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Journal articles on the topic 'CCCTC-binding factor like'

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Published: 2 June 2025

Last updated: 31 July 2025

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1

Yang, Bobae, Tae-Gyun Kim, Sueun Kim, and Hyoung-Pyo Kim. "CCCTC-binding factor regulates the development and function of dendritic cells." Journal of Immunology 202, no. 1_Supplement (2019): 118.5. http://dx.doi.org/10.4049/jimmunol.202.supp.118.5.

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Abstract Dendritic cells (DCs) are professional antigen presenting cells, which present antigen to cognate T cells. DC activation through diverse toll-like receptors is prerequisite for triggering efficient immune responses to foreign antigens. CCCTC-binding factor (CTCF) is a DNA binding protein that regulates 3D genome structure which is believed to be important to control of gene expression. Here we described that CTCF is required for development and function in DCs. CTCF is critically required for the FLT3L-dependent CD11c+ DCs (FL-DCs) development, unlike for those in the GM-CSF-dependent

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2

Zhang, He, Beibei Niu, Ji-Fan Hu, et al. "Interruption of intrachromosomal looping by CCCTC binding factor decoy proteins abrogates genomic imprinting of human insulin-like growth factor II." Journal of Cell Biology 193, no. 3 (2011): 475–87. http://dx.doi.org/10.1083/jcb.201101021.

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Monoallelic expression of IGF2 is regulated by CCCTC binding factor (CTCF) binding to the imprinting control region (ICR) on the maternal allele, with subsequent formation of an intrachromosomal loop to the promoter region. The N-terminal domain of CTCF interacts with SUZ12, part of the polycomb repressive complex-2 (PRC2), to silence the maternal allele. We synthesized decoy CTCF proteins, fusing the CTCF deoxyribonucleic acid–binding zinc finger domain to CpG methyltransferase Sss1 or to enhanced green fluorescent protein. In normal human fibroblasts and breast cancer MCF7 cell lines, the CT

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3

Bintu, Bogdan, Leslie J. Mateo, Jun-Han Su, et al. "Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells." Science 362, no. 6413 (2018): eaau1783. http://dx.doi.org/10.1126/science.aau1783.

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The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding s

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Fu, Vivian X., Steven R. Schwarze, Michelle L. Kenowski, Scott LeBlanc, John Svaren, and David F. Jarrard. "A Loss of Insulin-like Growth Factor-2 Imprinting Is Modulated by CCCTC-binding Factor Down-regulation at Senescence in Human Epithelial Cells." Journal of Biological Chemistry 279, no. 50 (2004): 52218–26. http://dx.doi.org/10.1074/jbc.m405015200.

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The imprinted insulin-like growth factor-2 (IGF2) gene is an auto/paracrine growth factor expressed only from the paternal allele in adult tissues. In tissues susceptible to aging-related cancers, including the prostate, a relaxation ofIGF2imprinting is found, suggesting a permissive role for epigenetic alterations in cancer development. To determine whetherIGF2imprinting is altered in cellular aging and senescence, human prostate epithelial and urothelial cells were passaged serially in culture to senescence. Allelic analyses using anIGF2polymorphism demonstrated a complete conversion of theI

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5

Gillen, Austin E., and Ann Harris. "The role of CTCF in coordinating the expression of single gene loci." Biochemistry and Cell Biology 89, no. 5 (2011): 489–94. http://dx.doi.org/10.1139/o11-040.

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The CCCTC-binding factor (CTCF), which binds insulator elements in vertebrates, also facilitates coordinated gene expression at several gene clusters, including the β-globin, Igf2/H19 (insulin like growth factor 2/H19 noncoding RNA), and major histocompatibility complex (MHC) class II loci. CTCF controls expression of these genes both by enabling insulator function and facilitating higher order chromatin interactions. While the role of CTCF in gene regulation is best studied at these multi-gene loci, there is also evidence that CTCF contributes to the regulated expression of single genes. Here

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6

Oiwa, Nestor Norio, Kunhe Li, Claudette E. Cordeiro, and Dieter W. Heermann. "Prediction and comparative analysis of CTCF binding sites based on a first principle approach." Physical Biology 19, no. 3 (2022): 036005. http://dx.doi.org/10.1088/1478-3975/ac5dca.

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Abstract We calculated the patterns for the CCCTC transcription factor (CTCF) binding sites across many genomes on a first principle approach. The validation of the first principle method was done on the human as well as on the mouse genome. The predicted human CTCF binding sites are consistent with the consensus sequence, ChIP-seq data for the K562 cell, nucleosome positions for IMR90 cell as well as the CTCF binding sites in the mouse HOXA gene. The analysis of Homo sapiens, Mus musculus, Sus scrofa, Capra hircus and Drosophila melanogaster whole genomes shows: binding sites are organized in

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7

Miyata, Kenichi, Yoshinori Imai, Satoshi Hori, et al. "Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer." Proceedings of the National Academy of Sciences 118, no. 35 (2021): e2025647118. http://dx.doi.org/10.1073/pnas.2025647118.

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Cellular senescence causes a dramatic alteration of chromatin organization and changes the gene expression profile of proinflammatory factors, thereby contributing to various age-related pathologies through the senescence-associated secretory phenotype (SASP). Chromatin organization and global gene expression are maintained by the CCCTC-binding factor (CTCF); however, the molecular mechanism underlying CTCF regulation and its association with SASP gene expression remains unclear. We discovered that noncoding RNA (ncRNA) derived from normally silenced pericentromeric repetitive sequences direct

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8

Voutsadakis, Ioannis. "Molecular Lesions of Insulator CTCF and Its Paralogue CTCFL (BORIS) in Cancer: An Analysis from Published Genomic Studies." High-Throughput 7, no. 4 (2018): 30. http://dx.doi.org/10.3390/ht7040030.

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CTCF (CCCTC-binding factor) is a transcription regulator with hundreds of binding sites in the human genome. It has a main function as an insulator protein, defining together with cohesins the boundaries of areas of the genome called topologically associating domains (TADs). TADs contain regulatory elements such as enhancers which function as regulators of the transcription of genes inside the boundaries of the TAD while they are restricted from regulating genes outside these boundaries. This paper will examine the most common genetic lesions of CTCF as well as its related protein CTCFL (CTCF-

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9

Sun, Ge, Chunyu Wang, Shengli Wang та ін. "An H3K4me3 reader, BAP18 as an adaptor of COMPASS-like core subunits co-activates ERα action and associates with the sensitivity of antiestrogen in breast cancer". Nucleic Acids Research 48, № 19 (2020): 10768–84. http://dx.doi.org/10.1093/nar/gkaa787.

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Abstract Estrogen receptor alpha (ERα) signaling pathway is essential for ERα-positive breast cancer progression and endocrine therapy resistance. Bromodomain PHD Finger Transcription Factor (BPTF) associated protein of 18kDa (BAP18) has been recognized as a crucial H3K4me3 reader. However, the whole genomic occupation of BAP18 and its biological function in breast cancer is still elusive. Here, we found that higher expression of BAP18 in ERα-positive breast cancer is positively correlated with poor prognosis. ChIP-seq analysis further demonstrated that the half estrogen response elements (ERE

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10

Mohanta, Tapan Kumar, Awdhesh Kumar Mishra, and Ahmed Al-Harrasi. "The 3D Genome: From Structure to Function." International Journal of Molecular Sciences 22, no. 21 (2021): 11585. http://dx.doi.org/10.3390/ijms222111585.

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The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding fact

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11

Willmer, Tarryn, Asive Myataza, Oelfah Patel, Rabia Johnson, and Carmen Pheiffer. "A HIGH-FAT, HIGH-SUGAR DIET INDUCES INSULIN-LIKE GROWTH FACTOR 2 HYPER- METHYLATION IN MALE WISTAR RATS." Journal of the ASEAN Federation of Endocrine Societies 37, no. 2 (2022): 63. https://doi.org/10.15605/jafes.037.afes.98.

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OBJECTIVEThe prevalence of obesity and insulin resistance (IR) has increased at an exponential rate worldwide. Although several mechanisms such as dysregulation of the epigenome have been implicated, the disease pathophysiology remains to be fully elucidated. The primary objective of this study was to elucidate DNA methylation profiles and gene regulatory networks that are altered in the skeletal muscle (SM) during the development of obesity and IR in male Wistar rats. METHODOLOGYMale Wistar rats (n=20) were fed either a high-fat, high- sugar (HFHS) or a standard diet (STD) for 12 weeks. SM wa

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Szabó, Piroska E., Gerd P. Pfeifer, and Jeffrey R. Mann. "Parent-of-Origin-Specific Binding of Nuclear Hormone Receptor Complexes in the H19-Igf2 Imprinting Control Region." Molecular and Cellular Biology 24, no. 11 (2004): 4858–68. http://dx.doi.org/10.1128/mcb.24.11.4858-4868.2004.

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ABSTRACT Parent-of-origin-specific expression of the mouse insulin-like growth factor 2 gene (Igf2) and the closely linked H19 gene located on distal chromosome 7 is regulated by a 2.4-kb imprinting control region (ICR) located upstream of the H19 gene. In somatic cells, the maternally and paternally derived ICRs are hypo- and hypermethylated, respectively, with the former binding the insulator protein CCCTC-binding factor (CTCF) and acting to block access of enhancers to the Igf2 promoter. Here we report on a detailed in vivo footprinting analysis—using ligation-mediated PCR combined with in

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Eberhart, Charles, Lujain Alaali, and Su Chan Lee. "CSIG-33. BCOR LOSS PROMOTES RETINOBLASTOMA GROWTH AND DISSEMINATION BY MODULATING INSULIN-LIKE GROWTH FACTOR 2." Neuro-Oncology 24, Supplement_7 (2022): vii46. http://dx.doi.org/10.1093/neuonc/noac209.182.

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Abstract While loss of RB function is the most common genetic alteration in the pediatric embryonal eye tumor retinoblastoma, mutations leading to BCL-6 corepressor (BCOR) loss of function are the second most common alteration. BCOR mutations are found in more aggressive tumors, and are associated with metastasis and poor prognosis. We investigated the effects of BCOR loss or overexpression in retinoblastoma cells in order to better understand its functional role, and to determine if it represents a new therapeutic target in these tumors. Six established retinoblastoma cell lines were examined

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14

Amelio, Antonio L., Peterjon K. McAnany, and David C. Bloom. "A Chromatin Insulator-Like Element in the Herpes Simplex Virus Type 1 Latency-Associated Transcript Region Binds CCCTC-Binding Factor and Displays Enhancer-Blocking and Silencing Activities." Journal of Virology 80, no. 5 (2006): 2358–68. http://dx.doi.org/10.1128/jvi.80.5.2358-2368.2006.

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ABSTRACT A previous study demonstrated that the latency-associated transcript (LAT) promoter and the LAT enhancer/reactivation critical region (rcr) are enriched in acetyl histone H3 (K9, K14) during herpes simplex virus type 1 (HSV-1) latency, whereas all lytic genes analyzed (ICP0, UL54, ICP4, and DNA polymerase) are not (N. J. Kubat, R. K. Tran, P. McAnany, and D. C. Bloom, J. Virol. 78:1139-1149, 2004). This suggests that the HSV-1 latent genome is organized into histone H3 (K9, K14) hyperacetylated and hypoacetylated regions corresponding to transcriptionally permissive and transcriptiona

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Darrow, Emily M., Miriam H. Huntley, Olga Dudchenko, et al. "Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture." Proceedings of the National Academy of Sciences 113, no. 31 (2016): E4504—E4512. http://dx.doi.org/10.1073/pnas.1609643113.

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During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The

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Lin, Chia-Hung, Yun-Shien Lee, Yu-Yao Huang, and Chi-Neu Tsai. "Methylation status of vault RNA 2-1 promoter is a predictor of glycemic response to glucagon-like peptide-1 analog therapy in type 2 diabetes mellitus." BMJ Open Diabetes Research & Care 9, no. 1 (2021): e001416. http://dx.doi.org/10.1136/bmjdrc-2020-001416.

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IntroductionTherapeutic efficiency of glucagon-like peptide-1 (GLP-1) analog is about 50%–70% in type 2 diabetes mellitus (T2DM). Discovery of potential genetic biomarkers for prediction of treatment efficiency of GLP-1 analog before therapy is still necessary. We assess whether DNA methylation was associated with glycemic response to GLP-1 analog therapy in patients with poorly controlled T2DM.Research design and methodsGenomic DNA was extracted from the peripheral blood of training (n=10) and validation (n=128) groups of patients with T2DM receiving GLP-1 analogs. DNA methylome was analyzed

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Alireza, Heidari, Locci Elena, and Raymond Silvia. "Combinatorial Approaches with Checkpoint Inhibitors to Enhance Anti-Tumor Immunity as Advantages of Targeting the Tumor Immune Microenvironment over Blocking Immune Checkpoint in Cancer Immunotherapy." Instant Journal of Hematology and Oncology 4, no. 1 (2021): 501–47. https://doi.org/10.36811/ijho.2021.110021.

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Aging is a condition in which the cell cycle is essentially irreversible and is caused by a variety of stressors such as obesity, radiation and chemotherapy. Aging cells that accumulate in the body during this period communicate with surrounding tissues through the production of proinflammatory proteins, called the SASP, and play a number of physiological and pathological roles. In the elderly, inflammatory agents of SASP increase various age-related diseases, including cancer; therefore, clarification of the SASP monitoring mechanism is essential for the development of new prevention and trea

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Paris, Christian, Ieisha Pentland, Ian Groves, et al. "CCCTC-Binding Factor Recruitment to the Early Region of the Human Papillomavirus 18 Genome Regulates Viral Oncogene Expression." Journal of Virology 89, no. 9 (2015): 4770–85. http://dx.doi.org/10.1128/jvi.00097-15.

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ABSTRACTHost cell differentiation-dependent regulation of human papillomavirus (HPV) gene expression is required for productive infection. The host cell CCCTC-binding factor (CTCF) functions in genome-wide chromatin organization and gene regulation. We have identified a conserved CTCF binding site in the E2 open reading frame of high-risk HPV types. Using organotypic raft cultures of primary human keratinocytes containing high-risk HPV18 genomes, we show that CTCF recruitment to this conserved site regulates viral gene expression in differentiating epithelia. Mutation of the CTCF binding site

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Singh, Pankaj, Liqian Zhu, Mason A. Shipley, Ziyun A. Ye, and Donna M. Neumann. "The HSV-1 encoded CCCTC-binding factor, CTRL2, impacts the nature of viral chromatin during HSV-1 lytic infection." PLOS Pathogens 20, no. 10 (2024): e1012621. http://dx.doi.org/10.1371/journal.ppat.1012621.

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HSV-1 genomes are rapidly heterochromatinized following entry by host cells to limit viral gene expression. Efficient HSV-1 genome replication requires mechanisms that de-repress chromatin associated with the viral genome. CCCTC-binding factors, or CTCF insulators play both silencing and activating roles in cellular transcriptional regulation. Importantly, the HSV-1 genome encodes several CTCF insulators that flank IE genes, implying that individual HSV-1 encoded CTCF insulators regulate IE transcription during all stages of the HSV-1 life cycle. We previously reported that the HSV-1 encoded C

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Ferguson, Jack, Karen Campos-León, Ieisha Pentland, et al. "The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression." PLOS Pathogens 17, no. 11 (2021): e1010032. http://dx.doi.org/10.1371/journal.ppat.1010032.

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The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading frame (ORF) of human papillomavirus (HPV) 18 and functions to repress viral oncogene expression in undifferentiated keratinocytes by co-ordinating an epigenetically repressed chromatin loop within HPV episomes. Keratinocyte differentiation disrupts CTCF-dependent chromatin looping of HPV18 episomes

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Siegler, Benedikt Hermann, Jan Niklas Thon, Marc Altvater, et al. "Abdominal surgery induces long-lasting changes in expression and binding of CTCF with impact on Major Histocompatibility Complex II transcription in circulating human monocytes." PLOS ONE 18, no. 10 (2023): e0293347. http://dx.doi.org/10.1371/journal.pone.0293347.

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Background Postoperative immunosuppression has been recognized as an important driver of surgery-related morbidity and mortality. It is characterized by lymphocyte depression and impaired monocyte capability to present foreign antigens to T-cells via Major Histocompatibility Complex, Class II (MHC-II) molecules. In patients with postoperative abdominal sepsis, we previously detected a persisting differential binding of the CCCTC-Binding Factor (CTCF), a superordinate regulator of transcription, inside the MHC-II region with specific impact on human leucocyte antigen (HLA) gene expression. In t

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Ogata, Toshihiko, Takuyo Kozuka, and Tadahito Kanda. "Identification of an Insulator in AAVS1, a Preferred Region for Integration of Adeno-Associated Virus DNA." Journal of Virology 77, no. 16 (2003): 9000–9007. http://dx.doi.org/10.1128/jvi.77.16.9000-9007.2003.

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ABSTRACT In latent adeno-associated virus (AAV) infection, the viral genome is integrated preferentially into the human chromosome 19 q arm at a specific region designated AAVS1, which has an open chromatin conformation as indicated by the presence of a DNase I-hypersensitive site (DHS-S1). We examined whether an insulator, which defines the domain of gene expression by directionally blocking the action of enhancers and by preventing the spread of heterochomatin, is present near the DHS-S1 in the middle of a 2.6-kbp AAVS1-related DNA fragment used in this study. The fragment, cloned into an Ep

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Gu, Dan, Ting Cao, Shijie Yi, Ya Liu, and Chao Fan. "CCCTC-Binding Factor Mediates the Transcription of Insulin-Like Growth Factor Binding Protein 5 Through EZH2 in Ulcerative Colitis." Digestive Diseases and Sciences, June 15, 2022. http://dx.doi.org/10.1007/s10620-022-07566-w.

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Olbrich, Teresa, Maria Vega-Sendino, Desiree Tillo, et al. "CTCF is a barrier for 2C-like reprogramming." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-25072-x.

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AbstractTotipotent cells have the ability to generate embryonic and extra-embryonic tissues. Interestingly, a rare population of cells with totipotent-like potential, known as 2 cell (2C)-like cells, has been identified within ESC cultures. They arise from ESC and display similar features to those found in the 2C embryo. However, the molecular determinants of 2C-like conversion have not been completely elucidated. Here, we show that the CCCTC-binding factor (CTCF) is a barrier for 2C-like reprogramming. Indeed, forced conversion to a 2C-like state by the transcription factor DUX is associated

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Pugacheva, Elena. "Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions." August 1, 2015. https://doi.org/10.5281/zenodo.21405.

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CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in mutually exclusive manners in DNA binding and transcriptional regulation. In this study we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2

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Yi, Chongil, Yuka Kitamura, So Maezawa, Satoshi H. Namekawa, and Bradley R. Cairns. "ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network." Nature Structural & Molecular Biology, March 3, 2025. https://doi.org/10.1038/s41594-025-01509-5.

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Abstract Spermatogonial stem cells balance self-renewal with differentiation and spermatogenesis to ensure continuous sperm production. Here, we identify roles for the transcription factor zinc finger and BTB domain-containing protein 16 (ZBTB16; also known as promyelocytic leukemia zinc finger (PLZF)) in juvenile mouse undifferentiated spermatogonia (uSPG) in promoting self-renewal and cell-cycle progression to maintain uSPG and transit-amplifying states. Notably, ZBTB16, Spalt-like transcription factor 4 (SALL4) and SRY-box transcription factor 3 (SOX3) colocalize at over 12,000 promoters re

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Ma, Dong‐Bo, Hui Zhang, Xi‐Ling Wang, and Qiu‐Ge Wu. "METTL3 aggravates cell damage induced by Streptococcus pneumoniae via the NEAT1/CTCF/MUC19 axis." Kaohsiung Journal of Medical Sciences, May 16, 2024. http://dx.doi.org/10.1002/kjm2.12843.

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AbstractDisruption of the alveolar barrier can trigger acute lung injury. This study elucidated the association of methyltransferase‐like 3 (METTL3) with Streptococcus pneumoniae (SP)‐induced apoptosis and inflammatory injury of alveolar epithelial cells (AECs). AECs were cultured and then infected with SP. Furthermore, the expression of METTL3, interleukin (IL)‐10, IL‐6, tumor necrosis factor‐alpha (TNF‐α), monocyte chemoattractant protein‐1 (MCP‐1), long noncoding RNA nuclear paraspeckle assembly transcript 1 (NEAT1), mucin 19 (MUC19), N6‐methyladenosine (m6A), and NEAT1 after m6A modificati

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Rivero-Hinojosa, Samuel, Sungyun Kang, Victor V. Lobanenkov, and Gabriel E. Zentner. "Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells." Scientific Reports 7, no. 1 (2017). http://dx.doi.org/10.1038/srep41279.

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Abstract Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCF&BORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells. BORIS-bound regions (CTCF&BORIS and BORIS-onl

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Goodman, Michael Aaron, Paritha Arumugam, Devin Marie Pillis, et al. "Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential." Journal of Virology 92, no. 1 (2017). http://dx.doi.org/10.1128/jvi.01639-17.

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ABSTRACTStrong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in “enhancerless” self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that

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Cheng, Liang, Chenwei Yang, Junlin Lu, et al. "Oncogenic SLC2A11–MIF fusion protein interacts with polypyrimidine tract binding protein 1 to facilitate bladder cancer proliferation and metastasis by regulating mRNA stability." MedComm 5, no. 9 (2024). http://dx.doi.org/10.1002/mco2.685.

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AbstractChimeric RNAs, distinct from DNA gene fusions, have emerged as promising therapeutic targets with diverse functions in cancer treatment. However, the functional significance and therapeutic potential of most chimeric RNAs remain unclear. Here we identify a novel fusion transcript of solute carrier family 2‐member 11 (SLC2A11) and macrophage migration inhibitory factor (MIF). In this study, we investigated the upregulation of SLC2A11–MIF in The Cancer Genome Atlas cohort and a cohort of patients from Sun Yat‐Sen Memorial Hospital. Subsequently, functional investigations demonstrated tha

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Fang, Celestia, Zhenjia Wang, Cuijuan Han, et al. "Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation." Genome Biology 21, no. 1 (2020). http://dx.doi.org/10.1186/s13059-020-02152-7.

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Abstract Background The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, hitherto there is no comprehensive survey of genome-wide CTCF bin

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Janssen, Sanne Marlijn, Roy Moscona, Mounib Elchebly, et al. "BORIS/CTCFL promotes a switch from a proliferative towards an invasive phenotype in melanoma cells." Cell Death Discovery 6, no. 1 (2020). http://dx.doi.org/10.1038/s41420-019-0235-x.

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AbstractMelanoma is among the most aggressive cancers due to its tendency to metastasize early. Phenotype switching between a proliferative and an invasive state has been suggested as a critical process for metastasis, though the mechanisms that regulate state transitions are complex and remain poorly understood. Brother of Regulator of Imprinted Sites (BORIS), also known as CCCTC binding factor-Like (CTCFL), is a transcriptional modulator that becomes aberrantly expressed in melanoma. Yet, the role of BORIS in melanoma remains elusive. Here, we show that BORIS is involved in melanoma phenotyp

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Dong, Xiaotao, Rong Guo, Tianrong Ji, et al. "YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency." Nucleic Acids Research, April 15, 2022. http://dx.doi.org/10.1093/nar/gkac230.

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Abstract Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. Moreover, Yy1 depletion triggers a series of epigenetic crosstalk activities, including changes in DNA methylation, histone modifications and high-order chromatin structur

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Liao, Lihong, Xiuyun Zhou, Meihui Zhang та ін. "Epigenetic modification of IGF2/H19 imprinting control region regulates PGC-1α/PI3K/AKT2 pathway in a rat model of intrauterine growth restriction". Chinese Medical Journal, 5 листопада 2024. http://dx.doi.org/10.1097/cm9.0000000000003324.

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Abstract Background: Intrauterine growth restriction (IUGR) is associated with adverse metabolic outcomes during adulthood. Histone modifications and changes in DNA methylation-affected genes are important for fetal development. This study aimed to confirm the epigenetic mechanisms in IUGR. Methods: IUGR models were established in Sprague–Dawley rats using a maternal nutritional restriction approach during pregnancy. The abundance of insulin-like growth factor 2 (IGF2), phosphoinositide 3-kinase (PI3K), AKT serine/threonine kinase 2 (AKT2), and PPAR gamma coactivator 1 alpha (PGC-1α) was exami

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Yang, Jie, John R. Horton, Bin Liu, et al. "Structures of CTCF–DNA complexes including all 11 zinc fingers." Nucleic Acids Research, July 13, 2023. http://dx.doi.org/10.1093/nar/gkad594.

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Abstract The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12–15-bp CORE sequence, some of the CTCF binding sites contain 5′ upstream and/or 3′ downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1–ZF7 and ZF3–ZF11 in complex with DNA that incorporates the CORE sequence together with either 3′ downstream or 5′ upstream motifs. Like conventional tandem ZF array proteins, ZF1–ZF7 follow the ri

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Nishizawa-Jotaki, Shino, Kenichi Sakurai, Akifumi Eguchi, Hiromi Tanabe, Masahiro Watanabe, and Chisato Mori. "Association between mercury in cord serum and sex-specific DNA methylation in cord tissues." Journal of Developmental Origins of Health and Disease, April 3, 2020, 1–8. http://dx.doi.org/10.1017/s2040174420000161.

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Abstract Prenatal exposure to mercury in utero causes abnormal foetal growth and adverse outcomes. DNA methylation is currently considered a possible mechanism through which this occurs. However, few studies have investigated the association between prenatal exposure to mercury and DNA methylation in detail. This study aimed to clarify the relationship between prenatal exposure to total mercury (Hg) and DNA methylation and its associations with sex-specific characteristics in male and female offspring. In a birth cohort study known as the Chiba study of Mother and Child Health, the DNA methyla

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Dobrica, Mihaela Olivia, Christy Susan Varghese, James Michael Harris, et al. "CTCF regulates hepatitis B virus cccDNA chromatin topology." Journal of General Virology 105, no. 1 (2024). http://dx.doi.org/10.1099/jgv.0.001939.

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Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein, CCCTC-binding factor (CTCF), is a key regulator of cellular transcription by maintaining epigenetic boundaries, nucleosome phasing, stabilisation of long-range chromatin loops and directing alternative exon splicing. We previously reported that CTCF binds two conserved motifs within Enhancer I of the HBV genome and represses viral transcription, however, the underlying mechanisms were not identified.

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Sun, Jifeng, Hao Wang, Ran Zhang, et al. "IGF2BP3/CTCF Axis–Dependent NT5DC2 Promotes M2 Macrophage Polarization to Enhance the Malignant Progression of Lung Squamous Cell Carcinomas." Clinical Respiratory Journal 18, no. 11 (2024). http://dx.doi.org/10.1111/crj.70031.

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ABSTRACTBackgroundLung squamous cell carcinoma (LUSC) is a type of lung cancer that develops in the squamous cells. It is known to be promoted by the activation of various signaling pathways and the dysregulation of key regulatory molecules. One such molecule, 5′‐nucleotidase domain containing 2 (NT5DC2), has been identified as a critical regulator in various cancers including lung cancer. However, there are no data regarding its role in LUSC.MethodsThe mRNA expression of insulin‐like growth factor 2 mRNA–binding protein 3 (IGF2BP3), CCCTC‐binding factor (CTCF), and NT5DC2 was analyzed using q

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Shen, Tian, Tao Lei, Lin Chen, et al. "Gardenoside Hinders Caspase-1-Mediated Hepatocyte Pyroptosis Through the CTCF/DPP4 Signaling Pathway." Frontiers in Physiology 12 (September 8, 2021). http://dx.doi.org/10.3389/fphys.2021.669202.

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Non-alcoholic fatty liver disease (NAFLD)is accompanied by typical inflammatory damage and cell death. As a pro-inflammatory form of cell death, pyroptosis participates in important pathological processes involved in NAFLD. Regulatory roles of both CCCTC-binding factor (CTCF) and dipeptidyl peptidase-4 (DPP4) have been reported in NAFLD, but it is still unclear whether the mechanism of action of gardenoside, a potential therapeutic for NAFLD, can be driven via these proteins. In this study, the direct interaction between CTCF and DPP4 was first confirmed by a dual-luciferase reporter assay sys

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Elena Locci and Silvia Raymond. "Combinatorial Approaches with Checkpoint Inhibitors to Enhance Anti-Tumor Immunity as Advantages of Targeting the Tumor Immune Microenvironment over Blocking Immune Checkpoint in Cancer Immunotherapy." Instant Journal of Hematology and Oncology, October 13, 2021, 501–47. http://dx.doi.org/10.36811/ijho.2021.110021.

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Aging is a condition in which the cell cycle is essentially irreversible and is caused by a variety of stressors such as obesity, radiation and chemotherapy. Aging cells that accumulate in the body during this period communicate with surrounding tissues through the production of proinflammatory proteins, called the SASP, and play a number of physiological and pathological roles. In the elderly, inflammatory agents of SASP increase various age-related diseases, including cancer; therefore, clarification of the SASP monitoring mechanism is essential for the development of new prevention and trea

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Ghieh, F., A. L. Barbotin, N. Swierkowski-Blanchard, et al. "Whole-exome sequencing in patients with maturation arrest: a potential additional diagnostic tool for prevention of recurrent negative testicular sperm extraction outcomes." Human Reproduction, April 12, 2022. http://dx.doi.org/10.1093/humrep/deac057.

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Abstract STUDY QUESTION Could whole-exome sequencing (WES) be useful in clinical practice for men with maturation arrest (MA) after a first testicular sperm extraction (TESE)? SUMMARY ANSWER WES in combination with TESE yields substantial additional information and may potentially be added as a test to predict a negative outcome of a recurrent TESE in patients with MA. WHAT IS KNOWN ALREADY At present, the only definitive contraindications for TESE in men with non-obstructive azoospermia (NOA) are a 46,XX karyotype and microdeletions in the azoospermia factor a (AZFa) and/or AZFb regions. Afte

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Groves, Ian J., Stephen M. Matthews, and Christine M. O’Connor. "Host-encoded CTCF regulates human cytomegalovirus latency via chromatin looping." Proceedings of the National Academy of Sciences 121, no. 10 (2024). http://dx.doi.org/10.1073/pnas.2315860121.

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Human cytomegalovirus (HCMV) is a prevalent pathogen that establishes life-long latent infection in hematopoietic cells. While this infection is usually asymptomatic, immune dysregulation leads to viral reactivation, which can cause significant morbidity and mortality. However, the mechanisms underpinning reactivation remain incompletely understood. The HCMV major immediate early promoter (MIEP)/enhancer is a key factor in this process, as its transactivation from a repressed to active state helps drive viral gene transcription necessary for reactivation from latency. Numerous host transcripti

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Preston-Alp, Sarah, Lisa Beatrice Caruso, Chenhe Su, et al. "Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer." mBio, August 22, 2023. http://dx.doi.org/10.1128/mbio.00396-23.

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ABSTRACT Epstein-Barr virus (EBV) is associated with 10% of human gastric carcinomas, which are distinguished by a CpG island methylator phenotype. In gastric carcinoma tumors and cell lines, the EBV genome also exhibits a high degree of 5-methyl cytosine (5mC) marks, which are propagated by host DNA methyltransferases (DNMT) with each cell cycle. Therefore, we sought to determine the effect of DNMT inhibition by the small molecule Decitabine (DCB) on EBV genomic 5mC and chromatin structure in two tumor-derived gastric cancer cell lines, YCCEL1 and SNU719. Decitabine effects on EBV genomic 5mC

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Kaminski, Paul, Shiyuan Hong, Takeyuki Kono, Paul Hoover та Laimonis Laimins. "Topoisomerase 2β Induces DNA Breaks To Regulate Human Papillomavirus Replication". mBio 12, № 1 (2021). http://dx.doi.org/10.1128/mbio.00005-21.

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ABSTRACT Topoisomerases regulate higher-order chromatin structures through the transient breaking and religating of one or both strands of the phosphodiester backbone of duplex DNA. TOP2β is a type II topoisomerase that induces double-strand DNA breaks at topologically associated domains (TADS) to relieve torsional stress arising during transcription or replication. TADS are anchored by CCCTC-binding factor (CTCF) and SMC1 cohesin proteins in complexes with TOP2β. Upon DNA cleavage, a covalent intermediate DNA-TOP2β (TOP2βcc) is transiently generated to allow for strand passage. The tyrosyl-DN

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