ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters

ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters

Response: Mapping Nucleosome Positions Using ChIP-Seq Data

+300 and +480, respectively. RNA POL II sits right on the TSS. In the upstream region, we observe no periodic signal indicative of regular nucleosome positioning (phasing) across promoters. The closest nucleosomes are located around position −180 leaving a minimal nucleosome-free promoter region of 150 bp. As the respective peaks of the H3K4me3 and H2A.Z signals coincide, it seems likely that t...

Design of synthetic yeast promoters via tuning of nucleosome architecture

Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate that nucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novo design of synthetic promoters. Initially, we use our approac...

Computational analysis of ChIP-seq data.

Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics of ChIP-seq data and introduces a computat...

CistromeFinder for ChIP-seq and DNase-seq data reuse

SUMMARY Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing have greatly accelerated the understanding of transcriptional and epigenetic regulation, although data reuse for the community of experimental biologists has been challenging. We created a data portal CistromeFinder that can help query, evaluate and visualize publicly available Chromatin im...