Description
These tracks show the results of the ChIP-Seq analyses of architectural proteins (also known as insulators) from Kc167 cells. The regions that are enriched in the architectural proteins were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2.
The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:
| Accession | Insulators | Reference |
|---|
| GSE32584 | BEAF-32, Cp190, CTCF | Yang J et al., Nat Commun. 2013 |
| GSE39521 | Myc | Yang J et al., Nat Commun. 2013 |
| GSE39664 | Dref | Gurudatta BV et al., Cell Cycle. 2013 |
| GSE62904 | Cap-H2, CBP, Chro, fs(1)h, l(3)mbt, pzg, TfIIIC, vtd | Li L et al., Mol Cell. 2015 |
| GSE80700 | GAF, Ibf1, Ibf2, Nup98, pita, ZIPIC | Cubeñas-Potts C et al., Nucleic Acids Res. 2017 |
References
Yang J, Sung E, Donlin-Asp PG, Corces VG. A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins. Nat Commun. 2013;4:1464.
Gurudatta BV, Yang J, Van Bortle K, Donlin-Asp PG, Corces VG. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle. Cell Cycle. 2013 May 15;12(10):1605-15.
Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Ong CT, Cubeñas-Potts C, Hu M, Lei EP, Bosco G, Qin ZS, Corces VG. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell. 2015 Apr 16;58(2):216-31.
Cubeñas-Potts C, Rowley MJ, Lyu X, Li G, Lei EP, Corces VG. Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res. 2017 Feb 28;45(4):1714-1730.
Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.