Regulation, functions and transmission of bivalent chromatin during mammalian development

TA Macrae, J Fothergill-Robinson… - … reviews Molecular cell …, 2023 - nature.com
Cells differentiate and progress through development guided by a dynamic chromatin
landscape that mediates gene expression programmes. During development, mammalian …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

M Yao, S Zhang, Q Lu, X Chen, SY Zhang… - Molecular …, 2022 - Wiley Online Library
Vast global declines of freshwater and marine fish diversity and population abundance pose
serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA …

Improved CUT&RUN chromatin profiling tools

MP Meers, TD Bryson, JG Henikoff, S Henikoff - elife, 2019 - elifesciences.org
Previously, we described a novel alternative to chromatin immunoprecipitation, CUT&RUN,
in which unfixed permeabilized cells are incubated with antibody, followed by binding of a …

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

PJ Skene, JG Henikoff, S Henikoff - Nature protocols, 2018 - nature.com
Cleavage under targets and release using nuclease (CUT&RUN) is an epigenomic profiling
strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases …

An efficient targeted nuclease strategy for high-resolution map** of DNA binding sites

PJ Skene, S Henikoff - elife, 2017 - elifesciences.org
We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a
chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal …

Epigenetics and aging

S Pal, JK Tyler - Science advances, 2016 - science.org
Over the past decade, a growing number of studies have revealed that progressive changes
to epigenetic information accompany aging in both dividing and nondividing cells …

[HTML][HTML] Transcriptome-wide measurement of translation by ribosome profiling

NJ McGlincy, NT Ingolia - Methods, 2017 - Elsevier
Translation is one of the fundamental processes of life. It comprises the assembly of
polypeptides whose amino acid sequence corresponds to the codon sequence of an …

Nuclear mechanosensing drives chromatin remodelling in persistently activated fibroblasts

CJ Walker, C Crocini, D Ramirez, AR Killaars… - Nature biomedical …, 2021 - nature.com
Fibrotic disease is caused by the continuous deposition of extracellular matrix by persistently
activated fibroblasts (also known as myofibroblasts), even after the resolution of the injury …

Polyploidy, the nucleotype, and novelty: the impact of genome doubling on the biology of the cell

JJ Doyle, JE Coate - International journal of plant sciences, 2019 - journals.uchicago.edu
Polyploidy is a key mechanism of genome evolution and speciation, particularly in plants.
Many aspects of polyploidy have been elucidated with the tools that have become available …