38,652 research outputs found
Epigenetic Regulation Of Gene Expression Domains In Pluripotent Stem Cells
Transcriptional and histone modification profiles were analysed in detail across
several regions of the mouse genome in order to examine how tissue-specificity is
determined at early stages of development and how it is maintained during cell
commitment. The analysis was mainly focused on a 2 Mb gene-dense region containing
68 known closely situated genes, having very diverse expression patterns.
Transcriptional profiling of this region showed that clustered tissue-restricted and
housekeeping genes are associated with clearly defined monovalent or bivalent
epigenetic domains. In ES cells, the actively transcribed housekeeping genes were
enriched for histone H3K4me1, H3K4me2, H3K4me3, H3K9ac and binding of Pol II.
Most of the silent tissue-restricted genes were marked by bivalent domains and had
background levels of Pol II. In few cases, substantial levels of Pol II were found at
inactive genes situated close to housekeeping genes, suggesting that transcriptional
read-through could be occurring at these genes in ES cells. Epigenetic profiling of the
gene-dense region in LPS-activated B cells showed that B cells have a very similar
histone modification profile to ES cells. Specifically, the analysis showed that bivalent
domains which were thought to be a defining characteristic of pluripotent stem cells are
equally prevalent in B cells, suggesting that the epigenetic marking of silent genes is
quite similar in these two very different cell types. Analysis of a large gene-poor region
containing four genes encoding GABAA neurotransmitter receptor subunits showed that
the this locus acquires a large bivalent domain of approximately 1.3 Mb following
differentiation of ES cells into NS cells and astrocytes. The results obtained in this study
demonstrate the complex and diverse nature of histone modifications at tissue-restricted
genes and suggest that trans-acting factors are responsible for generating highly specific
combinations of histone modifications at each individual gene at different stages of cell
differentiation
Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.
Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes. While on gene level histone modifications are known to change during differentiation, very little is known about the quantitative fluctuations in bulk histone modifications during development. To investigate this issue we analysed histones isolated from four different developmental stages of Xenopus laevis by mass spectrometry. In toto, we quantified 59 modification states on core histones H3 and H4 from blastula to tadpole stages. During this developmental period, we observed in general an increase in the unmodified states, and a shift from histone modifications associated with transcriptional activity to transcriptionally repressive histone marks. We also compared these naturally occurring patterns with the histone modifications of murine ES cells, detecting large differences in the methylation patterns of histone H3 lysines 27 and 36 between pluripotent ES cells and pluripotent cells from Xenopus blastulae. By combining all detected modification transitions we could cluster their patterns according to their embryonic origin, defining specific histone modification profiles (HMPs) for each developmental stage. To our knowledge, this data set represents the first compendium of covalent histone modifications and their quantitative flux during normogenesis in a vertebrate model organism. The HMPs indicate a stepwise maturation of the embryonic epigenome, which may be causal to the progressing restriction of cellular potency during development
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation.
SummaryChromatin modifications have been implicated in the self-renewal and differentiation of embryonic stem cells (ESCs). However, the function of histone variant H2A.Z in ESCs remains unclear. We show that H2A.Z is highly enriched at promoters and enhancers and is required for both efficient self-renewal and differentiation of murine ESCs. H2A.Z deposition leads to an abnormal nucleosome structure, decreased nucleosome occupancy, and increased chromatin accessibility. In self-renewing ESCs, knockdown of H2A.Z compromises OCT4 binding to its target genes and leads to decreased binding of MLL complexes to active genes and of PRC2 complex to repressed genes. During differentiation of ESCs, inhibition of H2A.Z also compromises RA-induced RARα binding, activation of differentiation markers, and the repression of pluripotency genes. We propose that H2A.Z mediates such contrasting activities by acting as a general facilitator that generates access for a variety of complexes, both activating and repressive
A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types
Chromatin is a highly compact and dynamic nuclear structure that consists of
DNA and associated proteins. The main organizational unit is the nucleosome,
which consists of a histone octamer with DNA wrapped around it. Histone
proteins are implicated in the regulation of eukaryote genes and they carry
numerous reversible post-translational modifications that control DNA-protein
interactions and the recruitment of chromatin binding proteins.
Heterochromatin, the transcriptionally inactive part of the genome, is densely
packed and contains histone H3 that is methylated at Lys 9 (H3K9me). The
propagation of H3K9me in nucleosomes along the DNA in chromatin is antagonizing
by methylation of H3 Lysine 4 (H3K4me) and acetylations of several lysines,
which is related to euchromatin and active genes. We show that the related
histone modifications form antagonized domains on a coarse scale. These histone
marks are assumed to be initiated within distinct nucleation sites in the DNA
and to propagate bi-directionally. We propose a simple computer model that
simulates the distribution of heterochromatin in human chromosomes. The
simulations are in agreement with previously reported experimental observations
from two different human cell lines. We reproduced different types of barriers
between heterochromatin and euchromatin providing a unified model for their
function. The effect of changes in the nucleation site distribution and of
propagation rates were studied. The former occurs mainly with the aim of
(de-)activation of single genes or gene groups and the latter has the power of
controlling the transcriptional programs of entire chromosomes. Generally, the
regulatory program of gene transcription is controlled by the distribution of
nucleation sites along the DNA string.Comment: 24 pages,9 figures, 1 table + supplementary materia
Epigenetic aberrations and cancer
The correlation between epigenetic aberrations and disease underscores the importance of epigenetic mechanisms. Here, we review recent findings regarding chromatin modifications and their relevance to cancer
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Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages.
To elucidate the transcriptional 'landscape' that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitor cells spanning the earliest stages of B lymphoid and T lymphoid specification. Over 3,000 genes encoding previously unknown long non-coding RNAs (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage specific and were more lineage specific than those of protein-coding genes. Protein-coding genes co-expressed with neighboring lncRNA genes showed enrichment for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships among the earliest progenitor cells in the human bone marrow and thymus
Chromatin insulator elements: establishing barriers to set heterochromatin boundaries
Epigenomic profiling has revealed that substantial portions of genomes in higher eukaryotes are organized into extensive domains of transcriptionally repressive chromatin. The boundaries of repressive chromatin domains can be fixed by DNA elements known as barrier insulators, to both shield neighboring gene expression and to maintain the integrity of chromosomal silencing. Here, we examine the current progress in identifying vertebrate barrier elements and their binding factors. We overview the design of the reporter assays used to define enhancer-blocking and barrier insulators. We look at the mechanisms vertebrate barrier proteins, such as USF1 and VEZF1, employ to counteract Polycomb- and heterochromatin-associated repression. We also undertake a critical analysis of whether CTCF could also act as a barrier protein. There is good evidence that barrier elements in vertebrates can form repressive chromatin domain boundaries. Future studies will determine whether barriers are frequently used to define repressive domain boundaries in vertebrates
Spatial clustering and common regulatory elements correlate with coordinated gene expression
Many cellular responses to surrounding cues require temporally concerted
transcriptional regulation of multiple genes. In prokaryotic cells, a
single-input-module motif with one transcription factor regulating multiple
target genes can generate coordinated gene expression. In eukaryotic cells,
transcriptional activity of a gene is affected by not only transcription
factors but also the epigenetic modifications and three-dimensional chromosome
structure of the gene. To examine how local gene environment and transcription
factor regulation are coupled, we performed a combined analysis of time-course
RNA-seq data of TGF-\b{eta} treated MCF10A cells and related epigenomic and
Hi-C data. Using Dynamic Regulatory Events Miner (DREM), we clustered
differentially expressed genes based on gene expression profiles and associated
transcription factors. Genes in each class have similar temporal gene
expression patterns and share common transcription factors. Next, we defined a
set of linear and radial distribution functions, as used in statistical
physics, to measure the distributions of genes within a class both spatially
and linearly along the genomic sequence. Remarkably, genes within the same
class despite sometimes being separated by tens of million bases (Mb) along
genomic sequence show a significantly higher tendency to be spatially close
despite sometimes being separated by tens of Mb along the genomic sequence than
those belonging to different classes do. Analyses extended to the process of
mouse nervous system development arrived at similar conclusions. Future studies
will be able to test whether this spatial organization of chromosomes
contributes to concerted gene expression.Comment: 30 pages, 9 figures, accepted in PLoS Computational Biolog
Computational modeling to elucidate molecular mechanisms of epigenetic memory
How do mammalian cells that share the same genome exist in notably distinct
phenotypes, exhibiting differences in morphology, gene expression patterns, and
epigenetic chromatin statuses? Furthermore how do cells of different phenotypes
differentiate reproducibly from a single fertilized egg? These are fundamental
problems in developmental biology. Epigenetic histone modifications play an
important role in the maintenance of different cell phenotypes. The exact
molecular mechanism for inheritance of the modification patterns over cell
generations remains elusive. The complexity comes partly from the number of
molecular species and the broad time scales involved. In recent years
mathematical modeling has made significant contributions on elucidating the
molecular mechanisms of DNA methylation and histone covalent modification
inheritance. We will pedagogically introduce the typical procedure and some
technical details of performing a mathematical modeling study, and discuss
future developments.Comment: 36 pages, 4 figures, 2 tables, book chapte
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