Higher-order folding of heterochromatin: Protein bridges span the nucleosome arrays

Grigoryev, Sergei A.

doi:10.1139/o01-030

Cited by 22 publications

(11 citation statements)

References 119 publications

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“…Linker DNA at the entry/exit site of the nucleosome becomes more condensed, and extensive lateral interactions form between chromatin fibers (reviewed in Ref. 9). Such changes are driven by developmentally regulated factors.…”

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confidence: 99%

“…This abundant nuclear protein accumulates in terminally differentiating chicken blood cells, binds to heterochromatin, and promotes its condensation during terminal cell differentiation (14,15). MENT belongs to a structurally diverse but functionally related group of proteins, including Sir3p, Tup1p, and MeCP2, that assemble tight higher order chromatin structures in repressed chromatin (3,9,16). The mechanism(s) of chromatin compaction by these proteins and the structural features that mediate chromatin remodeling remain unknown.…”

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confidence: 99%

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Role of the M-loop and Reactive Center Loop Domains in the Folding and Bridging of Nucleosome Arrays by MENT

Springhetti

Istomina

Whisstock

et al. 2003

Journal of Biological Chemistry

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MENT is a developmentally regulated heterochromatin-associated protein that condenses chromatin in terminally differentiated avian blood cells. Its homology to the serpin protein family suggests that the conserved serpin reactive center loop (RCL) and the unique M-loop are important for its function. To examine the role of these domains, we studied the interaction of wild-type and mutant MENT with naked DNA and biochemically defined nucleosome arrays reconstituted from 12-mer repeats containing nucleosome positioning sequences. Wild-type MENT folded the naked DNA duplexes into closely juxtaposed parallel structures ("tramlines"). Deletion of the M-loop, but not inactivation of the RCL, prevented tramline formation and the cooperative interaction of MENT with DNA. Reconstitution of wildtype MENT with nucleosome arrays caused their tight folding and self-association. M-loop deletion inhibited nucleosome array folding, whereas the inactive RCL mutant was competent to fold the nucleosome arrays, but had a significantly impaired ability to cause their self-association. Bifunctional chemical cross-linking of MENT revealed oligomerization of wild-type MENT in the presence of chromatin and DNA. This oligomerization was severely reduced in the RCL mutant. We propose that the mechanism of MENT-induced heterochromatin formation involves two independent events: bringing together nucleosome linkers within a chromatin fiber and formation of protein bridges between chromatin fibers. Ordered binding of MENT to linker DNA via its unique M-loop domain promotes the folding of chromatin, whereas bridging of chromatin fibers is facilitated by MENT oligomerization mediated by the RCL.In eukaryotic chromatin, DNA is coiled around histone octamers to form nucleosome arrays, which are further packed into compact higher order structures (for review, see Refs. 1-4). Two major types of chromatin are distinguished by their packing density: open, less compact euchromatin and highly condensed heterochromatin (5, 6). Heterochromatin contains predominantly repressed genes and spreads to the bulk of nuclear chromatin during terminal cell differentiation when most of the genome becomes inactive (7,8).Heterochromatin spreading in terminally differentiated cells is associated with profound remodeling of higher order chromatin structure. Linker DNA at the entry/exit site of the nucleosome becomes more condensed, and extensive lateral interactions form between chromatin fibers (reviewed in Ref. 9). Such changes are driven by developmentally regulated factors. Surprisingly, the expression of major non-histone proteins that promote heterochromatin-specific repression in proliferating cells, such as Ikaros and heterochromatin protein 1, declines in terminally differentiated cells (10, 11) and thus cannot account for heterochromatin spreading.As developing avian blood cells enter the final maturation stage and RNA and protein synthesis declines, few proteins capable of carrying out chromatin condensation are up-regulated. Nucleated erythrocytes in verteb...

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confidence: 99%

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confidence: 99%

Role of the M-loop and Reactive Center Loop Domains in the Folding and Bridging of Nucleosome Arrays by MENT

Springhetti

Istomina

Whisstock

et al. 2003

Journal of Biological Chemistry

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“…Chromatin condensation is especially tight in heterochromatin, representing the repressed fraction of genetic material (30, 57). Heterochromatin becomes very abundant in the nuclei of terminally differentiated cells, where the majority of formerly active genes are repressed and condensed (20,21). In this paper we investigate how the unique properties of heterochromatin in terminally differentiated cells integrate the general mechanism of gene regulation by histone modifications.…”

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confidence: 99%

Insulation of the Chicken β-Globin Chromosomal Domain from a Chromatin-Condensing Protein, MENT

Istomina

Шушанов

Springhetti

et al. 2003

Molecular and Cellular Biology

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Active genes are insulated from developmentally regulated chromatin condensation in terminally differentiated cells. We mapped the topography of a terminal stage-specific chromatin-condensing protein, MENT, across the active chicken ␤-globin domain. We observed two sharp transitions of MENT concentration coinciding with the ␤-globin boundary elements. The MENT distribution profile was opposite to that of acetylated core histones but correlated with that of histone H3 dimethylated at lysine 9 (H3me2K9). Ectopic MENT expression in NIH 3T3 cells caused a large-scale and specific remodeling of chromatin marked by H3me2K9. MENT colocalized with H3me2K9 both in chicken erythrocytes and NIH 3T3 cells. Mutational analysis of MENT and experiments with deacetylase inhibitors revealed the essential role of the reaction center loop domain and an inhibitory affect of histone hyperacetylation on the MENT-induced chromatin remodeling in vivo. In vitro, the elimination of the histone H3 N-terminal peptide containing lysine 9 by trypsin blocked chromatin self-association by MENT, while reconstitution with dimethylated but not acetylated N-terminal domain of histone H3 specifically restored chromatin self-association by MENT. We suggest that histone H3 modification at lysine 9 directly regulates chromatin condensation by recruiting MENT to chromatin in a fashion that is spatially constrained from active genes by gene boundary elements and histone hyperacetylation.In eukaryotic cells, the DNA is repeatedly wrapped around histone octamers to form nucleosomes. Nucleosome arrays are packed through a hierarchy of folding levels into higher-order chromatin structures with a variable degree of condensation (for reviews, see references 32, 67, 68, and 70). Chromatin condensation is especially tight in heterochromatin, representing the repressed fraction of genetic material (30, 57). Heterochromatin becomes very abundant in the nuclei of terminally differentiated cells, where the majority of formerly active genes are repressed and condensed (20,21). In this paper we investigate how the unique properties of heterochromatin in terminally differentiated cells integrate the general mechanism of gene regulation by histone modifications.One of the most intriguing aspects in the process of heterochromatin formation is that chromatin condensation does not spread to the actively transcribed tissue-specific genes, which still maintain an open, nuclease-sensitive conformation (66). For example, in the chicken ␤-globin domain, a 30-kb region of active DNase-sensitive chromatin is separated from repressed and condensed chromatin by gene boundary elements (2, 11). The repressed chromatin is associated with a special pattern of histone modification, most notably a decreased level of histone H3 and H4 acetylation (28, 43) and an increased level of histone H3 methylated at lysine 9 (H3meK9) (42). The H3meK9 binds to the chromodomain of heterochromatin protein 1 (HP1) (49), and this association has been proposed to determine the repressed state of heteroc...

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“…(69) In cell types with extensively repressed and compact genomes such as erythrocyte nuclei, H1 is replaced by H5 and the total amount of linker histones is elevated.…”

Section: Histone Variants and Linkersmentioning

confidence: 99%

“…(69) This is aided by regular spacing of nucleosomes and by histone variants, MeCP2 (91) and the crosslinked, higher-order structures afforded by the dimerisation of HP1. The recent finding that HP1 may bind to two H3-K9 residues (92) underlines the latter's involvement in formation of higher order structures within heterochromatin.…”

Section: Condensationmentioning

confidence: 99%

Heterochromatin?many flavours, common themes

Craig

2004

Bioessays

115

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SummaryHeterochromatin remains condensed throughout the cell cycle, is generally transcriptionally inert and is built and maintained by groups of factors with each group member sharing a similar function. In mammals, these groups include sequence-specific transcriptional repressors, functional RNA and proteins involved in DNA and histone methylation. Heterochromatin is cemented together via interactions within and between each protein group and is maintained by the cell's replication machinery. It can be constitutive (permanent) or facultative (developmentally regulated) and be any size, from a gene promotor to a whole genome. By studying the formation of facultative heterochromatin, we have gained information about how heterochromatin is assembled. We have discovered that there are many different architectural plans for the building of heterochromatin, leading to a seemingly never-ending variety of heterochromatic loci, with each built according to a general rule.

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Higher-order folding of heterochromatin: Protein bridges span the nucleosome arrays

Cited by 22 publications

References 119 publications

Role of the M-loop and Reactive Center Loop Domains in the Folding and Bridging of Nucleosome Arrays by MENT

Role of the M-loop and Reactive Center Loop Domains in the Folding and Bridging of Nucleosome Arrays by MENT

Insulation of the Chicken β-Globin Chromosomal Domain from a Chromatin-Condensing Protein, MENT

Heterochromatin?many flavours, common themes

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