved in PcG-mediated silencing at Fab-7 and in the production of small RNAs at transgenic Fab-7 copies. In general, these mutations do not affect the recruitment of PcG components, but they are specifically required for the maintenance of long-range contacts between Fab-7 copies. Dicer-2, PIWI, and Argonaute1, three RNAi components, frequently colocalize with PcG bodies, and their mutation significantly reduces the frequency of PcG-dependent chromosomal associations of endogenous homeotic genes. This suggests a novel role for the RNAi machinery in regulating the nuclear organization of PcG chromatin targets.

Animals↗

PubMed2001

Above and within the genome: epigenetics past and present.

Epigenetic regulation involves the maintenance of a particular state of gene expression--most commonly, repression--in the face of repeated mitosis, and frequently meiosis. Remarkably, changes in such heritable expression states occur without an alteration of the primary DNA sequence. We present a brief history of research in epigenetics, beginning with pioneering work in the 1950s by B. McClintock and R. A. Brink on maize kernel color inheritance. We describe the complex biochemistry of DNA methylation--the molecular basis of most epigenetic regulation in mammalian genomes--and review data connecting it to targeted modification and remodeling of chromatin structure. Several prominent examples of epigenetically regulated loci--X chromosome inactivation, imprinting, repetitive DNA silencing, and aberrant methylation patterns in neoplasia--are reviewed along with a description of our current understanding of the underlying molecular mechanisms. A common theme that emerges is the complex integration of epigenetic regulatory pathways with the chromatin infrastructure over target DNA loci.

Chromatin↗

PubMed2026

Nuclear exosome targeting complexes modulate cohesin binding and enhancer-promoter interactions in 3D.

Three-dimensional long-range contacts between enhancers and promoters are thought to be largely determined by loop extrusion driven by the cohesin complex and insulator factors. However, recent evidence also suggests a role for noncoding RNAs, such as enhancer-associated RNAs and promoter upstream transcripts, in shaping enhancer-promoter connectivity. While the nuclear RNA exosome, together with targeting complexes, poly(A) tail exosome targeting connection and nuclear exosome targeting complex, controls the decay of noncoding RNAs, it remains unclear whether these complexes regulate three-dimensional chromatin contacts. Chromatin recruitment maps of the nuclear exosome targeting complex subunit ZCCHC8, the poly(A) tail exosome targeting connection subunit ZFC3H1, and the RNA helicase MTR4 in human cells reveal that these factors associate with sites of enhancer-promoter interactions. Depletion of these factors leads to the accumulation of ncRNAs, notably enhancer-associated RNAs and promoter upstream transcripts, and increases cohesin occupancy at these sites. Chromatin conformation capture analysis reveals that MTR4 modulates long-range enhancer-promoter contacts. Upon loss of MTR4, enhancer-promoter contacts increase while intraloop contacts decrease, suggesting that MTR4 facilitates loop extrusion. These data highlight a key interplay between cohesin-mediated enhancer-promoter interactions and the regulation of noncoding RNAs by nuclear RNA exosome targeting complexes that is consistent with a role for RNA in genome folding.

Cohesins↗

PubMed2004

Targeted inhibition of V(D)J recombination by a histone methyltransferase.

The tissue- and stage-specific assembly of antigen receptor genes by V(D)J recombination is regulated by changes in the chromatin accessibility of target gene segments. This dynamic remodeling process is coordinated by cis-acting promoters and enhancers, which function as accessibility control elements. The basic epigenetic mechanisms that activate or repress chromatin accessibility to V(D)J recombinase remain unclear. We now demonstrate that a histone methyltransferase overrides accessibility control element function and cripples V(D)J recombination of chromosomal gene segments. The recruited histone methyltransferase induces extensive revisions in the local chromatin environment, including altered histone modifications and de novo methylation of DNA. These findings indicate a key function for histone methyltransferases in the tissue- and stage-specific suppression of antigen receptor gene assembly during lymphocyte development.

Animals↗