Nuclear compartmentalization and gene activity

Francastel, Claire; Schübeler, Dirk; Martin, David I. K.; Groudine, Mark

doi:10.1038/35040083

Cited by 273 publications

(196 citation statements)

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“…On differentiation, the histone methylation and acetylation patterns closely match those seen in fibroblasts. These findings are consistent with previous studies and indicate that ES cells exhibit more permissive chromatin overall and that differentiation is associated with a move toward more highly silenced chromatin (4,15,(32)(33)(34)(35). Both the presence of highly permissive chromatin and the changes observed during differentiation support the hypothesis that these modification states are required for the maintenance of pluripotency.…”

Section: Discussionsupporting

confidence: 82%

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Phanstiel

Brumbaugh²,

Berggren³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

162

175

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Epigenetic regulation through chromatin is thought to play a critical role in the establishment and maintenance of pluripotency. Traditionally, antibody-based technologies were used to probe for specific posttranslational modifications (PTMs) present on histone tails, but these methods do not generally reveal the presence of multiple modifications on a single-histone tail (combinatorial codes). Here, we describe technology for the discovery and quantification of histone combinatorial codes that is based on chromatography and mass spectrometry. We applied this methodology to decipher 74 discrete combinatorial codes on the tail of histone H4 from human embryonic stem (ES) cells. Finally, we quantified the abundances of these codes as human ES cells undergo differentiation to reveal striking changes in methylation and acetylation patterns. For example, H4R3 methylation was observed only in the presence of H4K20 dimethylation; such context-specific patterning exemplifies the power of this technique.electron transfer dissociation ͉ epigenetics ͉ posttranslational modification ͉ histone code ͉ pluripotency P luripotency-the ability to differentiate into any specialized lineage-is the hallmark of embryonic stem (ES) cells and the basis for their experimental and therapeutic potential. The precise molecular mechanisms that define pluripotency remain elusive; however, a number of recent works suggest a central role for epigenetic regulation through chromatin (1-6). Either by recruiting or shielding certain factors, modifications on histone proteins modulate a gene's local environment and thereby regulate expression (7-12). Concerted changes in histone modification states occur during differentiation (13). For example, high levels of histone H3 and H4 acetylation are characteristic of pluripotent cells in mice and the abundance of these marks decreases during differentiation (14, 15). Methylation of R2, R17, and R26 of histone H3 by CARM1 also correlates with cell fate and potency (6). Cells with higher levels of methylation, at these residues, were enriched in the embryonic part of the blastocyst. Next, specific patterns of histone H3K4me3 and H3K27me3 are observed at promoter regions of genes that are regulated during differentiation (1, 2). Finally, demethylation of H3K27me3 is required for activation of certain HOX genes essential for proper development (16,17). The demethylase responsible interacts directly with MLL 2/3 complexes, which methylate histone H3K4 (18). Taken together these experiments have shed new light on the power of epigenetic regulation within ES cells; however, the precise details and role(s) of such combinatorial PTM patterns remain largely unknown.Technological limitations in our ability to discover and quantify combinatorial histone PTMs has, and continues to, present a major obstacle. Most of our knowledge of epigenetics has been derived by antibody-based approaches. Antibodies require a priori knowledge of individual modifications, are subject to epitope occlusion, and have difficulty distingu...

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Section: Discussionsupporting

confidence: 82%

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Phanstiel

Brumbaugh²,

Berggren³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

162

175

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“…Our findings that TFs encoded in specific chromosomes and within distinct regions show a strong preference to regulate genes on distinct chromosomes (and regions) open up several questions and expand our need to understand eukaryotic gene regulation at a higher level. The findings reported here are consistent with several molecular mechanisms, such as the genome-wide loop model of chromosomes (26), the presence of expression hubs (27) and transcription factories (28,29), and the nuclear gating hypothesis (30). With the development of experimental methods such as chromosome conformation capture (3C), 4C, 5C, and 6C, and the availability of genome-scale data on protein-DNA interactions from high-throughput experiments in other eukaryotes, our work provides a fundamental framework by which such questions can be systematically studied for higher eukaryotes.…”

Section: Discussionsupporting

confidence: 79%

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes

Janga

Collado‐Vides

Babu

2008

Proc. Natl. Acad. Sci. U.S.A.

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Genetic material in eukaryotes is tightly packaged in a hierarchical manner into multiple linear chromosomes within the nucleus. Although it is known that eukaryotic transcriptional regulation is complex and requires an intricate coordination of several molecular events both in space and time, whether the complexity of this process constrains genome organization is still unknown. Here, we present evidence for the existence of a higher-order organization of genes across and within chromosomes that is constrained by transcriptional regulation. In particular, we reveal that the target genes (TGs) of transcription factors (TFs) for the yeast, Saccharomyces cerevisiae, are encoded in a highly ordered manner both across and within the 16 chromosomes. We show that (i) the TGs of a majority of TFs show a strong preference to be encoded on specific chromosomes, (ii) the TGs of a significant number of TFs display a strong preference (or avoidance) to be encoded in regions containing particular chromosomal landmarks such as telomeres and centromeres, and (iii) the TGs of most TFs are positionally clustered within a chromosome. Our results demonstrate that specific organization of genes that allowed for efficient control of transcription within the nuclear space has been selected during evolution. We anticipate that uncovering such higher-order organization of genes in other eukaryotes will provide insights into nuclear architecture, and will have implications in genetic engineering experiments, gene therapy, and understanding disease conditions that involve chromosomal aberrations.gene order ͉ genome ͉ nuclear architecture ͉ systems biology ͉ network A lthough transcription in both prokaryotes and eukaryotes involves the evolutionarily conserved core RNA polymerase subunit, the whole process of transcriptional regulation is fundamentally different. In contrast to prokaryotes where transcription primarily relies on the cis-regulatory DNA sequences alone (1), eukaryotic transcription is regulated at least at three major levels (2, 3). The first is at the level of DNA sequence where the transcription factor (TF) associates with cis-regulatory elements to regulate transcription of the relevant gene (2). The second is at the level of chromatin, which allows segments within a chromosomal arm to switch between different transcriptional states, that is, between a state that suppresses transcription and one that allows for gene activation (2). This involves changes in nucleosome occupancy and chromatin structure, both of which are controlled by the interplay between remodeling complexes, histone modification, DNA methylation, and a variety of repressive and activating mechanisms (4, 5). The third is at the level of nuclear architecture, which includes organization of chromosomes into chromosomal territories, and the dynamic, temporal, and spatial organization of specific chromosomal loci-all of which are known to influence gene expression (6-11). Thus, unlike in prokaryotes, transcription in eukaryotes is an energy-intensive, multi...

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“…These sites would not have been identified using conventional promoter analyses, which are generally restricted to the region proximal to the transcription start site. BARX2 binding elements located distal to genes or within introns might function through long range interactions that involve looping of chromatin to bring distal elements within proximity of gene promoters (31), or by inducing permissive or repressive structures that propagate along the chromosome and affect the accessibility of gene promoters to the transcriptional machinery (32). Moreover, the high proportion of intronic BARX2 binding sites identified in this study raises the possibility that BARX2 affects transcript elongation through the intron by influencing local chromatin structure.…”

Section: Discussionmentioning

confidence: 85%

Identification of Novel Binding Elements and Gene Targets for the Homeodomain Protein BARX2

Stevens

Iacovoni

Edelman

et al. 2004

Journal of Biological Chemistry

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BARX2 is a homeobox transcription factor that influences cellular differentiation in various developmental contexts. To begin to identify the gene targets that mediate its effects, chromatin immunoprecipitation (ChIP) was used to isolate BARX2 binding sites from the human MCF7 breast cancer cell line. Cloning and sequencing of BARX2-ChIP-derived DNA fragments identified 60 potential BARX2 target loci that were proximal to or within introns of genes involved in cytoskeletal organization, cell adhesion, growth factor signaling, transcriptional regulation, and RNA metabolism. The sequences of over half of the fragments showed homology with the mouse genome, and several sequences could be mapped to orthologous human and mouse genes. Binding of BARX2 to 21 genomic loci examined was confirmed quantitatively by replicate ChIP assays. A combination of sequence analysis and electrophoretic mobility shift assays revealed homeodomain binding sites within several fragments that bind to BARX2 in vitro. The majority of BARX2 binding fragments tested (14/19), also affected transcription in luciferase reporter gene assays. Mutation analyses of three fragments showed that their transcriptional activities required the HBS, and suggested that BARX2 regulates gene expression by binding to DNA elements containing paired TAAT motifs that are separated by a poly(T) sequence. Inhibition of BARX2 expression in MCF7 cells led to reduced expression of eight genes associated with BARX2 binding sites, indicating that BARX2 directly regulates their expression. The data suggest that BARX2 can coordinate the expression of a network of genes that influence the growth of MCF7 cells.

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Nuclear compartmentalization and gene activity

Cited by 273 publications

References 79 publications

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes

Identification of Novel Binding Elements and Gene Targets for the Homeodomain Protein BARX2

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