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Polycomb group (PcG) proteins function within Polycomb repressive complexes (PRCs), which modify histones and other proteins and silence target genes. This Review highlights new insights into the role of PcG proteins in gene regulation, specifically in controlling self-renewal and differentiation of embryonic stem cells, and into how PRCs are targeted to chromatin.
Nucleosome-remodeling factors are instrumental in assembling and disassembling nucleosomes and moving nucleosomes along DNA in a process called nucleosome sliding. This Review summarizes recent progress in understanding of the basic nucleosome sliding mechanism and the interplay of the ATPase and accessory domains in optimizing and regulating nucleosome sliding.
To ensure replication success, DNA polymerases must negotiate encounters with actively transcribing RNA polymerases that share the genome. This Review highlights the strategies used by prokaryotic and eukaryotic cells to minimize the consequences of collisions between replication forks and transcription complexes to effect faithful DNA replication without compromising gene expression.
Global erasure and re-establishment of chromatin-based and DNA-based epigenetic marks occurs naturally in the mammalian life cycle, but it can also be artificially engineered using various reprogramming strategies. In this Review, recent advances in understanding how epigenetic remodeling contributes to cell-fate reprogramming in vivo and in vitro are summarized.
The properties of nucleosomes can be altered in various ways, including by covalent modification of histones. In this Review, the known properties of key histone modifications and the biological processes to which they are linked are examined to place the modifications in the context of nucleosome dynamics—that is, processes in which nucleosomes are translocated, unwrapped, evicted or replaced.
Nucleosome positioning is crucial for gene expression and other DNA-related processes. In this Review, the authors consider mechanisms by which the genomic pattern of nucleosome positioning is achieved and conclude that nucleosome positioning is determined by the combined effects of several factors including DNA sequence, DNA-binding proteins, nucleosome remodelers and the transcription machinery.
A fundamental property of genomes is their topological organization in three-dimensional space in the cell nucleus. New imaging technologies and genome-wide biochemical approaches combined with functional data are starting to reveal the functional implications of genome topology, as discussed in this Review, and will enable a better understanding of how genome organization influences gene function, and vice versa.
Long noncoding RNAs (lncRNAs) fulfill a variety of regulatory roles in gene expression, which are dictated by their RNA structure, chemistry and modular domain structure. In this Review, the focus is on the well-characterized ability for lncRNAs to function as epigenetic modulators as part of a broad epigenetic regulatory network.
DNA methylation is an epigenetic mark that is erased in the early embryo and then re-established at the time of implantation. In this Review, dynamics of DNA methylation during normal development in vivo are discussed, starting from fertilization through embryogenesis and postnatal growth, as well as abnormal methylation changes that occur in cancer.
Nucleosome assembly is crucial for the maintenance of genome stability and epigenetic information and is aided by histone chaperones. This Review discusses recent insights into the mechanisms and roles of histone chaperones in regulating nucleosome assembly and how alterations in nucleosome-assembly factors may be implicated in human diseases.
