Histone H1 Depletion in Mammals Alters Global Chromatin Structure but Causes Specific Changes in Gene Regulation
TL;DR: Results indicate that linker histones can participate in epigenetic regulation of gene expression by contributing to the maintenance or establishment of specific DNA methylation patterns.
About: This article is published in Cell.The article was published on 2005-12-29 and is currently open access. It has received 551 citations till now. The article focuses on the topics: Histone code & Histone methylation.
Citations
More filters
TL;DR: A map at single-base-pair resolution of methylated cytosines for Arabidopsis is generated by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology.
Abstract: Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.
2,108 citations
TL;DR: What high-resolution genome-wide maps of nucleosomes positions have taught us about how nucleosome positioning demarcates promoter regions and transcriptional start sites and how the composition and structure of promoter nucleosites facilitate or inhibit transcription is discussed.
Abstract: Knowing the precise locations of nucleosomes in a genome is key to understanding how genes are regulated. Recent 'next generation' ChIP-chip and ChIP-Seq technologies have accelerated our understanding of the basic principles of chromatin organization. Here we discuss what high-resolution genome-wide maps of nucleosome positions have taught us about how nucleosome positioning demarcates promoter regions and transcriptional start sites, and how the composition and structure of promoter nucleosomes facilitate or inhibit transcription. A detailed picture is starting to emerge of how diverse factors, including underlying DNA sequences and chromatin remodelling complexes, influence nucleosome positioning.
1,026 citations
TL;DR: The goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
Abstract: Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
926 citations
TL;DR: It is shown that most asymmetric methylation is facilitated byDDM1 and mediated by the methyltransferase CMT2 separately from RdDM, and that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1.
880 citations
Cites background from "Histone H1 Depletion in Mammals Alt..."
...Mice with reduced H1 specifically lose DNA methylation at the regulatory regions of several imprinted genes (Fan et al., 2005), whereas loss of H1 leads to extensive hypermethylation in the fungus Ascobolus immersus (Barra et al., 2000) and apparently stochastic methylation gains and losses in…...
[...]
...Mice with reduced H1 specifically lose DNAmethylation at the regulatory regions of several imprinted genes (Fan et al., 2005), whereas loss of H1 leads to extensive hypermethylation in the fungus Ascobolus immersus (Barra et al....
[...]
...…inhibits nucleosome mobility and transcription in vitro (Pennings et al., 1994; Robinson and Rhodes, 2006); and is associated with more compact, less accessible, and transcriptionally silent chromatin in vivo (Ascenzi and Gantt, 1999; Barra et al., 2000; Fan et al., 2005; Raghuram et al., 2009)....
[...]
..., 1994; Robinson and Rhodes, 2006); and is associated with more compact, less accessible, and transcriptionally silent chromatin in vivo (Ascenzi and Gantt, 1999; Barra et al., 2000; Fan et al., 2005; Raghuram et al., 2009)....
[...]
TL;DR: The compaction of genomic DNA into chromatin has profound implications for the regulation of key processes such as transcription, replication and DNA repair, and it is becoming clear that chromatin structures are not nearly as uniform and regular as previously assumed.
Abstract: Chromatin compaction has profound implications for the regulation of transcription, replication and DNA repair. Changes in nucleosome structure and stability — due to the incorporation of variant histones and post-translational modifications of histones — affect chromatin compaction. Chromatin structures are not nearly as uniform as previously assumed, which should be taken into account in the context of specific biological functions.
636 citations
References
More filters
TL;DR: A technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described, and these "oligolabeled" DNA fragments serve as efficient probes in filter hybridization experiments.
23,324 citations
"Histone H1 Depletion in Mammals Alt..." refers methods in this paper
...For NRL analysis of specific gene loci, DNA fragments were transferred after electrophoresis to charged nylon membranes (GeneScreen Plus, PerkinElmer) by standard capillary blot conditions, and Southern blot analyses were carried out as described (Feinberg and Vogelstein, 1983)....
[...]
01 Jan 1984
TL;DR: In this article, a technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described, where DNA fragments are purified from agarose gels directly by ethanol precipitation and are then denatured and labeled with the large fragment of DNA polymerase I, using random oligonucleotides as primers.
Abstract: A technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described. DNA fragments are purified from agarose gels directly by ethanol precipitation and are then denatured and labeled with the large fragment of DNA polymerase I, using random oligonucleotides as primers. Over 70% of the precursor triphosphate is routinely incorporated into complementary DNA, and specific activities of over 10(9) dpm/microgram of DNA can be obtained using relatively small amounts of precursor. These "oligolabeled" DNA fragments serve as efficient probes in filter hybridization experiments.
21,435 citations
TL;DR: Results indicate that while a 3-fold reduction in levels of genomic m5C has no detectable effect on the viability or proliferation of ES cells in culture, a similar reduction of DNA methylation in embryos causes abnormal development and embryonic lethality.
3,994 citations
Additional excerpts
...We also did not detect a difference in DNA methylation of endogenous C type retrovirus repeats (Li et al., 1992) (Figure 5D)....
[...]
TL;DR: The study of imprinting provides new insights into epigenetic gene modification during development, and is thought to influence the transfer of nutrients to the fetus and the newborn from the mother.
Abstract: Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about by epigenetic instructions--imprints--that are laid down in the parental germ cells. Imprinting is a particularly important genetic mechanism in mammals, and is thought to influence the transfer of nutrients to the fetus and the newborn from the mother. Consistent with this view is the fact that imprinted genes tend to affect growth in the womb and behaviour after birth. Aberrant imprinting disturbs development and is the cause of various disease syndromes. The study of imprinting also provides new insights into epigenetic gene modification during development.
2,212 citations
"Histone H1 Depletion in Mammals Alt..." refers background in this paper
...We next studied the H19-Igf2 and Gtl2-Dlk1 loci, where parent-of-origin-specific DNA methylation patterns have been shown to regulate expression of the genes (Reik and Walter, 2001; Schmidt et al., 2000; Verona et al., 2003)....
[...]
TL;DR: It is demonstrated that a normal level of DNA methylation is required for controlling differential expression of the paternal and maternal alleles of imprinted genes in mutant mice that are deficient in DNA methyltransferase activity.
Abstract: The paternal and maternal genomes are not equivalent and both are required for mammalian development. The difference between the parental genomes is believed to be due to gamete-specific differential modification, a process known as genomic imprinting. The study of transgene methylation has shown that methylation patterns can be inherited in a parent-of-origin-specific manner, suggesting that DNA methylation may play a role in genomic imprinting. The functional significance of DNA methylation in genomic imprinting was strengthened by the recent finding that CpG islands (or sites) in three imprinted genes, H19, insulin-like growth factor 2 (Igf-2), and Igf-2 receptor (Igf-2r), are differentially methylated depending on their parental origin. We have examined the expression of these three imprinted genes in mutant mice that are deficient in DNA methyltransferase activity. We report here that expression of all three genes was affected in mutant embryos: the normally silent paternal allele of the H19 gene was activated, whereas the normally active paternal allele of the Igf-2 gene and the active maternal allele of the Igf-2r gene were repressed. Our results demonstrate that a normal level of DNA methylation is required for controlling differential expression of the paternal and maternal alleles of imprinted genes.
2,081 citations
"Histone H1 Depletion in Mammals Alt..." refers result in this paper
...In agreement with previously published results (Dean et al., 1998; Li et al., 1993; Tucker et al., 1996; Warnecke et al., 1998), we found that most CpG dinucleotide sequences in this region are predominantly methylated in wild-type ES cells....
[...]