Nucleosomes are fundamental units of chromatin compaction, which organize ∼200 DNA base pairs using an octamer of histone proteins. Their ubiquitous presence in the cell nucleus since the first eukaryotes compelled the chromatin machinery to coevolve and learn how to exploit various modes of nucleosome dynamics and sense differences in nucleosome composition. Alterations to histone or DNA sequences, post-translational modifications (PTM) of histones, recruitment of chromatin proteins modulate nucleosome dyn amics and provide epigenetic regulation to the DNA processing pathways (transcription, replication, repair, etc.). Our understanding of this complex interplay between nucleosome composition, dynamics and functioning is constantly evolving through new insights and discoveries. In this review, we highlight recent contributions to the field while attempting to organize them in a unified framework.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1016/j.sbi.2018.11.006 | DOI Listing |
Nature
January 2025
Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
View Article and Find Full Text PDFMethods Mol Biol
November 2024
Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ, USA.
Identification of the occupancy of transcription factors (TFs) and nucleosomes across the genome yields insights into the regulation of gene expression patterns. While several independent techniques can be performed and then analyzed in composite to reveal this chromatin landscape, the use of micrococcal nuclease (MNase) digestion can resolve the footprints of nearly all chromatin proteins simultaneously. The protocol below describes the use of MNase to identify chromatin footprints of both TFs and nucleosomes in two vastly different cell types, Mouse embryonic stem cells (mESCs) and sperm, with differing levels of chromatin compaction.
View Article and Find Full Text PDFMethods Mol Biol
November 2024
Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
Eukaryotic DNA is organized in the nucleus in the form of chromatin. Nucleosomes, the fundamental unit of chromatin, are subject to many posttranslational modifications (PTMs) as well as compositional variations through incorporation of histone variants. These alterations play important roles in regulation of genome structure and activity.
View Article and Find Full Text PDFLife Sci Alliance
December 2024
NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya, Japan.
Wild soybean is the progenitor of cultivated soybean Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes.
View Article and Find Full Text PDFJ Biol Chem
September 2024
Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA. Electronic address:
Sirtuin 2 (Sirt2) is a member of the sirtuin family of NAD-dependent lysine deacylases and plays important roles in regulation of the cell cycle and gene expression. As a nucleocytoplasmic deacetylase, Sirt2 has been shown to target both histone and nonhistone acetylated protein substrates. The central catalytic domain of Sirt2 is flanked by flexible N and C termini, which vary in length and composition with alternative splicing.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!