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CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

Jesse D. Ziebarth, Anindya Bhattacharya, Yan Cui
2012 Nucleic Acids Research  
DATABASE CONTENT Sources of CTCF-binding sites We expanded the CTCFBSDB using data from a variety of sources containing CTCF-binding sites determined using genome-wide experimental methods, and CTCFBSDB  ...  Figure 1 . 1 Screenshot of an example webpage for a CTCF-binding sequence (ENCODE_OC_hg18_MCF-7_744758) in CTCFBSDB 2.0.  ... 
doi:10.1093/nar/gks1165 pmid:23193294 pmcid:PMC3531215 fatcat:shjkjekgxbemzdhlhr4s6ilpzu

CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators

L. Bao, M. Zhou, Y. Cui
2007 Nucleic Acids Research  
We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties.  ...  CTCF-binding sites were found to be commonly distributed along the vertebrate genomes.  ...  Lander for providing the predicted CTCF motifs and Dr Keji Zhao for providing the genomic coordinates of 20 262 CTCF-binding sites.  ... 
doi:10.1093/nar/gkm875 pmid:17981843 pmcid:PMC2238977 fatcat:hkwuws73qjc6dek6nzsodiuesq

TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide [article]

Kyster K. Nanan, David M. Sturgill, Maria F. Prigge, Morgan Thenoz, Allissa A. Dillman, Mariana D. Mandler, Shalini Oberdoerffer
2018 bioRxiv   pre-print
Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ∼13,000 new CTCF sites.  ...  The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength.  ...  Genome Biol 9, R137. Ziebarth, J.D.,Bhattacharya, A., and Cui, Y. (2013). CTCFBSDB 2.0: a database for CTCFbinding sites and genome organization. Nucleic Acids Res 41, D188-194.  ... 
doi:10.1101/480525 fatcat:migehw6eyfguldhohog5f6vyfa

Positive regulation of c-Myc by cohesin is direct, and evolutionarily conserved

Jenny M. Rhodes, Fiona K. Bentley, Cristin G. Print, Dale Dorsett, Ziva Misulovin, Emma J. Dickinson, Kathryn E. Crosier, Philip S. Crosier, Julia A. Horsfield
2010 Developmental Biology  
In zebrafish, cohesin binds to the transcription start sites of p53 and mdm2, and depletion of either Rad21 or CTCF increased their transcription.  ...  Cohesin bound the transcription start site plus an upstream predicted CTCF binding site at zebrafish myca.  ...  advice on ChIP and Mike Eccles for helpful discussions.  ... 
doi:10.1016/j.ydbio.2010.05.493 pmid:20553708 pmcid:PMC2941799 fatcat:rahduisgxfayljdncv66tamcma

A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

Julie Dubois-Chevalier, Frédérik Oger, Hélène Dehondt, François F. Firmin, Céline Gheeraert, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute
2014 Nucleic Acids Research  
Here, we show that, in addition to constitutively bound CTCF binding sites (CTS), the CTCF cistrome comprises a large proportion of sites showing highly dynamic binding patterns during the course of adipogenesis  ...  Our study reveals a dynamic CTCF chromatin binding landscape required for epigenomic remodeling of enhancers and transcriptional activation driving cell differentiation.  ...  We also acknowledge the CNRS U8199 genomics platform for the processing of hMeDIP-seq samples. B.S. is a member of the Institut Universitaire de France.  ... 
doi:10.1093/nar/gku780 pmid:25183525 pmcid:PMC4176165 fatcat:c6w242ndpnaprcsjzld73k3lfm

Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene

Zhongjing Su, Guangyu Liu, Bin Zhang, Ze Lin, Dongyang Huang
2021 Genes  
Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45.  ...  PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA.  ...  Acknowledgments: We thank Liyan Xu from Shantou University for her scientific and technical support and Xiaojun Xie from Shantou University for his critical reading of the manuscript.  ... 
doi:10.3390/genes12050759 pmid:34067766 pmcid:PMC8156488 fatcat:epl3ypaxzjhyjbkt3sir7ogjt4

Genomic Space of MGMT in Human Glioma Revisited: Novel Motifs, Regulatory RNAs, NRF1, 2, and CTCF Involvement in Gene Expression

Mohammed A Ibrahim Al-Obaide, Viswanath Arutla, Manny D Bacolod, Wei Wang, Ruiwen Zhang, Kalkunte S Srivenugopal
2021 International Journal of Molecular Sciences  
ChIP analysis verified the binding site in MGMT promoter for CTCF which regulates the genomic methylation and chromatin looping.  ...  Extensive genome database analyses showed that the MGMT genomic space was rich in and harbored many undescribed RNA regulatory sequences and recognition motifs.  ...  Acknowledgments: We thank Ibtisam Ismael Al-Obaidi and laboratory personnel for technical assistance. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22052492 pmid:33801310 pmcid:PMC7958331 fatcat:2df5kixhvbebtmb6blc6qqojj4

Functional signatures of evolutionarily young CTCF binding sites

Dhoyazan Azazi, Jonathan M. Mudge, Duncan T. Odom, Paul Flicek
2020 BMC Biology  
Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome  ...  Conclusions Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.  ...  Acknowledgements We thank Maša Roller for the support and for a critical reading of the manuscript and suggestions for its improvement.  ... 
doi:10.1186/s12915-020-00863-8 pmid:32988407 pmcid:PMC7520972 fatcat:5m5sy772d5dkpcg2x74zj2o7be

Identification and characterization of two functional variants in the human longevity gene FOXO3

Friederike Flachsbart, Janina Dose, Liljana Gentschew, Claudia Geismann, Amke Caliebe, Carolin Knecht, Marianne Nygaard, Nandini Badarinarayan, Abdou ElSharawy, Sandra May, Anne Luzius, Guillermo G. Torres (+22 others)
2017 Nature Communications  
In summary, we present experimental evidence for a functional link between common intronic variants in FOXO3 and human longevity.  ...  FOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown.  ...  The biobank PopGen and the PopGen 2.0 network are also financed by the BMBF (grant 01EY1103).  ... 
doi:10.1038/s41467-017-02183-y pmid:29234056 pmcid:PMC5727304 fatcat:xdqocw7xdbfxnmyrhqmqsk6dm4

CTCF Recruits Centromeric Protein CENP-E to the Pericentromeric/Centromeric Regions of Chromosomes through Unusual CTCF-Binding Sites

Tiaojiang Xiao, Patompon Wongtrakoongate, Cecelia Trainor, Gary Felsenfeld
2015 Cell Reports  
We identified CTCF sites in pericentric/centromeric DNA and found that, early in mitosis, CTCF binds and recruits CENP-E to these sites.  ...  Unlike most known CTCF genomic sites, the CTCF-binding sites in the pericentric/centromeric regions interact strongly with the C-terminal fingers of CTCF.  ...  Gaelle Lefevre and Dr. Gregory Riddick as well as other members of our laboratory for their help. We also thank Dr. Don W. Cleveland for the CENP-E plasmid.  ... 
doi:10.1016/j.celrep.2015.08.005 pmid:26321640 pmcid:PMC4633288 fatcat:gozmssrblnc6dn6suh2hmmalxa

The CCCTC-binding factor (CTCF)-forkhead box protein M1 axis regulates tumour growth and metastasis in hepatocellular carcinoma

Bin Zhang, Yajing Zhang, Xiaoping Zou, Anthony WH Chan, Rui Zhang, Terence Kin-Wah Lee, Hang Liu, Eunice Yuen-Ting Lau, Nicole Pui-Yu Ho, Paul BS Lai, Yue-Sun Cheung, Ka-Fai To (+7 others)
2017 Journal of Pathology  
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 tumour pathogenesis remains elusive.  ...  histological diagnosis; RZ, TKWL, EYTL, NPYH, XZ, VK, LMCC, ASC: contributed to animal studies; KWC, HKW: helped with microarray analysis; BCBK: responsible for the design and analysis of the experiments  ... 
doi:10.1002/path.4976 pmid:28862757 pmcid:PMC5725705 fatcat:f5aeer2gkzev7munnbmaxr3oty

Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer

Mahfuza Sharmin, Héctor Corrada Bravo, Sridhar Hannenhalli
2016 BMC Cancer  
These regions are generally enriched for CpG islands, Lamin Associated Domains and Large organized chromatin lysine modification domains, and are associated with stochastic variability in gene expression  ...  Result: We found that the classical promoter epigenomic mark -H3K4me3, is highly enriched at HMB boundaries, as are CTCF bound sites. HMB boundaries harbor distinct combinations of TF motifs.  ...  Acknowledgements Authors would like to thank Joyce Hasio, and Rukhsana Yeasmin for reading the manuscript and providing helpful comments.  ... 
doi:10.1186/s12885-016-2128-1 pmid:26868017 pmcid:PMC4750190 fatcat:enbzth57wnajfemupnezlplkwa

Integrative genomic analysis of human ribosomal DNA

Gabriel E. Zentner, Alina Saiakhova, Pavel Manaenkov, Mark D. Adams, Peter C. Scacheri
2011 Nucleic Acids Research  
Fourth, UBF, a positive regulator of rRNA transcription, binds to sites throughout the genome.  ...  Lastly, the insulator binding protein CTCF associates with the spacer promoter of rDNA, suggesting that transcriptional insulation plays a role in regulating the transcription of rRNA.  ...  We also thank Batool Akhtar-Zaidi, Greg Crawford, Terry Furey, and Iris Gonzalez for helpful discussions during the course of this project and Stephanie Doerner for helpful comments on the manuscript.  ... 
doi:10.1093/nar/gkq1326 pmid:21355038 pmcid:PMC3130253 fatcat:k6cnohcmpffxnmwfqtpq2p7bym

Deletion of the CTRL2 Insulator in HSV-1 Results in the Decreased Expression of Genes Involved in Axonal Transport and Attenuates Reactivation In Vivo

Pankaj Singh, Matthew F. Collins, Richard N. Johns, Kayley A. Manuel, Ziyun A. Ye, David C. Bloom, Donna M. Neumann
2022 Viruses  
Importantly, during reactivation, CTCF protein is evicted from the HSV-1 genome, especially from the CTRL2 insulator.  ...  CTCF insulators flank the LAT and IE regions of HSV-1 and during latency and maintain the integrity of transcriptional domains through a myriad of functions, including enhancer-blocking or barrier-insulator  ...  (A) The CTCFBDBS 2.0 program was used to identify the CTUS1B site as a putative CTCF-binding site.  ... 
doi:10.3390/v14050909 pmid:35632655 pmcid:PMC9144644 fatcat:vqt75baef5drvl25y2bebaobya

Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer [article]

Mahfuza Sharmin, Hector Corrada Bravo, Sridhar S. Hannenhalli
2015 biorxiv/medrxiv   pre-print
We analyzed a number of distinguishing features at the HMB boundaries including transcription factor (TF) binding motifs, various epigenomic marks, and chromatin structural features. Result.  ...  We found that the classical promoter epigenomic mark, H3K4me3, is highly enriched at HMB boundaries, as are CTCF bound sites. HMB boundaries harbor distinct combinations of TF motifs.  ...  Acknowledgements Authors would like to thank Joyce Hasio, and Rukhsana Yeasmin for reading the manuscript and providing helpful comments.  ... 
doi:10.1101/028803 fatcat:fi56i7k3kjcsrldvrfavq2elq4
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