ZFIN

ZFIN ID: ZDB-GENE-040624-5

ZFIN ID: ZDB-GENE-040624-5

CITATIONS (41 total)

Gene Name:	CCCTC-binding factor (zinc finger protein)
Gene Symbol:	ctcf

Franke, M., De la Calle-Mustienes, E., Neto, A., Almuedo-Castillo, M., Irastorza-Azcarate, I., Acemel, R.D., Tena, J.J., Santos-Pereira, J.M., Gómez-Skarmeta, J.L. (2021) CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression. Nature communications. 12:5415

Pérez-Rico, Y.A., Barillot, E., Shkumatava, A. (2020) Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish. iScience. 23:101046

Carmona-Aldana, F., Zampedri, C., Suaste-Olmos, F., Murillo-de-Ozores, A., Guerrero, G., Arzate-Mejía, R., Maldonado, E., Navarro, R., Chimal-Monroy, J., Recillas-Targa, F. (2018) CTCF knockout reveals an essential role for this protein during the zebrafish development. Mechanisms of Development. 154:51-59

Meier, M., Grant, J., Dowdle, A., Thomas, A., Gerton, J., Collas, P., O'Sullivan, J.M., Horsfield, J.A. (2017) Cohesin facilitates zygotic genome activation in zebrafish. Development (Cambridge, England). 145(1)

Aanes, H., Winata, C., Moen, L.F., Østrup, O., Mathavan, S., Collas, P., Rognes, T., and Aleström, P. (2014) Normalization of RNA-sequencing data from samples with varying mRNA levels. PLoS One. 9(2):e89158

Marsman, J., O'Neill, A.C., Kao, B.R., Rhodes, J.M., Meier, M., Antony, J., Mönnich, M., and Horsfield, J.A. (2014) Cohesin and CTCF differentially regulate spatiotemporal runx1 expression during zebrafish development. Biochimica et biophysica acta. Gene regulatory mechanisms. 1839(1):50-61

Huang, H.T., Kathrein, K.L., Barton, A., Gitlin, Z., Huang, Y.H., Ward, T.P., Hofmann, O., Dibiase, A., Song, A., Tyekucheva, S., Hide, W., Zhou, Y., and Zon, L.I. (2013) A network of epigenetic regulators guides developmental haematopoiesis in vivo. Nature cell biology. 15(12):1516-1525

Lee, M.T., Bonneau, A.R., Takacs, C.M., Bazzini, A.A., Divito, K.R., Fleming, E.S., and Giraldez, A.J. (2013) Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature. 503(7476):360-4

Delgado-Olguin, P., Brand-Arzamendi, K., Scott, I.C., Jungblut, B., Stainier, D.Y., Bruneau, B.G., and Recillas-Targa, F. (2011) CTCF Promotes Muscle Differentiation by Modulating the Activity of Myogenic Regulatory Factors. The Journal of biological chemistry. 286(14):12483-94

Sander, J.D., Dahlborg, E.J., Goodwin, M.J., Cade, L., Zhang, F., Cifuentes, D., Curtin, S.J., Blackburn, J.S., Thibodeau-Beganny, S., Qi, Y., Pierick, C.J., Hoffman, E., Maeder, M.L., Khayter, C., Reyon, D., Dobbs, D., Langenau, D.M., Stupar, R.M., Giraldez, A.J., Voytas, D.F., Peterson, R.T., Yeh, J.R., Joung, J.K. (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nature Methods. 8:67-9

Tena, J.J., Alonso, M.E., de la Calle-Mustienes, E., Splinter, E., de Laat, W., Manzanares, M., and Gómez-Skarmeta, J.L. (2011) An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nature communications. 2:310

Rhodes, J.M., Bentley, F.K., Print, C.G., Dorsett, D., Misulovin, Z., Dickinson, E.J., Crosier, K.E., Crosier, P.S., and Horsfield, J.A. (2010) Positive regulation of c-Myc by cohesin is direct, and evolutionarily conserved. Developmental Biology. 344(2):637-649

Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. Journal of experimental zoology. Part B, Molecular and developmental evolution. 308(5):655-668

Pugacheva, E.M., Kwon, Y.W., Hukriede, N.A., Pack, S., Flanagan, P.T., Ahn, J.C., Park, J.A., Choi, K.S., Kim, K.W., Loukinov, D., Dawid, I.B., and Lobanenkov, V.V. (2006) Cloning and characterization of zebrafish CTCF: Developmental expression patterns, regulation of the promoter region, and evolutionary aspects of gene organization. Gene. 375:26-36

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

Additional Citations (26):

ZFIN Staff (2024) Association of Ensembl transcripts with ZFIN genes. Semi-automated Curation.

ZFIN Staff (2023) Automated Curation of UniProt Database Links. Automated Data Submission.

ZFIN Staff (2020) Addition of links from ZFIN to Expression Atlas. Semi-automated Curation.

ZFIN Staff (2019) Analysis of data directly submitted to the Zebrafish International Resource Center (ZIRC). ZFIN Direct Data Submission.

ZFIN Staff (2017) Curation of PANTHER Gene IDs. Automated Data Submission.

ZFIN Staff (2017) Curation of Alliance of Genome Resources Database Links. Automated Data Submission.

ZFIN Staff (2015) Data Model Change: Sequence Targeting Reagents Removed from Environment. ZFIN Historical Data.

Busch-Nentwich, E., Kettleborough, R., Dooley, C. M., Scahill, C., Sealy, I., White, R., Herd, C., Mehroke, S., Wali, N., Carruthers, S., Hall, A., Collins, J., Gibbons, R., Pusztai, Z., Clark, R., and Stemple, D.L. (2013) Sanger Institute Zebrafish Mutation Project mutant data submission. ZFIN Direct Data Submission.

ZFIN Staff (2013) Semi-automated association of ENSDARG identifiers with ZFIN genes for the ZMP project. Semi-automated Curation.

Gaudet, P., Livstone, M., Thomas, P., The Reference Genome Project (2010) Annotation inferences using phylogenetic trees. Automated Data Submission.

ZIRC and ZFIN Staff (2008) Mutant and Transgenic Line Submissions 2008. ZFIN Direct Data Submission.

Ensembl curators, GOA curators (2006) Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara. Manually curated data.

Phenotype Annotation (1994-2006) (2006) Mutant Data Curated from Older Literature. ZFIN Historical Data.

ZFIN Staff (2006) Curation of Ensembl Database Links. Automated Data Submission.

Amsterdam, A., Nissen, R.M., Sun, Z., Swindell, E., Farrington, S., and Hopkins, N. (2005) Submission and curation of data from an insertional mutagenesis screen. ZFIN Direct Data Submission.

Thisse, B., Thisse, C. (2004) Fast Release Clones: A High Throughput Expression Analysis. ZFIN Direct Data Submission.

ZFIN Staff (2004) ZGC Data Curation and Association in ZFIN by ZFIN Staff. Semi-automated Curation.

Zebrafish Nomenclature Committee (2003) Nomenclature Data Curation (2003-2010). Nomenclature Committee Submission.

ZFIN Staff (2003) Submission and Curation of Mutant and Transgenic Lines. ZFIN Direct Data Submission.

ZFIN Staff (2003) Curation of VEGA Database Links. Automated Data Submission.

ZFIN Staff (2003) Curation of orthology data. Manually curated data.

ZFIN Staff (2003) Curation of unpublished nucleotide sequence accession numbers. Manually curated data.

ZFIN Staff (2002) Gene Ontology Annotation Through Association of UniProt Keywords with GO Terms. Automated Data Submission.

ZFIN Staff (2002) Curation of NCBI Gene Data Via Shared RNA Sequence IDs. Automated Data Submission.

ZFIN Staff (2002) Scientific Curation. Manually curated data.

ZFIN Staff (2002) Curation of EMBL records. Automated Data Submission.