[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 …

The bivalent genome: characterization, structure, and regulation

E Blanco, M González-Ramírez, A Alcaine-Colet… - Trends in Genetics, 2020 - cell.com
An intricate molecular machinery is at the core of gene expression regulation in every cell.
During the initial stages of organismal development, the coordinated activation of diverse …

Efficient low-cost chromatin profiling with CUT&Tag

HS Kaya-Okur, DH Janssens, JG Henikoff, K Ahmad… - Nature protocols, 2020 - nature.com
Abstract We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

CA Meyer, XS Liu - Nature Reviews Genetics, 2014 - nature.com
Next-generation sequencing (NGS) technologies have been used in diverse ways to
investigate various aspects of chromatin biology by identifying genomic loci that are bound …

Regulatory activity is the default DNA state in eukaryotes

I Luthra, C Jensen, XE Chen, AL Salaudeen… - Nature Structural & …, 2024 - nature.com
Genomes encode for genes and non-coding DNA, both capable of transcriptional activity.
However, unlike canonical genes, many transcripts from non-coding DNA have limited …

[HTML][HTML] Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8+ T cell differentiation

BE Russ, M Olshanksy, HS Smallwood, J Li, AE Denton… - Immunity, 2014 - cell.com
The molecular mechanisms that regulate the rapid transcriptional changes that occur during
cytotoxic T lymphocyte (CTL) proliferation and differentiation in response to infection are …

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 …

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

J Feichtinger, I Hernández, C Fischer… - Biotechnology and …, 2016 - Wiley Online Library
The most striking characteristic of CHO cells is their adaptability, which enables efficient
production of proteins as well as growth under a variety of culture conditions, but also results …

[HTML][HTML] Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

V Chaitankar, G Karakülah, R Ratnapriya… - Progress in retinal and …, 2016 - Elsevier
The advent of high throughput next generation sequencing (NGS) has accelerated the pace
of discovery of disease-associated genetic variants and genomewide profiling of expressed …

[HTML][HTML] Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering

Y You, A Sawikowska, M Neumann, D Pose… - Nature …, 2017 - nature.com
Plants can produce organs throughout their entire life from pluripotent stem cells located at
their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of …