Prendergast, Laura Reinberg, Danny
Published in
Genes & development
Major advances in the chromatin and epigenetics fields have uncovered the importance of core histones, histone variants and their post-translational modifications (PTMs) in modulating chromatin structure. However, an acutely understudied related feature of chromatin structure is the role of linker histone H1. Previous assumptions of the functional ...
Panda, Amitesh Zylicz, Jan J Pasque, Vincent
Published in
Cells
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromati...
Liu, Xingyu Zhang, Ying Wen, Zhihui Hao, Yan Banks, Charles A S Lange, Jeffrey J Slaughter, Brian D Unruh, Jay R Florens, Laurence Abmayr, Susan M
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Published in
Proceedings of the National Academy of Sciences of the United States of America
Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunct...
Ding, Tao Zhu, Liyuan Fang, Yuxin Liu, Yangluorong Tang, Wei Zou, Peng
Published in
Angewandte Chemie (International ed. in English)
The spatial arrangement of chromosome within the nucleus is linked to genome function and gene expression regulation. Existing genome-wide mapping methods often rely on chemically crosslinking DNA with protein baits, which raises concerns of artifacts being introduced during cell fixation. By genetically targeting a photosensitizer protein to speci...
Lezmi, Elyad Weissbein, Uri Golan-Lev, Tamar Nissim-Rafinia, Malka Meshorer, Eran Benvenisty, Nissim
Published in
Stem cell reports
Chromatin regulators play fundamental roles in controlling pluripotency and differentiation. We examined the effect of mutations in 703 genes from nearly 70 chromatin-modifying complexes on human embryonic stem cell (ESC) growth. While the vast majority of chromatin-associated complexes are essential for ESC growth, the only complexes that conferre...
Stevens, Kathryn M Swadling, Jacob B Hocher, Antoine Bang, Corinna Gribaldo, Simonetta Schmitz, Ruth A Warnecke, Tobias
Published in
Proceedings of the National Academy of Sciences of the United States of America
Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome r...
Barish, Scott Barakat, Tahsin Stefan Michel, Brittany C Mashtalir, Nazar Phillips, Jennifer B Valencia, Alfredo M Ugur, Berrak Wegner, Jeremy Scott, Tiana M Bostwick, Brett
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Published in
American journal of human genetics
SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identif...
Sönmezer, Can Kleinendorst, Rozemarijn Imanci, Dilek Barzaghi, Guido Villacorta, Laura Schübeler, Dirk Benes, Vladimir Molina, Nacho Krebs, Arnaud Regis
Published in
Molecular cell
Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements (CREs). Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we present a DNA footprinting method that detects individual molecular int...
Reimer, Kirsten A Neugebauer, Karla M
Published in
Current protocols in molecular biology
Long read sequencing technologies now allow high-quality sequencing of RNAs (or their cDNAs) that are hundreds to thousands of nucleotides long. Long read sequences of nascent RNA provide single-nucleotide-resolution information about co-transcriptional RNA processing events-e.g., splicing, folding, and base modifications. Here, we describe how to ...
Espejo, Isabel Di Croce, Luciano Aranda, Sergi
Published in
BioEssays : news and reviews in molecular, cellular and developmental biology
Chromatin-bound proteins underlie several fundamental cellular functions, such as control of gene expression and the faithful transmission of genetic and epigenetic information. Components of the chromatin proteome (the "chromatome") are essential in human life, and mutations in chromatin-bound proteins are frequently drivers of human diseases, suc...