A high-resolution protein architecture of the budding yeast genome

MJ Rossi, PK Kuntala, WKM Lai, N Yamada, N Badjatia… - Nature, 2021 - nature.com
The genome-wide architecture of chromatin-associated proteins that maintains chromosome
integrity and gene regulation is not well defined. Here we use chromatin …

[HTML][HTML] Quantitative ChIP-Seq normalization reveals global modulation of the epigenome

DA Orlando, MW Chen, VE Brown, S Solanki, YJ Choi… - Cell reports, 2014 - cell.com
Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel
DNA sequencing (ChIP-seq) is a prevailing methodology used to investigate chromatin …

An interactive environment for agile analysis and visualization of ChIP-sequencing data

M Lerdrup, JV Johansen, S Agrawal-Singh… - Nature structural & …, 2016 - nature.com
To empower experimentalists with a means for fast and comprehensive chromatin
immunoprecipitation sequencing (ChIP-seq) data analyses, we introduce an integrated …

[HTML][HTML] Practical guidelines for the comprehensive analysis of ChIP-seq data

T Bailey, P Krajewski, I Ladunga… - PLoS computational …, 2013 - journals.plos.org
Mapping the chromosomal locations of transcription factors, nucleosomes, histone
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …

Recombination initiation maps of individual human genomes

F Pratto, K Brick, P Khil, F Smagulova, GV Petukhova… - Science, 2014 - science.org
Introduction The dramatic events of meiotic recombination culminate in the exchange of
genetic information between parental chromosomes and ensure the production of …

[HTML][HTML] Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

KS Myers, H Yan, IM Ong, D Chung, K Liang… - PLoS …, 2013 - journals.plos.org
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across
bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors …

Reprogramming of the histone H3. 3 landscape in the early mouse embryo

T Ishiuchi, S Abe, K Inoue, WKA Yeung, Y Miki… - Nature structural & …, 2021 - nature.com
Epigenetic reprogramming of the zygote involves dynamic incorporation of histone variant
H3. 3. However, the genome-wide distribution and dynamics of H3. 3 during early …

Defining bacterial regulons using ChIP-seq

KS Myers, DM Park, NA Beauchene, PJ Kiley - Methods, 2015 - Elsevier
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a
powerful method that identifies protein–DNA binding sites in vivo. Recent studies have …

A comprehensive comparison of tools for differential ChIP-seq analysis

S Steinhauser, N Kurzawa, R Eils… - Briefings in …, 2016 - academic.oup.com
ChIP-seq has become a widely adopted genomic assay in recent years to determine binding
sites for transcription factors or enrichments for specific histone modifications. Beside …

The PfAP2‐G2 transcription factor is a critical regulator of gametocyte maturation

S Singh, JM Santos, LM Orchard… - Molecular …, 2021 - Wiley Online Library
Differentiation from asexual blood stages to mature sexual gametocytes is required for the
transmission of malaria parasites. Here, we report that the ApiAP2 transcription factor, PfAP2 …