[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 …
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
Absence of a simple code: how transcription factors read the genome
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 …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Impact of cytosine methylation on DNA binding specificities of human transcription factors
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 …
sequence consisting of four nucleotide bases. One of the bases, cytosine, is commonly …
The N6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and Hypertrophy
Background: N 6-Methyladenosine (m6A) methylation is the most prevalent internal
posttranscriptional modification on mammalian mRNA. The role of m6A mRNA methylation …
posttranscriptional modification on mammalian mRNA. The role of m6A mRNA methylation …
Genome-wide quantitative enhancer activity maps identified by STARR-seq
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 …
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 …
DNA sequencing (ChIP-seq) is a prevailing methodology used to investigate chromatin …
YAP1 exerts its transcriptional control via TEAD-mediated activation of enhancers
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 …
YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is …
Evolutionary changes in promoter and enhancer activity during human corticogenesis
Human higher cognition is attributed to the evolutionary expansion and elaboration of the
human cerebral cortex. However, the genetic mechanisms contributing to these …
human cerebral cortex. However, the genetic mechanisms contributing to these …
Practical guidelines for the comprehensive analysis of ChIP-seq data
Mapping the chromosomal locations of transcription factors, nucleosomes, histone
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
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
Background Development of eukaryotic organisms is controlled by transcription factors that
trigger specific and global changes in gene expression programs. In plants, MADS-domain …
trigger specific and global changes in gene expression programs. In plants, MADS-domain …