Formaldehyde crosslinking: a tool for the study of chromatin complexes

EA Hoffman, BL Frey, LM Smith, DT Auble - Journal of Biological Chemistry, 2015 - ASBMB
Formaldehyde has been used for decades to probe macromolecular structure and function
and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is …

Using single‐cell genomics to understand developmental processes and cell fate decisions

JA Griffiths, A Scialdone, JC Marioni - Molecular systems biology, 2018 - embopress.org
High‐throughput‐omics techniques have revolutionised biology, allowing for thorough and
unbiased characterisation of the molecular states of biological systems. However, cellular …

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

CD Richardson, GJ Ray, MA DeWitt, GL Curie… - Nature …, 2016 - nature.com
Targeted genomic manipulation by Cas9 can efficiently generate knockout cells and
organisms via error-prone nonhomologous end joining (NHEJ), but the efficiency of precise …

[HTML][HTML] Protein group modification and synergy in the SUMO pathway as exemplified in DNA repair

I Psakhye, S Jentsch - Cell, 2012 - cell.com
Protein modification by SUMO affects a wide range of protein substrates. Surprisingly,
although SUMO pathway mutants display strong phenotypes, the function of individual …

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

L Teytelman, DM Thurtle, J Rine… - Proceedings of the …, 2013 - National Acad Sciences
Chromatin immunoprecipitation (ChIP) is the gold-standard technique for localizing nuclear
proteins in the genome. We used ChIP, in combination with deep sequencing (Seq), to study …

[HTML][HTML] Acetylation is indispensable for p53 activation

Y Tang, W Zhao, Y Chen, Y Zhao, W Gu - Cell, 2008 - cell.com
The activation of the tumor suppressor p53 facilitates the cellular response to genotoxic
stress; however, the p53 response can only be executed if its interaction with its inhibitor …

Uniform transitions of the general RNA polymerase II transcription complex

A Mayer, M Lidschreiber, M Siebert, K Leike… - Nature structural & …, 2010 - nature.com
We present genome-wide occupancy profiles for RNA polymerase (Pol) II, its
phosphorylated forms and transcription factors in proliferating yeast. Pol II exchanges …

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

R Blecher-Gonen, Z Barnett-Itzhaki, D Jaitin… - Nature protocols, 2013 - nature.com
Dynamic protein binding to DNA elements regulates genome function and cell fate. Although
methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect …

Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation

AA Joshi, K Struhl - Molecular cell, 2005 - cell.com
Eaf3, a component of the NuA4 histone acetylase and Rpd3 histone deacetylase
complexes, is important for the global pattern of histone acetylation in Saccharomyces …

Epigenetic instability due to defective replication of structured DNA

P Sarkies, C Reams, LJ Simpson, JE Sale - Molecular cell, 2010 - cell.com
The accurate propagation of histone marks during chromosomal replication is proposed to
rely on the tight coupling of replication with the recycling of parental histones to the daughter …