Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation

R Nakato, K Shirahige - Briefings in bioinformatics, 2017 - academic.oup.com
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect
protein/DNA-binding and histone-modification sites across an entire genome. Recent …

The ensembl regulatory build

DR Zerbino, SP Wilder, N Johnson, T Juettemann… - Genome biology, 2015 - Springer
Most genomic variants associated with phenotypic traits or disease do not fall within gene
coding regions, but in regulatory regions, rendering their interpretation difficult. We collected …

[HTML][HTML] H3K4me3 breadth is linked to cell identity and transcriptional consistency

BA Benayoun, EA Pollina, D Ucar, S Mahmoudi… - Cell, 2014 - cell.com
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to
mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that …

The role of fatty acid β-oxidation in lymphangiogenesis

BW Wong, X Wang, A Zecchin, B Thienpont… - Nature, 2017 - nature.com
Lymphatic vessels are lined by lymphatic endothelial cells (LECs), and are critical for health.
However, the role of metabolism in lymphatic development has not yet been elucidated …

CTCF-mediated functional chromatin interactome in pluripotent cells

L Handoko, H Xu, G Li, CY Ngan, E Chew… - Nature …, 2011 - nature.com
Mammalian genomes are viewed as functional organizations that orchestrate spatial and
temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been …

diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates

L Shen, NY Shao, X Liu, I Maze, J Feng, EJ Nestler - PloS one, 2013 - journals.plos.org
ChIP-seq is increasingly being used for genome-wide profiling of histone modification
marks. It is of particular importance to compare ChIP-seq data of two different conditions …

Telomerase directly regulates NF-κB-dependent transcription

A Ghosh, G Saginc, SC Leow, E Khattar, EM Shin… - Nature cell …, 2012 - nature.com
Although elongation of telomeres is thought to be the prime function of reactivated
telomerase in cancers, this activity alone does not account for all of the properties that …

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

VC Seitan, AJ Faure, Y Zhan, RP McCord… - Genome …, 2013 - genome.cshlp.org
Chromosome conformation capture approaches have shown that interphase chromatin is
partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological …

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 …

Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant

S Denissov, H Hofemeister, H Marks, A Kranz… - …, 2014 - journals.biologists.com
Trimethylation of histone H3 lysine 4 (H3K4me3) at the promoters of actively transcribed
genes is a universal epigenetic mark and a key product of Trithorax group action. Here, we …