CTCF/cohesin-binding sites are frequently mutated in cancer

Nature Genetics

Volumn 47, Issue 7, 2015, Pages 818-821

  Katainen, Riku ^a   Dave, Kashyap ^b   Pitkänen, Esa ^a   Palin, Kimmo ^a   Kivioja, Teemu ^a   Välimäki, Niko ^a   Gylfe, Alexandra E ^a   Ristolainen, Heikki ^a   Hänninen, Ulrika A ^a   Cajuso, Tatiana ^a   Kondelin, Johanna ^a   Tanskanen, Tomas ^a   Mecklin, Jukka Pekka ^c   Järvinen, Heikki ^d   Renkonen Sinisalo, Laura ^a,d   Lepistö, Anna ^d   Kaasinen, Eevi ^a   Kilpivaara, Outi ^a   Tuupanen, Sari ^a   Enge, Martin ^b   Taipale, Jussi ^a,b   Aaltonen, Lauri A ^a   more..

^a UNIVERSITY OF HELSINKI   (Finland)

^b KAROLINSKA INSTITUTE   (Sweden)

^c UNIVERSITY OF EASTERN FINLAND   (Finland)

^d HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; DNA; DNA POLYMERASE; EXONUCLEASE; TRANSCRIPTION FACTOR CTCF; CCCTC-BINDING FACTOR; CELL CYCLE PROTEIN; NONHISTONE PROTEIN; REPRESSOR PROTEIN;

ARTICLE; BINDING SITE; CANCER GENETICS; CHROMATIN IMMUNOPRECIPITATION; COLORECTAL CANCER; DNA FLANKING REGION; DNA REPLICATION; DNA REPLICATION TIMING; ENHANCER REGION; GENE MUTATION; GENOME; GENOMIC INSTABILITY; HOMEOSTASIS; MULTIPLE CANCER; MUTATION RATE; POINT MUTATION; PRIORITY JOURNAL; SOMATIC MUTATION; COLORECTAL TUMOR; CONSENSUS SEQUENCE; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; HUMAN; PHYSIOLOGY; REGULATORY SEQUENCE;

BINDING SITES; CELL CYCLE PROTEINS; CHROMOSOMAL PROTEINS, NON-HISTONE; COLORECTAL NEOPLASMS; CONSENSUS SEQUENCE; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; POINT MUTATION; REGULATORY SEQUENCES, NUCLEIC ACID; REPRESSOR PROTEINS;

EID: 84933278077     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3335     Document Type: Article

References (29)

1. Kagey, M.H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430-435 (2010).
2. Yan, J. et al. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 154, 801-813 (2013).
3. Parelho, V. et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422-433 (2008).
4. Rubio, E.D. et al. CTCF physically links cohesin to chromatin. Proc. Natl. Acad. Sci. USA 105, 8309-8314 (2008).
5. Wendt, K.S. et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796-801 (2008).
6. Rao, S.S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014).
7. Kon, A. et al. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat. Genet. 45, 1232-1237 (2013).
8. Leiserson, M.D. et al. Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat. Genet. 47, 106-114 (2015).
9. Huang, F.W. et al. Highly recurrent TERT promoter mutations in human melanoma. Science 339, 957-959 (2013).
10. Mansour, M.R. et al. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science 346, 1373-1377 (2014).
11. Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
12. Chen, C.L. et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res. 20, 447-457 (2010).
13. Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
14. Hoffman, M.M. et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 41, 827-841 (2013).
15. Hudson, T.J. et al. International network of cancer genome projects. Nature 464, 993-998 (2010).
16. Guillou, E. et al. Cohesin organizes chromatin loops at DNA replication factories. Genes Dev. 24, 2812-2822 (2010).
17. Helleday, T., Eshtad, S. & Nik-Zainal, S. Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet. 15, 585-598 (2014).
18. Dulak, A.M. et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat. Genet. 45, 478-486 (2013).
19. Satou, K., Kawai, K., Kasai, H., Harashima, H. & Kamiya, H. Mutagenic effects of 8-hydroxy-dGTP in live mammalian cells. Free Radic. Biol. Med. 42, 1552-1560 (2007).
20. Narendra, V. et al. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science 347, 1017-1021 (2015).
21. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
22. DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
23. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213-219 (2013).
24. Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Campbell, P.J. & Stratton, M.R. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246-259 (2013).
25. Rhee, H.S. & Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419 (2011).
26. Guo, Y. et al. Discovering homotypic binding events at high spatial resolution. Bioinformatics 26, 3028 (2010).
27. Jolma, A. et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20, 861-873 (2010).
28. Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013).
29. Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).