keyword
MENU ▼
Read by QxMD icon Read
search

CTCF

keyword
https://www.readbyqxmd.com/read/28938112/non-coding-transcription-instructs-chromatin-folding-and-compartmentalization-to-dictate-enhancer-promoter-communication-and-t-cell-fate
#1
Takeshi Isoda, Amanda J Moore, Zhaoren He, Vivek Chandra, Masatoshi Aida, Matthew Denholtz, Jan Piet van Hamburg, Kathleen M Fisch, Aaron N Chang, Shawn P Fahl, David L Wiest, Cornelis Murre
It is now established that Bcl11b specifies T cell fate. Here, we show that in developing T cells, the Bcl11b enhancer repositioned from the lamina to the nuclear interior. Our search for factors that relocalized the Bcl11b enhancer identified a non-coding RNA named ThymoD (thymocyte differentiation factor). ThymoD-deficient mice displayed a block at the onset of T cell development and developed lymphoid malignancies. We found that ThymoD transcription promoted demethylation at CTCF bound sites and activated cohesin-dependent looping to reposition the Bcl11b enhancer from the lamina to the nuclear interior and to juxtapose the Bcl11b enhancer and promoter into a single-loop domain...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28938092/ctcf-mediated-enhancer-promoter-interaction-is-a-critical-regulator-of-cell-to-cell-variation-of-gene-expression
#2
Gang Ren, Wenfei Jin, Kairong Cui, Joseph Rodrigez, Gangqing Hu, Zhiying Zhang, Daniel R Larson, Keji Zhao
Recent studies indicate that even a homogeneous population of cells display heterogeneity in gene expression and response to environmental stimuli. Although promoter structure critically influences the cell-to-cell variation of gene expression in bacteria and lower eukaryotes, it remains unclear what controls the gene expression noise in mammals. Here we report that CTCF decreases cell-to-cell variation of expression by stabilizing enhancer-promoter interaction. We show that CTCF binding sites are interwoven with enhancers within topologically associated domains (TADs) and a positive correlation is found between CTCF binding and the activity of the associated enhancers...
September 21, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28931413/topological-organization-and-dynamic-regulation-of-human-trna-genes-during-macrophage-differentiation
#3
Kevin Van Bortle, Douglas H Phanstiel, Michael P Snyder
BACKGROUND: The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing...
September 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28928744/ccctc-binding-factor-locks-premature-igh-germline-transcription-and-restrains-class-switch-recombination
#4
Ester Marina-Zárate, Arantxa Pérez-García, Almudena R Ramiro
In response to antigenic stimulation B cells undergo class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) to replace the primary IgM/IgD isotypes by IgG, IgE, or IgA. CSR is initiated by activation-induced cytidine deaminase (AID) through the deamination of cytosine residues at the switch (S) regions of IgH. B cell stimulation promotes germline transcription (GLT) of specific S regions, a necessary event prior to CSR because it facilitates AID access to S regions. Here, we show that CCCTC-binding factor (CTCF)-deficient mice are severely impaired in the generation of germinal center B cells and plasma cells after immunization in vivo, most likely due to impaired cell survival...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28898712/inhibition-of-the-lytic-cycle-of-kaposi-s-sarcoma-associated-herpesvirus-by-cohesin-factors-following-de-novo-infection
#5
Zsolt Toth, Richard J Smindak, Bernadett Papp
Establishment of Kaposi's sarcoma-associated herpesvirus (KSHV) latency following infection is a multistep process, during which polycomb proteins are recruited onto the KSHV genome, which is crucial for the genome-wide repression of lytic genes during latency. Strikingly, only a subset of lytic genes are expressed transiently in the early phase of infection prior to the binding of polycomb proteins onto the KSHV genome, which raises the question what restricts lytic gene expression in the first hours of infection...
September 9, 2017: Virology
https://www.readbyqxmd.com/read/28886334/new-insights-into-genome-structure-genes-of-a-feather-stick-together
#6
Denes Hnisz, Richard A Young
DNA structuring proteins such as CTCF facilitate DNA loop formation and are presumed to be among the major determinants of eukaryotic genome structure. Recent studies, including Rowley et al. (2017), suggest that gene activation and repression play fundamentally important roles in structuring the genome independently of CTCF.
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28865451/genome-wide-computational-analysis-of-potential-long-noncoding-rna-mediated-dna-dna-rna-triplexes-in-the-human-genome
#7
Saakshi Jalali, Amrita Singh, Souvik Maiti, Vinod Scaria
BACKGROUND: Only a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there have been detailed investigations on lncRNA-miRNA and lncRNA-protein interactions, the interaction of lncRNAs with DNA have not been studied extensively. In the present study, we explore whether lncRNAs could modulate genomic regulation by interacting with DNA through the formation of highly stable DNA:DNA:RNA triplexes...
September 2, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28863138/5c-analysis-of-the-epidermal-differentiation-complex-locus-reveals-distinct-chromatin-interaction-networks-between-gene-rich-and-gene-poor-tads-in-skin-epithelial-cells
#8
Krzysztof Poterlowicz, Joanne L Yarker, Igor Malashchuk, Brian R Lajoie, Andrei N Mardaryev, Michal R Gdula, Andrey A Sharov, Terumi Kohwi-Shigematsu, Vladimir A Botchkarev, Michael Y Fessing
Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28862757/ctcf-foxm1-axis-regulates-tumor-growth-and-metastasis-in-hepatocellular-carcinoma
#9
Bin Zhang, Yajing Zhang, Xiaoping Zou, Anthony W H Chan, Rui Zhang, Terence Kin-Wah Lee, Hang Liu, Eunice Yuen-Ting Lau, Nicole Pui-Yu Ho, Paul B S Lai, Yue-Sun Cheung, Ka-Fai To, Hoi Kin Wong, Kwong Wai Choy, Vincent W Keng, Larry M C Chow, Kenrick K Y Chan, Alfred S Cheng, Ben C B Ko
CCCTC-binding factor (CTCF) is a DNA-binding protein that interacts with a large number of highly divergent target sequences throughout the genome. It is implicated in a variety of functions, including chromatin organization and transcriptional control. The functional role of CTCF in tumor pathogenesis remains elusive. We showed that CTCF is frequently upregulated in a subset of primary hepatocellular carcinoma (HCC) compared with non-tumoral liver. Overexpression of CTCF was associated with shorter disease-free survival of patients...
September 1, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28857086/ccctc-binding-factor-is-essential-to-the-maintenance-and-quiescence-of-hematopoietic-stem-cells-in-mice
#10
Tae-Gyun Kim, Sueun Kim, Soyeon Jung, Mikyoung Kim, Bobae Yang, Min-Geol Lee, Hyoung-Pyo Kim
Hematopoiesis involves a series of lineage differentiation programs initiated in hematopoietic stem cells (HSCs) found in bone marrow (BM). To ensure lifelong hematopoiesis, various molecular mechanisms are needed to maintain the HSC pool. CCCTC-binding factor (CTCF) is a DNA-binding, zinc-finger protein that regulates the expression of its target gene by organizing higher order chromatin structures. Currently, the role of CTCF in controlling HSC homeostasis is unknown. Using a tamoxifen-inducible CTCF conditional knockout mouse system, we aimed to determine whether CTCF regulates the homeostatic maintenance of HSCs...
August 25, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28855971/the-effect-of-nipped-b-like-nipbl-haploinsufficiency-on-genome-wide-cohesin-binding-and-target-gene-expression-modeling-cornelia-de-lange-syndrome
#11
Daniel A Newkirk, Yen-Yun Chen, Richard Chien, Weihua Zeng, Jacob Biesinger, Ebony Flowers, Shimako Kawauchi, Rosaysela Santos, Anne L Calof, Arthur D Lander, Xiaohui Xie, Kyoko Yokomori
BACKGROUND: Cornelia de Lange syndrome (CdLS) is a multisystem developmental disorder frequently associated with heterozygous loss-of-function mutations of Nipped-B-like (NIPBL), the human homolog of Drosophila Nipped-B. NIPBL loads cohesin onto chromatin. Cohesin mediates sister chromatid cohesion important for mitosis but is also increasingly recognized as a regulator of gene expression. In CdLS patient cells and animal models, expression changes of multiple genes with little or no sister chromatid cohesion defect suggests that disruption of gene regulation underlies this disorder...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28846746/ctcf-counter-regulates-cardiomyocyte-development-and-maturation-programs-in-the-embryonic-heart
#12
Melisa Gomez-Velazquez, Claudio Badia-Careaga, Ana Victoria Lechuga-Vieco, Rocio Nieto-Arellano, Juan J Tena, Isabel Rollan, Alba Alvarez, Carlos Torroja, Eva F Caceres, Anna R Roy, Niels Galjart, Paul Delgado-Olguin, Fatima Sanchez-Cabo, Jose Antonio Enriquez, Jose Luis Gomez-Skarmeta, Miguel Manzanares
Cardiac progenitors are specified early in development and progressively differentiate and mature into fully functional cardiomyocytes. This process is controlled by an extensively studied transcriptional program. However, the regulatory events coordinating the progression of such program from development to maturation are largely unknown. Here, we show that the genome organizer CTCF is essential for cardiogenesis and that it mediates genomic interactions to coordinate cardiomyocyte differentiation and maturation in the developing heart...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28826674/evolutionarily-conserved-principles-predict-3d-chromatin-organization
#13
M Jordan Rowley, Michael H Nichols, Xiaowen Lyu, Masami Ando-Kuri, I Sarahi M Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G Corces
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C...
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28822906/the-impact-of-htlv-1-on-the-cellular-genome
#14
REVIEW
Lucy Cook, Anat Melamed, Hiroko Yaguchi, Charles Rm Bangham
Human T-lymphotropic virus type-1 (HTLV-1) is the causative agent of adult T-cell leukaemia/lymphoma (ATL), an aggressive CD4+ T-cell malignancy. The mechanisms of leukaemogenesis in ATL are incompletely understood. Insertional mutagenesis has not previously been thought to contribute to the pathogenesis of ATL. However, the recent discovery that HTLV-1 binds the key chromatin architectural protein CTCF raises the hypothesis that HTLV-1 deregulates host gene expression by causing abnormal chromatin looping, bringing the strong HTLV-1 promoter-enhancer near to host genes that lie up to 2Mb from the integrated provirus...
August 17, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28819414/depletion-of-ctcf-in-breast-cancer-cells-selectively-induces-cancer-cell-death-via-p53
#15
Ji-Yeon Lee, Muhammad Mustafa, Clara Yuri Kim, Myoung Hee Kim
CCCTC-binding factor (CTCF), a ubiquitous 11-zinc finger multifunctional protein, has distinct molecular functions, such as transcriptional activation, repression, and chromatin barrier activity, in a locus-specific manner. Elevated CTCF levels in breast cancer cells are known to contribute to tumorigenesis; however, the underlying mechanism remains elusive. We investigated the effect of CTCF expression on breast cancer cell survival and elucidated its mechanism. CTCF depletion in MCF-7 cells led to a decreased cell growth and proliferation, surpassing the growth of normal cells under co-culture system of MCF-7-GFP and MCF10A...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28813658/ccctc-binding-factor-translates-interleukin-2-and-%C3%AE-ketoglutarate-sensitive-metabolic-changes-in-t%C3%A2-cells-into-context-dependent-gene-programs
#16
Danielle A Chisolm, Daniel Savic, Amanda J Moore, Andre Ballesteros-Tato, Beatriz León, David K Crossman, Cornelis Murre, Richard M Myers, Amy S Weinmann
Despite considerable research connecting cellular metabolism with differentiation decisions, the underlying mechanisms that translate metabolite-sensitive activities into unique gene programs are still unclear. We found that aspects of the interleukin-2 (IL-2)-sensitive effector gene program in CD4(+) and CD8(+) T cells in type 1 conditions (Th1) were regulated by glutamine and alpha-ketoglutarate (αKG)-induced events, in part through changes in DNA and histone methylation states. We further identified a mechanism by which IL-2- and αKG-sensitive metabolic changes regulated the association of CCCTC-binding factor (CTCF) with select genomic sites...
August 15, 2017: Immunity
https://www.readbyqxmd.com/read/28811569/transcriptional-response-to-stress-is-pre-wired-by-promoter-and-enhancer-architecture
#17
Anniina Vihervaara, Dig Bijay Mahat, Michael J Guertin, Tinyi Chu, Charles G Danko, John T Lis, Lea Sistonen
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene's response to stress is determined...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28803781/myc-regulates-chromatin-decompaction-and-nuclear-architecture-during-b-cell-activation
#18
Kyong-Rim Kieffer-Kwon, Keisuke Nimura, Suhas S P Rao, Jianliang Xu, Seolkyoung Jung, Aleksandra Pekowska, Marei Dose, Evan Stevens, Ewy Mathe, Peng Dong, Su-Chen Huang, Maria Aurelia Ricci, Laura Baranello, Ying Zheng, Francesco Tomassoni Ardori, Wolfgang Resch, Diana Stavreva, Steevenson Nelson, Michael McAndrew, Adriel Casellas, Elizabeth Finn, Charles Gregory, Brian Glenn St Hilaire, Steven M Johnson, Wendy Dubois, Maria Pia Cosma, Eric Batchelor, David Levens, Robert D Phair, Tom Misteli, Lino Tessarollo, Gordon Hager, Melike Lakadamyali, Zhe Liu, Monique Floer, Hari Shroff, Erez Lieberman Aiden, Rafael Casellas
50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input...
August 17, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#19
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28796949/mecp2-and-ctcf-enhancing-the-cross-talk-of-silencers
#20
Juan Ausio, Philippe T Georgel
This paper provides a brief introductory review of the most recent advances in our knowledge about structural and functional aspects of two transcriptional regulators: the methyl-CpG protein binding 2 (MeCP2), a protein whose mutated forms are involved in Rett syndrome and CCCTC-binding factor (CTCF), a constitutive transcriptional insulator. This is followed by a description of the post-translational modifications (PTMs) affecting these two proteins and an analysis of their known interacting partners. A special emphasis is placed on the recent studies connecting these two proteins focusing on the still poorly understood potential structural and functional interactions between the two of them on the chromatin substrate...
August 10, 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
keyword
keyword
21995
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"