Description

This track shows TAF1 binding in fibroblastoid (IMR90) cells as assayed by ChIP-chip using a NimbleGen microarray. The companion LI TAF Sites track shows binding sites derived from these experiments.

TAF1, a protein found at the start of transcribed genes, is a general transcription factor that is a key part of the pre-initiation complex found on the promoter. It is more fully known as TBP-associated factor 1 of the TFIID complex or by its molecular weight as TAF250.

To survey the entire human genome in an unbiased fashion, a total of 38 high-density oligonucleotide arrays (NimbleGen platform) were fabricated, representing approximately 1.45 billion base pairs of non-repetitive DNA with 50-mer oligonucleotides positioned at every 100 base pairs throughout the human genome (UCSC hg16). Using this array, genome-wide location analysis of TAF1 was conducted employing ChIP-chip using chromatin extracted from primary fibroblast IMR90 cells.

Methods

Chromatin from IMR90 cells lines was cross-linked, precipitated with TAF1 antibody (sc-735, Santa Cruz), sheared, amplified and hybridized to 38 high-density oligonucleotide arrays (NimbleGen). These arrays contain a total of 14,535,659 50-mer oligonucleotides positioned at every 100 base pairs through the human genome (UCSC hg16). track.

The raw data are available from GEO GSE2672.

The raw data are available from GEO GSE2672.

Verification

The peaks from genome scan experiments were verified using condensed arrays, as described in the Methods section. The verification data may be viewed in the LI TAF1 Valid track.

References

Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. A high-resolution map of active promoters in the human genome. Nature. 2005 Aug 11;436:876-80.