CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

被引：8

作者：

Dozmorov, Mikhail G. ^{[1
,2
]}

Mu, Wancen ^{[3
]}

Davis, Eric S. ^{[4
]}

Lee, Stuart ^{[5
,6
]}

Triche, Timothy J. ^{[7
,8
,9
]}

Phanstiel, Douglas H. ^{[4
,10
,11
,12
,13
]}

Love, Michael, I ^{[3
,14
]}

机构：

[1] Virginia Commonwealth Univ, Dept Biostat, Richmond, VA 23298 USA

[2] Virginia Commonwealth Univ, Dept Pathol, Richmond, VA 23284 USA

[3] Univ North Carolina Chapel Hill, Dept Biostat, Chapel Hill, NC 27514 USA

[4] Univ North Carolina Chapel Hill, Curriculum Bioinformat & Computat Biol, Chapel Hill, NC 27599 USA

[5] Monash Univ, Dept Econometr & Business Stat, Clayton, Vic 3168, Australia

[6] Walter & Eliza Hall Inst Med Res, Mol Med Div, Parkville, Vic 3052, Australia

[7] Van Andel Res Inst, Ctr Epigenet, Grand Rapids, MI 49503 USA

[8] Michigan State Univ, Coll Human Med, Dept Pediat, E Lansing, MI 90033 USA

[9] Univ Southern Calif, Keck Sch Med, Dept Translat Genom, Los Angeles, CA 90033 USA

[10] Univ North Carolina Chapel Hill, Thurston Arthrit Res Ctr, Chapel Hill, NC 27599 USA

[11] Univ North Carolina Chapel Hill, Dept Cell Biol & Physiol, Chapel Hill, NC 27599 USA

[12] Univ North Carolina Chapel Hill, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA

[13] Univ North Carolina Chapel Hill, Curriculum Genet & Mol Biol, Chapel Hill, NC 27599 USA

[14] Univ North Carolina Chapel Hill, Dept Genet, Chapel Hill, NC 27514 USA

来源：

BIOINFORMATICS ADVANCES | 2022年 / 2卷 / 01期

关键词：

HUMAN GENOME; TRANSCRIPTION; ORGANIZATION; VERSATILE; SEQUENCE; MAP;

D O I：

10.1093/bioadv/vbac097

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome's 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. We recommend filtering strategies for CTCF binding motifs and demonstrate that liftOver is a viable alternative to convert CTCF coordinates between assemblies. Our comprehensive data resource and usage recommendations can serve to harmonize and strengthen the reproducibility of genomic studies utilizing CTCF binding data.

引用

页数：3

共 25 条

[1] MEME SUITE: tools for motif discovery and searching [J].

Bailey, Timothy L. ;

Boden, Mikael ;

Buske, Fabian A. ;

Frith, Martin ;

Grant, Charles E. ;

Clementi, Luca ;

Ren, Jingyuan ;

Li, Wilfred W. ;

Noble, William S. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W202-W208

[2] CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators [J].

Bao, Lei ;

Zhou, Mi ;

Cui, Yan .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D83-D87

[3] JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles [J].

Castro-Mondragon, Jaime A. ;

Riudavets-Puig, Rafael ;

Rauluseviciute, Ieva ;

Lemma, Roza Berhanu ;

Turchi, Laura ;

Blanc-Mathieu, Romain ;

Lucas, Jeremy ;

Boddie, Paul ;

Khan, Aziz ;

Perez, Nicolas Manosalva ;

Fornes, Oriol ;

Leung, Tiffany Y. ;

Aguirre, Alejandro ;

Hammal, Fayrouz ;

Schmelter, Daniel ;

Baranasic, Damir ;

Ballester, Benoit ;

Sandelin, Albin ;

Lenhard, Boris ;

Vandepoele, Klaas ;

Wasserman, Wyeth W. ;

Parcy, Francois ;

Mathelier, Anthony .

NUCLEIC ACIDS RESEARCH, 2022, 50 (D1) :D165-D173

[4] Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome [J].

Chen, Hebing ;

Tian, Yao ;

Shu, Wenjie ;

Bo, Xiaochen ;

Wang, Shengqi .

PLOS ONE, 2012, 7 (07)

[5] Epigenetic priors for identifying active transcription factor binding sites [J].

Cuellar-Partida, Gabriel ;

Buske, Fabian A. ;

McLeay, Robert C. ;

Whitington, Tom ;

Noble, William Stafford ;

Bailey, Timothy L. .

BIOINFORMATICS, 2012, 28 (01) :56-62

[6] CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features [J].

Essien, Kobby ;

Vigneau, Sebastien ;

Apreleva, Sofia ;

Singh, Larry N. ;

Bartolomei, Marisa S. ;

Hannenhalli, Sridhar .

GENOME BIOLOGY, 2009, 10 (11)

[7] Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA [J].

Hashimoto, Hideharu ;

Wang, Dongxue ;

Horton, John R. ;

Zhang, Xing ;

Corces, Victor G. ;

Cheng, Xiaodong .

MOLECULAR CELL, 2017, 66 (05) :711-+

[8] DNA-Binding Specificities of Human Transcription Factors [J].

Jolma, Arttu ;

Yan, Jian ;

Whitington, Thomas ;

Toivonen, Jarkko ;

Nitta, Kazuhiro R. ;

Rastas, Pasi ;

Morgunova, Ekaterina ;

Enge, Martin ;

Taipale, Mikko ;

Wei, Gonghong ;

Palin, Kimmo ;

Vaquerizas, Juan M. ;

Vincentelli, Renaud ;

Luscombe, Nicholas M. ;

Hughes, Timothy R. ;

Lemaire, Patrick ;

Ukkonen, Esko ;

Kivioja, Teemu ;

Taipale, Jussi .

CELL, 2013, 152 (1-2) :327-339

[9] Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome [J].

Kim, Tae Hoon ;

Abdullaev, Ziedulla K. ;

Smith, Andrew D. ;

Ching, Keith A. ;

Loukinov, Dmitri I. ;

Green, Roland D. ;

Zhang, Michael Q. ;

Lobanenkov, Victor V. ;

Ren, Bing .

CELL, 2007, 128 (06) :1231-1245

[10] HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis [J].

Kulakovskiy, Ivan V. ;

Vorontsov, Ilya E. ;

Yevshin, Ivan S. ;

Sharipov, Ruslan N. ;

Fedorova, Alla D. ;

Rumynskiy, Eugene I. ;

Medvedeva, Yulia A. ;

Magana-Mora, Arturo ;

Bajic, Vladimir B. ;

Papatsenko, Dmitry A. ;

Kolpakov, Fedor A. ;

Makeev, Vsevolod J. .

NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) :D252-D259

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