[HTML][HTML] Methods for ChIP-seq analysis: A practical workflow and advanced applications

R Nakato, T Sakata - Methods, 2021 - Elsevier
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …

Absence of a simple code: how transcription factors read the genome

M Slattery, T Zhou, L Yang, ACD Machado… - Trends in biochemical …, 2014 - cell.com
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Y Yin, E Morgunova, A Jolma, E Kaasinen, B Sahu… - Science, 2017 - science.org
INTRODUCTION Nearly all cells in the human body share the same primary genome
sequence consisting of four nucleotide bases. One of the bases, cytosine, is commonly …

The N6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and Hypertrophy

LE Dorn, L Lasman, J Chen, X Xu, TJ Hund… - Circulation, 2019 - Am Heart Assoc
Background: N 6-Methyladenosine (m6A) methylation is the most prevalent internal
posttranscriptional modification on mammalian mRNA. The role of m6A mRNA methylation …

Genome-wide quantitative enhancer activity maps identified by STARR-seq

CD Arnold, D Gerlach, C Stelzer, ŁM Boryń, M Rath… - Science, 2013 - science.org
Genomic enhancers are important regulators of gene expression, but their identification is a
challenge, and methods depend on indirect measures of activity. We developed a method …

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 …

YAP1 exerts its transcriptional control via TEAD-mediated activation of enhancers

C Stein, AF Bardet, G Roma, S Bergling, I Clay… - PLoS …, 2015 - journals.plos.org
YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated
YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is …

Evolutionary changes in promoter and enhancer activity during human corticogenesis

SK Reilly, J Yin, AE Ayoub, D Emera, J Leng, J Cotney… - Science, 2015 - science.org
Human higher cognition is attributed to the evolutionary expansion and elaboration of the
human cerebral cortex. However, the genetic mechanisms contributing to these …

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 …

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

A Pajoro, P Madrigal, JM Muiño, JT Matus, J Jin… - Genome biology, 2014 - Springer
Background Development of eukaryotic organisms is controlled by transcription factors that
trigger specific and global changes in gene expression programs. In plants, MADS-domain …