The mammalian epigenome.

By Bradley E. Bernstein, Alexander Meissner, Eric S. Lander. Cell, 2007

2,148 citations recorded by the source corpus.

Chemical modifications to DNA and histone proteins form a complex regulatory network that modulates chromatin structure and genome function. The epigenome refers to the complete description of these potentially heritable changes across the genome. The composition of the epigenome within a given cell is a function of genetic determinants, lineage, and environment. With the sequencing of the human genome completed, investigators now seek a comprehensive view of the epigenetic changes that determine how genetic information is made manifest across an incredibly varied background of developmental stages, tissue types, and disease states. Here we review current research efforts, with an emphasis on large-scale studies, emerging technologies, and challenges ahead.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/33b28b048ab70ca2f34b948e6dd5badba10c020f

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Citations in the corpus

Aberrant epigenetic landscape in cancer: how cellular identity goes awry. (2010, background): “We now knowa considerable amount about the characterization of global levels of histone modifications in differentiated mammalian tissues, mainly thanks to the development of large-scale techniques (ChIP-Seq, ChIP on chip, among others) (Barski et al., 2007; Bernstein et al., 2007).”
Discovery and characterization of chromatin states for systematic annotation of the human genome (2010, background): “More than a dozen positions of multiple histone proteins can undergo a number of modifications, such as acetylation and mono-, di- or tri-methylatio”
Chromatin organization marks exon-intron structure (2009, background): “Nucleosome occupancy is modulated by means of specific modifications of histone tails, including acetylation, methylation, phosphorylation and ubiquitinatio”
Transcriptional control of the inflammatory response (2009, background): “Dynamic chromatin remodelling Recent studies have highlighted an important role for chromatin in the control of inflammatory gene expressio”
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. (2008, positive): “Whereas methylation at CpG dinucleotides predominates in animals, in plant cells distinct pathways govern the methylation of cytosines throughout all sequence contexts (Bernstein et al., 2007; Henderson and Jacobsen, 2007).”
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. (2007, background): “Epigenetic modifications have profound effects on cell identity and cell-fate determination ( Bernstein et al., 2007; Surani, 2001).”
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome (2012, positive): “DISCUSSION Bisulfite sequencing has been broadly used to analyze the genomic distribution and abundance of 5mC (Bernstein et al., 2007; Clark et al., 1994; Lister et al., 2008; Meissner, 2010; Pelizzola and Ecker, 2011).”
Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics (2015, background): “Changes in epigenetic marks such as DNA methylation and histone modifications are being studied with genome-wide assays (Bernstein et al., 2007; Rivera and Ren, 2013), which have advanced our understanding of epigenomic cell states.”
CTCF: Master Weaver of the Genome (2009, positive): “…interplay between DNA sequence and a secondary layer of potentially heritable epigenetic marks (such as histone modifications and DNA methylation) that are dynamically accumulated throughout the lifetime of an organism in response to developmental and/or environmental cues (Bernstein et al., 2007).”
Persistent epigenetic differences associated with prenatal exposure to famine in humans (2008, background): “Methyl groups coupled to cytosines in cytosine-guanine (CpG) dinucleotides and modifications of histones that package the DNA are the two main molecular marks that compose this information and regulate chromatin structure and DNA accessibility (2).”
Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. (2008, background): “Since this ‘‘bivalency’’ was hypothesized to be an ESC-specific chromatin state that poises for differentiation-coupled activation (Bernstein et al., 2007), we wondered about the H3K4 methylation of progenitor- and terminal neuron-specific targets of Polycomb.”