scholarly journals Assessment of the CTCF Binding Sites and Repeat-Positions Upstream the Human H19 Gene

2018 ◽  
Author(s):  
Minou Bina
Keyword(s):  
Cpg Island ◽  
Ctcf Binding ◽  
Dependent Manner ◽  
Sequence Comparisons ◽  
Sequence Organization ◽  
Accurate Localization ◽  
H19 Gene ◽  
Chromatin Boundary ◽  
Clustal Omega ◽  
Ctcf Site

AbstractThe human H19 and IGF2 genes share an Imprinting Control Region (ICR) that regulates gene expression in a parent-of-origin dependent manner. Understanding of the ICR sequence organization is critical to accurate localization of disease-associated abnormalities including Beckwith-Wiedemann and Silver-Russell syndromes. Previous studies established that the ICR of the H19 - IGF2 imprinted domain included several repeated DNA segments. Using BLAST, BLAT, and Clustal Omega, I conducted detailed sequence comparisons to evaluate the annotation of the unique-repeats upstream of the H19 transcription start site (TSS) and to investigate the extent of similarities among the various repeats. Initial analyses confirmed the existence of two DNA segments consisting of two types of repeats (A and B). However, I find that one of the repeats (B7) is unlikely to be a partial repeat. I provide the genomic positions of the various repeats in the build hg19 of the human genome. I also evaluated the previously predicted CTCF sites (1 to 7) in the context of the ENCODE data: including the positions of DNase I HS clusters and results of ChIP assays. My evaluations did not support the existence of CTCF site 5. Furthermore, the ENCODE data revealed a previously unknown chromatin boundary (consisting of CTCF, RAD21, and SMC3), in a CpG island (CpG27) between the A1 repeat and the H19 TSS. Furthermore, a sequence within this boundary corresponds to a newly discovered CTCF site (I named it CTCF site 8). My discovery of this chromatin boundary in CpG27 entails mechanistic implications.

scholarly journals Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis

2020 ◽  
Vol 48 (6) ◽  
pp. 3119-3133 ◽  
Author(s):  
Ying Li ◽  
Ziwei Liao ◽  
Huacheng Luo ◽  
Aissa Benyoucef ◽  
Yuanyuan Kang ◽  
...  
Keyword(s):  
Chromatin Accessibility ◽  
Jurkat Cells ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Dependent Manner ◽  
Range Interaction ◽  
Chromatin Boundary ◽  
Transcription Networks ◽  
Transcription Program ◽  
Promoter Interaction

Abstract Aberrant activation of the TAL1 is associated with up to 60% of T-ALL cases and is involved in CTCF-mediated genome organization within the TAL1 locus, suggesting that CTCF boundary plays a pathogenic role in T-ALL. Here, we show that −31-Kb CTCF binding site (−31CBS) serves as chromatin boundary that defines topologically associating domain (TAD) and enhancer/promoter interaction required for TAL1 activation. Deleted or inverted −31CBS impairs TAL1 expression in a context-dependent manner. Deletion of −31CBS reduces chromatin accessibility and blocks long-range interaction between the +51 erythroid enhancer and TAL1 promoter-1 leading to inhibition of TAL1 expression in erythroid cells, but not T-ALL cells. However, in TAL1-expressing T-ALL cells, the leukemia-prone TAL1 promoter-IV specifically interacts with the +19 stem cell enhancer located 19 Kb downstream of TAL1 and this interaction is disrupted by the −31CBS inversion in T-ALL cells. Inversion of −31CBS in Jurkat cells alters chromatin accessibility, histone modifications and CTCF-mediated TAD leading to inhibition of TAL1 expression and TAL1-driven leukemogenesis. Thus, our data reveal that −31CBS acts as critical regulator to define +19-enhancer and the leukemic prone promoter IV interaction for TAL1 activation in T-ALL. Manipulation of CTCF boundary can alter TAL1 TAD and oncogenic transcription networks in leukemogenesis.

scholarly journals Analysis of Sequence Upstream of the Endogenous H19 Gene Reveals Elements Both Essential and Dispensable for Imprinting

2002 ◽  
Vol 22 (8) ◽  
pp. 2450-2462 ◽  
Author(s):  
Joanne L. Thorvaldsen ◽  
Mellissa R. W. Mann ◽  
Okechukwu Nwoko ◽  
Kristen L. Duran ◽  
Marisa S. Bartolomei
Keyword(s):  
Repetitive Elements ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Insulator Activity ◽  
Binding Factor ◽  
Additional Sequence ◽  
H19 Gene ◽  
Full Activation ◽  
Ctcf Site

ABSTRACT Imprinting of the linked and oppositely expressed mouse H19 and Igf2 genes requires a 2-kb differentially methylated domain (DMD) that is located 2 kb upstream of H19. This element is postulated to function as a methylation-sensitive insulator. Here we test whether an additional sequence 5′ of H19 is required for H19 and Igf2 imprinting. Because repetitive elements have been suggested to be important for genomic imprinting, the requirement of a G-rich repetitive element that is located immediately 3′ to the DMD was first tested in two targeted deletions: a 2.9-kb deletion (ΔDMDΔG) that removes the DMD and G-rich repeat and a 1.3-kb deletion (ΔG) removing only the latter. There are also four 21-bp GC-rich repetitive elements within the DMD that bind the insulator-associated CTCF (CCCTC-binding factor) protein and are implicated in mediating methylation-sensitive insulator activity. As three of the four repeats of the 2-kb DMD were deleted in the initial 1.6-kb ΔDMD allele, we analyzed a 3.8-kb targeted allele (Δ3.8kb-5′H19), which deletes the entire DMD, to test the function of the fourth repeat. Comparative analysis of the 5′ deletion alleles reveals that (i) the G-rich repeat element is dispensable for imprinting, (ii) the ΔDMD and ΔDMDΔG alleles exhibit slightly more methylation upon paternal transmission, (iii) removal of the 5′ CTCF site does not further perturb H19 and Igf2 imprinting, suggesting that one CTCF-binding site is insufficient to generate insulator activity in vivo, (iv) the DMD sequence is required for full activation of H19 and Igf2, and (v) deletion of the DMD disrupts H19 and Igf2 expression in a tissue-specific manner.

Structural models for the self-assembly and microtubule interactions of gamma-, delta- and epsilon-tubulin

2001 ◽  
Vol 114 (2) ◽  
pp. 413-422 ◽  
Author(s):  
Y.F. Inclan ◽  
E. Nogales
Keyword(s):  
Self Assembly ◽  
Structural Models ◽  
Dependent Manner ◽  
Gamma Delta ◽  
Sequence Comparisons ◽  
Alpha Tubulin ◽  
A Cell ◽  
Gamma Tubulin ◽  
Cycle Dependent ◽  
Key Residues

alphabeta-tubulin heterodimers self-assemble to form microtubules nucleated by gamma-tubulin in the cell. Gamma-tubulin is believed to recruit the alphabeta-tubulin dimers that form the minus ends of microtubules, but the molecular mechanism of this action remains a matter of heated controversy. Still less is known about the function and molecular interactions of delta-tubulin and epsilon-tubulin. delta-tubulin may seed the formation of the C triplet tubules in the basal bodies of Chlamydomonas and epsilon-tubulin is known to localize to the centrosome in a cell cycle-dependent manner. Using the structure of alphabeta tubulin as a model, we have analyzed the sequences of gamma-, delta- and epsilon-tubulin in regions corresponding to different polymerization interfaces in the tubulin alphabeta dimer. The sequence comparisons sometimes show clear conservation, pointing to similar types of contacts being functionally important for the new tubulin considered. Conversely, certain surfaces show marked differences that rule out equivalent interactions for non-microtubular tubulins. This sequence/structure analysis has led us to structural models of how these special tubulins may be involved in protein-protein contacts that affect microtubule self-assembly. delta-tubulin most likely interacts longitudinally with alpha-tubulin at the minus ends of microtubules, while epsilon-tubulin most likely binds to the plus end of beta-tubulin. Conservation of key residues in gamma-tubulin suggests that it is capable of longitudinal self-assembly. The implications for the protofilament and template models of nucleation are considered.

Methylation of the ESR1 CpG island in the colorectal mucosa is an ‘all or nothing’ process in healthy human colon, and is accelerated by dietary folate supplementation in the mouse

2005 ◽  
Vol 33 (4) ◽  
pp. 709-711 ◽  
Author(s):  
N.J. Belshaw ◽  
G.O. Elliott ◽  
E.A. Williams ◽  
J.C. Mathers ◽  
L. Buckley ◽  
...  
Keyword(s):  
Cpg Island ◽  
Cancer Cell Line ◽  
Human Colon ◽  
Colorectal Cancer Cell Line ◽  
Dependent Manner ◽  
Folate Supplementation ◽  
Healthy Human ◽  
Dietary Folate ◽  
Human Dna ◽  
Age Dependent

ESR1 is frequently silenced by CGI (CpG island) methylation, both in human colorectal tumours and, in an age-dependent manner, in healthy mucosa. It is not clear, however, whether methylation of individual cytosines occurs randomly within the epithelial genome, or preferentially within individual cells as an ‘all-or-nothing’ phenomenon. CGI methylation can be quantified in human DNA residues recovered from faecal samples. We used bisulphite genomic sequencing of human DNA from this source and from a colorectal cancer cell line (SW48) to show that the ESR1 CGI is methylated in an allele-specific manner. This provides support for the ‘all or none’ mechanism for methylation of this gene, and shows how age-dependent methylation of the ESR1 CGI leads rapidly to silencing of the gene within the cells, and hence the colonic crypt within which it occurs. Preliminary studies with a rodent model suggest the rate of age-dependent methylation of ESR1 is modifiable by dietary folate.

scholarly journals 3'HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression

2021 ◽  
Author(s):  
Pamela Himadewi ◽  
Xue Qing David Wang ◽  
Fan Feng ◽  
Haley Gore ◽  
Yushuai Liu ◽  
...  
Keyword(s):  
Binding Site ◽  
Progenitor Cells ◽  
Globin Gene ◽  
Fetal Hemoglobin ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Distal Enhancer ◽  
Erythroid Progenitor ◽  
Hematopoietic Stem ◽  
Ctcf Site

Mutations in the adult β-globin gene can lead to a variety of hemoglobinopathies, including sickle cell disease and β-thalassemia. An increase in fetal hemoglobin expression throughout adulthood, a condition named Hereditary Persistence of Fetal Hemoglobin (HPFH), has been found to ameliorate hemoglobinopathies. Deletional HPFH occurs through the excision of a significant portion of the 3 prime end of the β-globin locus, including a CTCF binding site termed 3'HS1. Here, we show that the deletion of this CTCF site alone induces fetal hemoglobin expression in both adult CD34+ hematopoietic stem and progenitor cells and HUDEP-2 erythroid progenitor cells. This induction is driven by the ectopic access of a previously postulated distal enhancer located in the OR52A1 gene downstream of the locus, which can also be insulated by the inversion of the 3'HS1 CTCF site. This suggests that genetic editing of this binding site can have therapeutic implications to treat hemoglobinopathies.

Lead induces the up-regulation of the protein arginine methyltransferase 5 possibly by its promoter demethylation

2018 ◽  
Vol 475 (16) ◽  
pp. 2653-2666 ◽  
Author(s):  
Krishna Ghosh ◽  
Biji Chatterjee ◽  
Santosh R. Kanade
Keyword(s):  
Cpg Island ◽  
Proximal Region ◽  
Dependent Manner ◽  
Protein Arginine Methyltransferase ◽  
Arginine Methyltransferase ◽  
Arginine Residues ◽  
Pb Exposure ◽  
Mcf 7 ◽  
Protein Arginine Methyltransferase 5

The studies on lead (Pb) exposure linking to epigenetic modulations are caused by its differential actions on global DNA methylation and histone modifications. These epigenetic changes may result in increased accessibility of the transcription factors to promoter DNA-binding elements leading to activation and expression of the gene. The protein arginine methyltransferase 5 (PRMT5) and its partner methylosome protein 50 (MEP50) together catalyze the mono- and symmetric dimethylation of arginine residues in many histone and non-histone protein substrates. Moreover, it is overexpressed in many forms of cancer. In the present study, the effects of Pb on the PRMT5 and MEP50 expression and formation of the symmetrically dimethylated arginine (SDMA), the catalytic product of the PRMT5–MEP50 complex were analyzed in vitro after exposing the A549 and MCF-7 cells. The results show that exposure to 0.1 and 1 µM of Pb strongly enhanced the expression of both PRMT5 and MEP50 transcript and protein leading to increased SDMA levels globally with H4R3 being increasingly symmetrically dimethylated in a dose-dependent manner after 48 h of Pb exposure in both cell types. The methylation-specific PCR also revealed that the CpG island present on the PRMT5 promoter proximal region was increasingly demethylated as the dose of Pb increased in a 48-h exposure window in both cells, with MCF-7 being more responsive to Pb-mediated PRMT5 promoter demethylation. The bisulfite sequencing confirmed this effect. The findings therefore indicate that Pb exposure increasing the PRMT5 expression might be one of the contributing epigenetic factors in the lead-mediated disease processes as PRMT5 has a versatile role in cellular functions and oncogenesis.

Role of MBD2 in gene regulation and tumorigenesis

2005 ◽  
Vol 33 (6) ◽  
pp. 1537-1540 ◽  
Author(s):  
J. Berger ◽  
A. Bird
Keyword(s):  
Dna Methyltransferase ◽  
Cpg Island ◽  
Gene Dosage ◽  
Cpg Islands ◽  
Transcriptional Repressor ◽  
Epigenetic Mechanism ◽  
Tumour Suppressor Genes ◽  
Dependent Manner ◽  
Cpg Dinucleotides ◽  
Mbd Protein

DNA methylation is an epigenetic mechanism involved in transcriptional silencing of imprinted genes, genes located on the inactive X chromosome, and a number of tumour suppressor genes in cancer. MBD (methyl-CpG-binding domain) proteins selectively bind to methylated DNA and recruit chromatin remodelling and transcriptional repressor complexes, thereby establishing a repressive chromatin state. MBD2, a member of the MBD protein family, binds to methylated promoter CpG islands (clusters of high-density CpG dinucleotides) and acts as a methylation-dependent transcriptional repressor. Previous work has demonstrated that decreased CpG island methylation in mice lacking the DNA methyltransferase DNMT1 is associated with impaired tumorigenesis when crossed on the tumour-susceptible ApcMin/+ background. Mbd2 deficiency also dramatically reduces adenoma burden and extends life span in a gene dosage-dependent manner in this mouse model. Mbd2 is therefore essential for tumorigenesis in the murine intestine, although it is dispensable for the viability of the host animals. These findings validate MBD2 as a potential target for therapeutic intervention in colorectal cancer.

scholarly journals Epigenetic Inactivation of Acetyl-Co A acetyltransferase 1 promotes the proliferation and metastasis of nasopharyngeal carcinoma via decreasing ketogenesis

2020 ◽  
Author(s):  
Yunliang Lu ◽  
Xiaohui Zhou ◽  
Weilin Zhao ◽  
Zhipeng Liao ◽  
Bo Li ◽  
...  
Keyword(s):  
Cell Lines ◽  
Colony Formation ◽  
Ketone Body ◽  
Epithelial Mesenchymal Transition ◽  
Cpg Island ◽  
Dependent Manner ◽  
Mesenchymal Transition ◽  
Ketone Body Metabolism

Abstract Background Acy1 Coenzyme A Acyltransferases1 (ACAT1) is a key enzyme in the metabolism of ketone bodies, but its expression and biological function in the pathogenesis of NPC remains underexplored. Methods The mRNA and protein expression levels of ACAT1 in NPC and normal control tissues were analyzed by qPCR and immunohistochemistry staining, respectively. GEO database was applied for meta-analysis of ACAT1 mRNA expression and DNA promoter methylation. The role of ACAT1 in NPC proliferation was examined by CCK8 and colony formation assays in vitro and tumorigenicity in vivo. The wound healing and transwell assays were used for analyzing the migratory and invasive ability. cDNA microarray analysis was performed to identify the genes involved in epithelial-mesenchymal transition and dysregulated by ACAT1. These changes were further confirmed by western blot. Results We found that ACAT1 is inactivated in NPC cell lines and primary tissues. DNA microarray data showed higher methylation in the CpG island region of ACAT1 in NPC than normal tissues. The demethylating reagent 5-aza-dC significantly restored the transcription of ACAT1 in NPC cell lines, suggesting that ACAT1 was inactivated by DNA promoter hypermethylation. Ectopic overexpression of ACAT1 remarkably suppressed the proliferation and colony formation of NPC cells in vitro. As well, the tumorigenesis of NPC cells overexpressing ACAT1 was decreased in vivo. In addition, the migratory and invasive capacities of NPC cells was inhibited by ACAT1 overexpression. Importantly, the higher level of ACAT1 was accompanied by an increased expression of CDH1, EPCAM, and a decreased expression of vimentin and SPARC. This strongly indicates that ACAT1 is able to affect the epithelial-mesenchymal transition in NPC, thereby controlling cellular motility. In addition, we found that ACAT1 expression increases the intracellular level of β-HB. Moreover, exogenous β-HB remarkably inhibits the growth of NPC cells in a dose-dependent manner. Conclusions We have discovered that the ketone body metabolism enzyme ACAT1 is epigenetically downregulated in NPC and acts as a potential tumor suppressor in NPC. Our findings highlight the possibility of using the modulation of ketone body metabolism as effective adjuvant therapy for NPC.

scholarly journals Environmental enrichment induces epigenomic and genome organization changes relevant for cognitive function

2021 ◽  
Author(s):  
Sergio Espeso-Gil ◽  
Aliaksei Holik ◽  
Sarah Bonnin ◽  
Shalu Jhanwar ◽  
Sandhya Chandrasekaran ◽  
...  
Keyword(s):  
Cognitive Function ◽  
Genome Organization ◽  
Environmental Enrichment ◽  
Neuronal Development ◽  
Chromatin Accessibility ◽  
Ctcf Binding ◽  
List Type ◽  
Dependent Manner ◽  
3D Genome ◽  
Induced Changes

SummaryIn early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 (inter-chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization.Highlights-Environmental enrichment (EE) alters chromatin conformation, CTCF binding, and spatially 3D genome changes, thereby regulating cognitive function during the first steps of life after birth.-Transcription-associated gene body marks H3K79me2 and H3K36me3 are differently influenced by EE in cortical brain cells and binding is exacerbated upon stimulation in an age-dependent manner.-EE-induced changes of 3D genome organization increase inter-chromosomal interactions of genes associated with synaptic transmission and AMPA receptor genes on chromosomes 7 and 17.

scholarly journals Differential Expression of α, β, and γ Protocadherin Isoforms During Differentiation, Aging, and Cancer

2021 ◽  
Author(s):  
Michael D. West ◽  
Ivan Labat ◽  
Jie Li ◽  
Pam Sim ◽  
Jeffrey Janus ◽  
...  
Keyword(s):  
Potential Role ◽  
Replicative Senescence ◽  
Cpg Island ◽  
Embryonic Stem ◽  
Neuronal Cell ◽  
Differential Regulation ◽  
Ctcf Binding ◽  
Cell Recognition ◽  
Cell Cell

AbstractThe cadherin family of cell surface glycoproteins plays a fundamental role in cell-cell recognition, thereby participating in diverse biological process such as embryonic morphogenesis and oncogenic transformation. The subset of clustered protocadherin (PCDH) genes generated from the α, β, and γ loci, have been widely studied for their potential role in neuronal cell-cell recognition and neurogenesis, however their broader role in normal embryonic development and cancer has not been examined in detail. We utilized human embryonic stem (hES) cells to model early human developmentin vitro, comparing PCDH isoform transcription in diverse types of embryonic progenitors with normal adult-derived and cancer counterparts. Embryonic progenitors express genes from the α and β cluster at levels comparable to that seen in the CNS, while fetal and adult-derived cells express primarily from the γ cluster. Replicative senescence left fibroblasts with markedly lower expression of all isoforms. We observe that an embryonic pattern of clustered protocadherin gene expression and associated CpG island methylation is commonly associated with cancer cell lines from diverse tissue types. The differential regulation of the α, β, and γ loci coincide with alternate regions of DNA accessibility at CTCF binding sites and lamina-associated domains and CPL expression correlated with the expression ofLMNAandLMNB1. These observations support a potential role for the differential regulation of genes within the clustered protocadherin locus in selective cell-cell adhesion during embryogenesis, regeneration, cancer and aging.

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