Mutations in the Insulator Protein Suppressor of Hairy Wing Induce Genome Instability

Mapping Intimacies ◽

10.1101/551002 ◽

2019 ◽

Cited By ~ 1

Author(s):

Shih-Jui Hsu ◽

Emily C. Stow ◽

James R. Simmons ◽

Heather A. Wallace ◽

Andrea Mancheno Lopez ◽

...

Keyword(s):

Genome Instability ◽

Critical Role ◽

Regulatory Sequences ◽

Gene Promoters ◽

Microtubule Organization ◽

Germline Development ◽

Insulator Protein ◽

Insulator Proteins ◽

Egg Chambers ◽

Chromosome Integrity

AbstractChromatin insulator proteins mediate the formation of contacts between distant insulator sites along chromatin fibers. Long-range contacts facilitate communication between regulatory sequences and gene promoters throughout the genome, allowing accurate gene transcription regulation during embryo development and cell differentiation. Lack of insulator function has detrimental effects often resulting in lethality. The Drosophila insulator protein Suppressor of Hairy wing [Su(Hw)] is not essential for viability, but plays a crucial role in female oogenesis. The mechanism(s) by which Su(Hw) promotes proper oogenesis remains unclear. To gain insight into the functional properties of chromatin insulators, we further characterize the oogenesis phenotypes of su(Hw) mutant females. We find that mutant egg chambers frequently display an irregular number of nurse cells, have poorly formed microtubule organization centers (MTOC) in the germarium, and show mislocalized Gurken (Grk) in later stages of oogenesis. Furthermore, eggshells produced by partially rescued su(Hw) mutant females exhibit dorsoventral patterning defects that are identical to defects found in spindle mutants or in piRNA pathway mutants. Further analysis reveals an excess of DNA damage in egg chambers, which is independent of activation of transposable elements, and that Gurken localization defects and oogenesis progression are partially rescued by mutations in mei-41 and chk1 genes. In addition, we show that Su(Hw) is required for chromosome integrity in dividing neuroblasts from larval brains. Together, these findings suggest that Su(Hw) plays a critical role in maintaining genome integrity during germline development in Drosophila females as well as in dividing somatic cells.

A novel regulatory element between the human FGA and FGG genes

Thrombosis and Haemostasis ◽

10.1160/th12-04-0274 ◽

2012 ◽

Vol 108 (09) ◽

pp. 427-434 ◽

Cited By ~ 7

Author(s):

Richard J. Fish ◽

Marguerite Neerman-Arbez

Keyword(s):

Gene Cluster ◽

Fluorescent Protein ◽

Regulatory Element ◽

Luciferase Reporter ◽

Transgenic Zebrafish ◽

Regulatory Sequences ◽

Gene Promoters ◽

Cvd Risk ◽

Enhancer Activity

SummaryHigh circulating fibrinogen levels correlate with cardiovascular disease (CVD) risk. Fibrinogen levels vary between people and also change in response to physiological and environmental stimuli. A modest proportion of the variation in fibrinogen levels can be explained by genotype, inferring that variation in genomic sequences that regulate the fibri-nogen genes (FGA, FGB and FGG) may affect hepatic fibrinogen production and perhaps CVD risk. We previously identified a conserved liver enhancer in the fibrinogen gene cluster (CNC12), between FGB and FGA. Genome-wide Chromatin immunoprecipitation-sequencing (ChIP-seq) demonstrated that transcription factors which bind fibrinogen gene promoters also interact with CNC12, as well as two potential fibrinogen enhancers (PFE), between FGA and FGG. Here we show that one of the PFE sequences has potent hepatocyte enhancer activity. Using a luciferase reporter gene system, we found that PFE2 enhances minimal promoter- and FGA promoter-driven gene expression in hepatoma cells, regardless of its orientation with respect to the promoters. A region within PFE2 bears a short series of conserved nucleotides which maintain enhancer activity without flanking sequence. We also demonstrate that PFE2 is a liver enhancer in vivo, driving enhanced green fluorescent protein expression in transgenic zebrafish larval livers. Our study shows that combining public domain ChIP-seq data with in vitro and in vivo functional tests can identify novel fibrinogen gene cluster regulatory sequences. Variation in such elements could affect fibrinogen production and influence CVD risk.

The vitamin K–dependent γ-glutamyl carboxylase gene contains a TATA-less promoter with a novel upstream regulatory element

Blood ◽

10.1182/blood-2002-12-3833 ◽

2003 ◽

Vol 102 (4) ◽

pp. 1333-1339 ◽

Cited By ~ 3

Author(s):

Elizabeth E. Romero ◽

Umaima Marvi ◽

Zachary E. Niman ◽

David A. Roth

Keyword(s):

Blood Coagulation ◽

Dna Sequence ◽

Vitamin K ◽

Nuclear Protein ◽

Regulatory Element ◽

Hepatoma Cell ◽

Critical Role ◽

Developmental Expression ◽

Regulatory Sequences ◽

Developmentally Regulated

Abstract The expression of the vitamin K–dependent γ-glutamyl carboxylase gene in liver is developmentally regulated. Since the gene product catalyzes an essential post-translational modification of the vitamin K–dependent blood coagulation proteins, the regulation of carboxylase expression is critical for hemostasis. We analyzed the activity of the rat carboxylase gene 5′-regulatory DNA sequences in rat hepatoma cell lines at different states of differentiation. These studies demonstrated that the 2.6-kb 5′-flanking sequence has differentiation-dependent transcriptional activity. Transient gene expression assays, examining the effects of nested deletions and site-directed mutagenesis of putative regulatory sequences, together with electrophoretic mobility shift assays (EMSAs) were used to identify sequences critical for the developmentally regulated transcription of the rat carboxylase gene. We identified a DNA sequence (–76 to –65; GTTCCGGCCTTC) not known to bind to transcription factors, yet which functions as an upstream promoter element. In vivo genomic DNA footprinting confirms the presence of nuclear protein–DNA interactions at this site in the endogenous carboxylase gene in differentiated hepatoma cells. Therefore, this DNA sequence has specific nuclear protein–binding activity and functional properties consistent with a regulatory element that plays a critical role in the developmental expression of the carboxylase gene, and hence the regulation of vitamin K–dependent blood coagulation protein synthesis.

Human rDNA Copy Number Is Unstable in Metastatic Breast Cancers

10.1101/623595 ◽

2019 ◽

Author(s):

Virginia Valori ◽

Katalin Tus ◽

Christina Laukaitis ◽

David T. Harris ◽

Lauren LeBeau ◽

...

Keyword(s):

Breast Cancer ◽

Copy Number Variation ◽

Copy Number ◽

Genome Instability ◽

Gene Clusters ◽

Genome Rearrangements ◽

Epigenetic Silencing ◽

Healthy Tissue ◽

Gene Promoters ◽

Number Variation

AbstractEpigenetic silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of epigenetic silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their etiology. We find support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumors and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation – both losses and gains of copies – compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed etiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.Authors’ StatementOne of the common hallmarks of cancer is genome instability, including hypermutation and changes to chromosome structure. Using tumor tissues obtained from women with invasive ductal carcinoma, we find that a sensitive area of the genome – the ribosomal DNA gene repeat cluster – shows hypervariability in copy number. The patterns we observe as not consistent with an adaptive loss leading to increased tumor growth, but rather we conclude that copy number variation at repeat DNA is a general consequence of reduced heterochromatin function in cancer progression.

Mutations in the insulator protein Suppressor of Hairy wing induce genome instability

Chromosoma ◽

10.1007/s00412-020-00743-8 ◽

2020 ◽

Vol 129 (3-4) ◽

pp. 255-274

Author(s):

Shih-Jui Hsu ◽

Emily C. Stow ◽

James R. Simmons ◽

Heather A. Wallace ◽

Andrea Mancheno Lopez ◽

...

Keyword(s):

Genome Instability ◽

Insulator Protein

An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters

Bioinformatics and Biology Insights ◽

10.4137/bbi.s29330 ◽

2015 ◽

Vol 9S4 ◽

pp. BBI.S29330

Author(s):

Stephen A. Ramsey

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Binding Sites ◽

Transcription Factor Binding ◽

Regulatory Sequences ◽

Gene Promoters ◽

Sequence Pattern ◽

Factor Binding Site ◽

Factor Binding

A Bayesian method for sampling from the distribution of matches to a precompiled transcription factor binding site (TFBS) sequence pattern (conditioned on an observed nucleotide sequence and the sequence pattern) is described. The method takes a position frequency matrix as input for a set of representative binding sites for a transcription factor and two sets of noncoding, 5’ regulatory sequences for gene sets that are to be compared. An empirical prior on the frequency A (per base pair of gene-vicinal, noncoding DNA) of TFBSs is developed using data from the ENCODE project and incorporated into the method. In addition, a probabilistic model for binding site occurrences conditioned on λ is developed analytically, taking into account the finite-width effects of binding sites. The count of TFBS β (conditioned on the observed sequence) is sampled using Metropolis-Hastings with an information entropybased move generator. The derivation of the method is presented in a step-by-step fashion, starting from specific conditional independence assumptions. Empirical results show that the newly proposed prior on β improves accuracy for estimating the number of TFBS within a set of promoter sequences.

Multi-BRCT Domain Protein Brc1 Links Rhp18/Rad18 and γH2A To Maintain Genome Stability during S Phase

Molecular and Cellular Biology ◽

10.1128/mcb.00260-17 ◽

2017 ◽

Vol 37 (22) ◽

Cited By ~ 2

Author(s):

Michael C. Reubens ◽

Sophie Rozenzhak ◽

Paul Russell

Keyword(s):

Genome Stability ◽

Genome Instability ◽

Replication Stress ◽

S Phase ◽

Dna Lesions ◽

Brct Domain ◽

Replication Forks ◽

Content Type ◽

Domain Protein ◽

Chromosome Integrity

ABSTRACT DNA replication involves the inherent risk of genome instability, since replisomes invariably encounter DNA lesions or other structures that stall or collapse replication forks during the S phase. In the fission yeast Schizosaccharomyces pombe, the multi-BRCT domain protein Brc1, which is related to budding yeast Rtt107 and mammalian PTIP, plays an important role in maintaining genome integrity and cell viability when cells experience replication stress. The C-terminal pair of BRCT domains in Brc1 were previously shown to bind phosphohistone H2A (γH2A) formed by Rad3/ATR checkpoint kinase at DNA lesions; however, the putative scaffold interactions involving the N-terminal BRCT domains 1 to 4 of Brc1 have remained obscure. Here, we show that these domains bind Rhp18/Rad18, which is an E3 ubiquitin protein ligase that has crucial functions in postreplication repair. A missense allele in BRCT domain 4 of Brc1 disrupts binding to Rhp18 and causes sensitivity to replication stress. Brc1 binding to Rhp18 and γH2A are required for the Brc1 overexpression suppression of smc6-74, a mutation that impairs the Smc5/6 structural maintenance of chromosomes complex required for chromosome integrity and repair of collapsed replication forks. From these findings, we propose that Brc1 provides scaffolding functions linking γH2A, Rhp18, and Smc5/6 complex at damaged replication forks.

Topoisomerase I Plays a Critical Role in Suppressing Genome Instability at a Highly Transcribed G-Quadruplex-Forming Sequence

PLoS Genetics ◽

10.1371/journal.pgen.1004839 ◽

2014 ◽

Vol 10 (12) ◽

pp. e1004839 ◽

Cited By ~ 29

Author(s):

Puja Yadav ◽

Victoria Harcy ◽

Juan Lucas Argueso ◽

Margaret Dominska ◽

Sue Jinks-Robertson ◽

...

Keyword(s):

Topoisomerase I ◽

Genome Instability ◽

Critical Role ◽

G Quadruplex

Inhibition of macrophage histone demethylase JMJD3 protects against abdominal aortic aneurysms

Journal of Experimental Medicine ◽

10.1084/jem.20201839 ◽

2021 ◽

Vol 218 (6) ◽

Author(s):

Frank M. Davis ◽

Lam C. Tsoi ◽

William J. Melvin ◽

Aaron denDekker ◽

Rachael Wasikowski ◽

...

Keyword(s):

Aortic Rupture ◽

Critical Role ◽

Abdominal Aortic Aneurysms ◽

Aortic Aneurysms ◽

Pharmacologic Therapy ◽

Gene Promoters ◽

Macrophage Phenotype ◽

Inflammatory Gene ◽

Abdominal Aortic

Abdominal aortic aneurysms (AAAs) are a life-threatening disease for which there is a lack of effective therapy preventing aortic rupture. During AAA formation, pathological vascular remodeling is driven by macrophage infiltration, and the mechanisms regulating macrophage-mediated inflammation remain undefined. Recent evidence suggests that an epigenetic enzyme, JMJD3, plays a critical role in establishing macrophage phenotype. Using single-cell RNA sequencing of human AAA tissues, we identified increased JMJD3 in aortic monocyte/macrophages resulting in up-regulation of an inflammatory immune response. Mechanistically, we report that interferon-β regulates Jmjd3 expression via JAK/STAT and that JMJD3 induces NF-κB–mediated inflammatory gene transcription in infiltrating aortic macrophages. In vivo targeted inhibition of JMJD3 with myeloid-specific genetic depletion (JMJD3f/fLyz2Cre+) or pharmacological inhibition in the elastase or angiotensin II–induced AAA model preserved the repressive H3K27me3 on inflammatory gene promoters and markedly reduced AAA expansion and attenuated macrophage-mediated inflammation. Together, our findings suggest that cell-specific pharmacologic therapy targeting JMJD3 may be an effective intervention for AAA expansion.

ARID1A loss derepresses human endogenous retrovirus-H to modulate BRD4-dependent transcription

10.1101/2021.06.28.450127 ◽

2021 ◽

Author(s):

Chunhong Yu ◽

Xiaoyun Lei ◽

Fang Chen ◽

Song Mao ◽

Lu Lv ◽

...

Keyword(s):

Colorectal Cancer ◽

Tumor Growth ◽

Tumor Suppressors ◽

Target Genes ◽

Critical Role ◽

Endogenous Retrovirus ◽

Early Embryogenesis ◽

Human Endogenous Retrovirus ◽

Regulatory Sequences ◽

3D Architecture

The transposable elements (TEs) through evolutionary exaptation have become an integral part of human genome, offering ample regulatory sequences and shaping chromatin 3D architecture. While the functional impacts of TE-derived sequences on early embryogenesis are recognized, their role in malignancy has only started to emerge. Here we show that many TEs, especially the pluripotency-related endogenous retrovirus H (HERVH), are abnormally activated in colorectal cancer (CRC) samples. The transcriptional upregulation of HERVH is associated with mutations of several tumor suppressors including ARID1A. Knockout of ARID1A in CRC cells leads to increased accessibility at HERVH loci and enhanced transcription, which is dependent on ARID1B. Suppression of HERVH in CRC cells and patient-derived organoids impairs tumor growth. Mechanistically, HERVH transcripts colocalize with nuclear BRD4 foci, modulate their dynamics, and co-regulate many target genes. Altogether, we uncover a critical role for ARID1A in restraining HERVH, which can promote tumorigenesis by stimulating BRD4-dependent transcription when ARID1A is mutated.

Deletion of Tet proteins results in quantitative disparities during ESC differentiation partially attributable to alterations in gene expression

10.21203/rs.2.9320/v2 ◽

2019 ◽

Author(s):

Michael J Reimer ◽

Kirthi Pulakanti ◽

Linzheng Shi ◽

Alex Abel ◽

Mingyu Liang ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Critical Role ◽

Embryonic Stem ◽

Dna Demethylation ◽

Intermediate Phenotype ◽

Gene Promoters ◽

Dna Hypermethylation ◽

Tet Proteins ◽

Tet Protein

Abstract Background: The Tet protein family (Tet1, Tet2, and Tet3) regulate DNA methylation through conversion of 5-methylcytosine to 5-hydroxymethylcytosine which can ultimately result in DNA demethylation and play a critical role during early mammalian development and pluripotency¬. While multiple groups have generated knockouts combining loss of different Tet proteins in murine embryonic stem cells (ESCs), differences in genetic background and approaches has made it difficult to directly compare results and discern the direct mechanism by which Tet proteins regulate the transcriptome. To address this concern, we utilized genomic editing in an isogenic pluripotent background which permitted a quantitative, flow-cytometry based measurement of pluripotency in combination with genome-wide assessment of gene expression and DNA methylation changes. Our ultimate goal was to generate a resource of large-scale datasets to permit hypothesis-generating experiments. Results: We demonstrate a quantitative disparity in the differentiation ability among Tet protein deletions, with Tet2 single knockout exhibiting the most severe defect, while loss of Tet1 ¬alone or combinations of Tet genes showed a quantitatively intermediate phenotype. Using a combination of transcriptomic and epigenomic approaches we demonstrate an increase in DNA hypermethylation and a divergence of transcriptional profiles in pluripotency among Tet deletions, with loss of Tet2 having the most profound effect in undifferentiated ESCs. Conclusions: We conclude that loss of Tet2 has the most dramatic effect both on the phenotype of ESCs and the transcriptome compared to other genotypes. While loss of Tet proteins increased DNA hypermethylation, especially in gene promoters, these changes in DNA methylation did not correlate with gene expression changes. Thus, while loss of different Tet proteins alters DNA methylation, this change does not appear to be directly responsible for transcriptome changes. Thus, loss of Tet proteins likely regulates the transcriptome epigenetically both through altering 5mC but also through additional mechanisms. Nonetheless, the transcriptome changes in pluripotent Tet2-/- ESCs compared to wild-type implies that the disparities in differentiation can be partially attributed to baseline alterations in gene expression.