scholarly journals Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis

2021 ◽  
Author(s):  
Parijat Senapati ◽  
Aditya Bhattacharya ◽  
Sadhan Das ◽  
Suchismita Dey ◽  
Deepthi Sudarshan ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcription Activation ◽  
Regulatory Elements ◽  
Histone Chaperone ◽  
Transcriptional Regulatory Elements ◽  
Expression Of Genes ◽  
Activation Potential ◽  
Hypersensitive Sites ◽  
Oral Cancer Cells

Nucleophosmin (NPM1) is a multifunctional histone chaperone that can activate acetylation-dependent transcription from chromatin templates in vitro. Acetylation of NPM1 by p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells and oral tumorigenesis is not fully elucidated. Using ChIP-seq analyses, we provide the first genome-wide profile of AcNPM1 and show that AcNPM1 is enriched at transcriptional regulatory elements. AcNPM1 co-occupies marks of active transcription at promoters and DNase I hypersensitive sites at enhancers. In addition, using a high-throughput protein interaction profiling approach, we show that NPM1 interacts with RNA Pol II, general transcription factors, mediator subunits, histone acetyltransferase complexes, and chromatin remodelers. NPM1 histone chaperone activity also contributes to its transcription activation potential. Further, NPM1 depletion leads to decreased AcNPM1 occupancy and reduced expression of genes required for proliferative, migratory and invasive potential of oral cancer cells. NPM1 depletion also abrogates the growth of orthotopic tumors in mice. Collectively, these results establish that AcNPM1 functions as a coactivator during during RNA polymerase II-driven transcription and regulates the expression of genes that promote oral tumorigenesis.

scholarly journals Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis

2019 ◽  
Author(s):  
Parijat Senapati ◽  
Suchismita Dey ◽  
Deepthi Sudarshan ◽  
Aditya Bhattacharya ◽  
Shyla G ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Histone Chaperone ◽  
Migration And Invasion ◽  
Chromatin Remodelers ◽  
Hypersensitive Sites ◽  
Active Transcription ◽  
Key Genes ◽  
Oral Cancer Cells ◽  
In Cells

ABSTRACTNucleophosmin (NPM1) is a multifunctional histone chaperone that can activate RNA Polymerase II-driven chromatin transcription. Acetylation of NPM1 by acetyltransferase p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells is not fully elucidated. Using ChIP-seq analyses, we show that AcNPM1 co-occupies marks of active transcription at promoters and DNase I hypersensitive sites at enhancers. Moreover, NPM1 interacts with proteins involved in transcription, including RNA Pol II, general transcription factors, mediator subunits, histone acetyltransferase complexes, and chromatin remodelers. Moreover, its histone chaperone also contributes to transcriptional activation. We further show that AcNPM1 regulates key genes required for proliferation, migration and invasion potential of oral cancer cells and knockdown of NPM1 mitigates these processes in cells as well as orthotopic tumors in mice. Collectively, these results establish that AcNPM1 functions as a coactivator and regulates the expression of key genes involved in oral tumorigenesis.

scholarly journals Enhancers mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer

2017 ◽  
Author(s):  
Darren K. Patten ◽  
Giacomo Corleone ◽  
Balázs Győrffy ◽  
Edina Erdős ◽  
Alina Saiakhova ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
Regulatory Elements ◽  
Phenotypic Heterogeneity ◽  
Endocrine Treatment ◽  
Clinical Samples ◽  
Luminal Breast Cancer ◽  
Breast Cancer Patients ◽  
Expression Of Genes

AbstractThe degree of intrinsic and interpatient phenotypic heterogeneity and its role in tumour evolution is poorly understood. Phenotypic divergence can be achieved via the inheritance of alternative transcriptional programs1,2. Cell-type specific transcription is maintained through the activation of epigenetically-defined regulatory regions including promoters and enhancers1,3,4. In this work, we annotated the epigenome of 47 primary and metastatic oestrogen-receptor (ERα)-positive breast cancer specimens from clinical samples, and developed strategies to deduce phenotypic heterogeneity from the regulatory landscape, identifying key regulatory elements commonly shared across patients. Highly shared regions contain a unique set of regulatory information including the motif for the transcription factor YY1. In vitro work shows that YY1 is essential for ERα transcriptional activity and defines the critical subset of functional ERα binding sites driving tumor growth in most luminal patients. YY1 also control the expression of genes that mediate resistance to endocrine treatment. Finally, we show that H3K27ac levels at active enhancer elements can be used as a surrogate of intra-tumor phenotypic heterogeneity, and to track expansion and contraction of phenotypic subpopulations throughout breast cancer progression. Tracking YY1 and SLC9A3R1 positive clones in primary and metastatic lesions, we show that endocrine therapies drive the expansion of phenotypic clones originally underrepresented at diagnosis. Collectively, our data show that epigenetic mechanisms significantly contribute to phenotypic heterogeneity and evolution in systemically treated breast cancer patients.

scholarly journals CTCF mediates insulator function at the CFTR locus

2007 ◽  
Vol 408 (2) ◽  
pp. 267-275 ◽  
Author(s):  
Neil P. Blackledge ◽  
Emma J. Carter ◽  
Joanne R. Evans ◽  
Victoria Lawson ◽  
Rebecca K. Rowntree ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Cftr Gene ◽  
Chromatin Domain ◽  
Transmembrane Conductance Regulator ◽  
Binding Factor ◽  
Hypersensitive Sites ◽  
Insulator Elements ◽  
Translational Start

Regulatory elements that lie outside the basal promoter of a gene may be revealed by local changes in chromatin structure and histone modifications. The promoter of the CFTR (cystic fibrosis transmembrane conductance regulator) gene is not responsible for its complex pattern of expression. To identify important regulatory elements for CFTR we have previously mapped DHS (DNase I-hypersensitive sites) across 400 kb spanning the locus. Of particular interest were two DHS that flank the CFTR gene, upstream at −20.9 kb with respect to the translational start site, and downstream at +15.6 kb. In the present study we show that these two DHS possess enhancer-blocking activity and bind proteins that are characteristic of known insulator elements. The DHS core at −20.9 kb binds CTCF (CCCTC-binding factor) both in vitro and in vivo; however, the +15.6 kb core appears to bind other factors. Histone-modification analysis across the CFTR locus highlights structural differences between the −20.9 kb and +15.6 kb DHS, further suggesting that these two insulator elements may operate by distinct mechanisms. We propose that these two DHS mark the boundaries of the CFTR gene functional unit and establish a chromatin domain within which the complex profile of CFTR expression is maintained.

scholarly journals Enhancer redundancy predicts gene pathogenicity and informs complex disease gene discovery

2018 ◽  
Author(s):  
Xinchen Wang ◽  
David B. Goldstein
Keyword(s):  
Complex Disease ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Disease Genes ◽  
Transcriptional Regulatory Elements ◽  
Regulatory Domains ◽  
Disease Gene Discovery ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Transcriptional Regulatory

AbstractNon-coding transcriptional regulatory elements are critical for controlling the spatiotemporal expression of genes. Here, we demonstrate that the number of bases in enhancers linked to a gene reflects its disease pathogenicity. Moreover, genes with redundant enhancer domains are depleted of cis-acting genetic variants that disrupt gene expression, and are buffered against the effects of disruptive non-coding mutations. Our results demonstrate that dosage-sensitive genes have evolved robustness to the disruptive effects of genetic variation by expanding their regulatory domains. This resolves a puzzle in the genetic literature about why disease genes are depleted of cis-eQTLs, suggesting that eQTL information may implicate the wrong genes at genome-wide association study loci, and establishes a framework for identifying non-coding regulatory variation with phenotypic consequences.

scholarly journals Conserved CTCF Insulator Elements Flank the Mouse and Human β-Globin Loci

2002 ◽  
Vol 22 (11) ◽  
pp. 3820-3831 ◽  
Author(s):  
Catherine M. Farrell ◽  
Adam G. West ◽  
Gary Felsenfeld
Keyword(s):  
Gene Clusters ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Functional Domain ◽  
Blocking Activity ◽  
Hypersensitive Sites ◽  
Enhancer Blocking ◽  
Olfactory Receptor Genes ◽  
Insulator Elements

ABSTRACT A binding site for the transcription factor CTCF is responsible for enhancer-blocking activity in a variety of vertebrate insulators, including the insulators at the 5′ and 3′ chromatin boundaries of the chicken β-globin locus. To date, no functional domain boundaries have been defined at mammalian β-globin loci, which are embedded within arrays of functional olfactory receptor genes. In an attempt to define boundary elements that could separate these gene clusters, CTCF-binding sites were searched for at the most distal DNase I-hypersensitive sites (HSs) of the mouse and human β-globin loci. Conserved CTCF sites were found at 5′HS5 and 3′HS1 of both loci. All of these sites could bind to CTCF in vitro. The sites also functioned as insulators in enhancer-blocking assays at levels correlating with CTCF-binding affinity, although enhancer-blocking activity was weak with the mouse 5′HS5 site. These results show that with respect to enhancer-blocking elements, the architecture of the mouse and human β-globin loci is similar to that found previously for the chicken β-globin locus. Unlike the chicken locus, the mouse and human β-globin loci do not have nearby transitions in chromatin structure but the data suggest that 3′HS1 and 5′HS5 may function as insulators that prevent inappropriate interactions between β-globin regulatory elements and those of neighboring domains or subdomains, many of which possess strong enhancers.

scholarly journals Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

2010 ◽  
Vol 30 (23) ◽  
pp. 5531-5544 ◽  
Author(s):  
Guoyu Ling ◽  
Aarathi Sugathan ◽  
Tali Mazor ◽  
Ernest Fraenkel ◽  
David J. Waxman
Keyword(s):  
High Throughput Sequencing ◽  
Strong Association ◽  
Regulatory Elements ◽  
Sequence Motifs ◽  
Transcriptional Regulatory Elements ◽  
Transcriptional Regulatory ◽  
Mammalian Tissues ◽  
Hypersensitive Sites ◽  
Regulatory Sites

ABSTRACT We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-related differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation, and disease. To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse livers and in livers of male mice feminized by continuous infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-related differences. Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male livers. We also identified broad genomic regions (up to ∼100 kb) showing sex-dependent hypersensitivity and similar patterns of GH responses. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100 kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism and several new candidates for further investigation. This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions.

scholarly journals Ligand-induced native G-quadruplex stabilization impairs transcription initiation

2021 ◽  
Author(s):  
Conghui Li ◽  
Honghong Wang ◽  
Zhinang Yin ◽  
Pingping Fang ◽  
Ruijing Xiao ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Transcription Initiation ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Drug Induced ◽  
Transcriptional Regulatory Elements ◽  
Genome Wide ◽  
Self Association

G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines, and G4s are distributed widely across the genome. G4 participates in multiple biological processes including gene transcription, and G4-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, genome-wide studies of the exact roles of G4s in transcriptional regulation are still lacking. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G4s with high resolution and specificity. We find that native G4 signals are cell type–specific and are associated with transcriptional regulatory elements carrying active epigenetic modifications. Drug-induced promoter-proximal RNA polymerase II pausing promotes nearby G4 formation. In contrast, G4 stabilization by G4-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, ligand-induced G4 stabilization modulates chromatin states and impedes transcription initiation via inhibition of general transcription factors loading to promoters. Together, our study reveals a reciprocal genome-wide regulation between native G4 dynamics and gene transcription, which will deepen our understanding of G4 biology toward therapeutically targeting G4s in human diseases.

scholarly journals Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functionalMYCsuperenhancers and enhancer RNAs

2020 ◽  
Vol 117 (35) ◽  
pp. 21618-21627 ◽  
Author(s):  
Angela Park ◽  
Soohwan Oh ◽  
Kyle L. Jung ◽  
Un Yung Choi ◽  
Hye-Ra Lee ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Kaposi's Sarcoma ◽  
Primary Effusion Lymphoma ◽  
Mrna Level ◽  
Kaposi’S Sarcoma ◽  
Regulatory Elements ◽  
Lytic Replication ◽  
Viral Reactivation ◽  
Transcriptional Regulatory Elements ◽  
Viral Lifecycle

Enhancers play indispensable roles in cell proliferation and survival through spatiotemporally regulating gene transcription. Active enhancers and superenhancers often produce noncoding enhancer RNAs (eRNAs) that precisely control RNA polymerase II activity. Kaposi’s sarcoma-associated herpesvirus (KSHV) is a human oncogenic gamma-2 herpesvirus that causes Kaposi’s sarcoma and primary effusion lymphoma (PEL). It is well characterized that KSHV utilizes host epigenetic machineries to control the switch between two lifecycles, latency and lytic replication. However, how KSHV impacts host epigenome at different stages of viral lifecycle is not well understood. Using global run-on sequencing (GRO-seq) and chromatin-immunoprecipitation sequencing (ChIP-seq), we profiled the dynamics of host transcriptional regulatory elements during latency and lytic replication of KSHV-infected PEL cells. This revealed that a number of critical host genes for KSHV latency, includingMYCproto-oncogene, were under the control of superenhancers whose activities were globally repressed upon viral reactivation. The eRNA-expressingMYCsuperenhancers were located downstream of theMYCgene in KSHV-infected PELs and played a key role inMYCexpression. RNAi-mediated depletion or dCas9-KRAB CRISPR inhibition ofeRNAexpression significantly reducedMYCmRNA level in PELs, as did the treatment of an epigenomic drug that globally blocks superenhancer function. Finally, while cellular IRF4 acted uponeRNAexpression and superenhancer function forMYCexpression during latency, KSHV viral IRF4 repressed cellularIRF4expression, decreasingMYCexpression and thereby, facilitating lytic replication. These results indicate that KSHV acts as an epigenomic driver that modifies host epigenomic status upon reactivation by effectively regulating host enhancer function.

Abstract 355: In Vivo Targeting Of GTF2B Selectively Inhibits Transcription Of Cardiomyopathy-related Genes And Partially Blunts Development Of Cardiac Hypertrophy

2013 ◽  
Vol 113 (suppl_1) ◽  
Author(s):  
Danish Sayed ◽  
Zhi Yang ◽  
Minzhen He ◽  
Maha Abdellatif
Keyword(s):  
Rna Polymerase Ii ◽  
Rna Splicing ◽  
De Novo ◽  
Transcriptional Profiling ◽  
Essential Genes ◽  
Pol Ii ◽  
Expression Of Genes ◽  
Essential Components

Transcriptional profiling of cardiac genome during hypertrophy identified two categories of genes with distinct modes of regulation. The first set of genes involved in the cells essential functions (e.g. RNA splicing) and whose transcription is expected to be incremental and contribute to the increasing cardiac mass is regulated by promoter clearance of RNA polymerase II (pol II). On the other hand, the second set that include genes with specialized function and show a robust increase in expression upon growth stimulus (cytoskeletal, extracellular matrix) are regulated by de novo pol II recruitment to promoters. Our goal was to identify the transcriptional mechanisms that distinguish these two sets of genes and then to selectively inhibit those that participate in contractile dysfunction, while preserving the expression of genes necessary for essential functions. General Transcription factor IIB (GTF2B), is one of the essential components of transcription machinery and is required for pol II recruitment. Thus, we hypothesized that inhibition of GTF2B would result in inhibition of only the specialized genes, sparing the essential genes. Our in vitro results with shRNA mediated inhibition of GTF2B in hypertrophying neonatal myocytes showed decreased expression of genes that required de novo pol II recruitment for transcription (eg. ACTA1), while no change was observed in the genes regulated by promoter clearance of pol II (Vdac1). Similarly, preliminary results with in vivo knockdown of GTF2B (~80% reduction in mRNA and ~36% in protein) via intravenous injection of modified antisense oligo in mice subjected to transaortic coarctation (TAC) showed inhibition of only cardiomyopathy-related genes that require pol II recruitment (ANF), while expression of essential genes (Vdac1) remained unchanged. Inhibition of GTF2B restricted increase in TAC-induced heart wt to 9%, compared to 29% in TAC hearts with control oligo. Echocardiography showed partial normalization of ejection fraction with GTF2B inhibitor during TAC from 61.5% to 66.4% compared to sham hearts with 71%. Thus, we conclude that by targeting GTF2B we can selectively restrict the expression of detrimental genes during hypertrophy, thereby delaying the onset of cardiac dysfunction and failure

scholarly journals Highly Restricted Localization of RNA Polymerase II within a Locus Control Region of a Tissue-Specific Chromatin Domain

2003 ◽  
Vol 23 (18) ◽  
pp. 6484-6493 ◽  
Author(s):  
Kirby D. Johnson ◽  
Jeffrey A. Grass ◽  
Changwon Park ◽  
Hogune Im ◽  
Kyunghee Choi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Histone Modification ◽  
Rna Polymerase Ii ◽  
Control Region ◽  
Locus Control Region ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Pol Ii ◽  
Reading Frame ◽  
Hypersensitive Sites

ABSTRACT RNA polymerase II (Pol II) can associate with regulatory elements far from promoters. For the murine β-globin locus, Pol II binds the β-globin locus control region (LCR) far upstream of the β-globin promoters, independent of recruitment to and activation of the βmajor promoter. We describe here an analysis of where Pol II resides within the LCR, how it is recruited to the LCR, and the functional consequences of recruitment. High-resolution analysis of the distribution of Pol II revealed that Pol II binding within the LCR is restricted to the hypersensitive sites. Blocking elongation eliminated the synthesis of genic and extragenic transcripts and eliminated Pol II from the βmajor open reading frame. However, the elongation blockade did not redistribute Pol II at the hypersensitive sites, suggesting that Pol II is recruited to these sites. The distribution of Pol II did not strictly correlate with the distributions of histone acetylation and methylation. As Pol II associates with histone-modifying enzymes, Pol II tracking might be critical for establishing and maintaining broad histone modification patterns. However, blocking elongation did not disrupt the histone modification pattern of the β-globin locus, indicating that Pol II tracking is not required to maintain the pattern.

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