These tracks show the results of the ChIP-Seq analyses of transcription factors that are associated with the core promoter. The peak calls and the log likelihood ratio evidence tracks were produced by MACS.
The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:
|GSE46630||M1BP||Li J and Gilmour DS, EMBO J. 2013|
|GSE40646||GAF, GAF-KD||Fuda NJ et al., PLoS Genet. 2015|
|GSE38594||GAF (Embryos)||Oh H et al., Cell Rep. 2013|
|GSE50374||GAF (Embryos; modENCODE)||modENCODE|
|GSE52029||TBP, TRF2||Wang YL et al., Genes Dev. 2014|
Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT.
GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet. 2015 Mar 27;11(3):e1005108.
Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD.
Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes.
Cell Rep. 2013 Feb 21;3(2):309-18.
Landt SG, et al.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Genome Res. 2012 Sep;22(9):1813-31.
Li J, Gilmour DS.
Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J. 2013 Jul 3;32(13):1829-41.
Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT.
TRF2, but not TBP, mediates the transcription of ribosomal protein genes.
Genes Dev. 2014 Jul 15;28(14):1550-5.
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.