Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions.

ABSTRACT:

Background

Characterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of genomic location (ChIP-seq) data, one can approach that question through the identification of characteristic patterns of transcription factor occupancy and histone modifications.

Results

Based on the ENCODE annotation and integration of sequence motifs as well as three-dimensional chromatin data, we have undertaken a re-analysis of occupancy and sequence patterns in human promoters. We identify clear groups of CAAT-box and E-box sequence motif containing promoters, as well as a group of promoters whose interaction with an enhancer appears to be mediated by C

SUBMITTER: Yang X 

PROVIDER: S-EPMC6238301 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature