Formation of Boundaries of Transcriptionally Silent Chromatin by Nucleosome-Excluding Structures

ABSTRACT The eukaryotic genome is divided into chromosomal domains of distinct gene activities. Transcriptionally silent chromatin tends to encroach upon active chromatin. Barrier elements that can block the spread of silent chromatin have been documented, but the mechanisms of their function are not resolved. We show that the prokaryotic LexA protein can function as a barrier to the propagation of transcriptionally silent chromatin in yeast. The barrier function of LexA correlates with its ability to disrupt local chromatin structure. In accord with this, (CCGNN) n and poly(dA-dT), both of which do not favor nucleosome formation, can also act as efficient boundaries of silent chromatin. Moreover, we show that a Rap1p-binding barrier element also disrupts chromatin structure. These results demonstrate that nucleosome exclusion is one of the mechanisms for the establishment of boundaries of silent chromatin domains.

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Faculty Opinions recommendation of Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1088778.541510 ◽

2007 ◽

Author(s):

Sui Huang

Keyword(s):

Noncoding Rnas ◽

Silent Chromatin ◽

Chromatin Domains

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Recovery of transcriptionally active chromatin restriction fragments by binding to organomercurial-agarose magnetic beads. A rapid and sensitive method for monitoring changes in higher order chromatin structure during gene activation and repression.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)49477-5 ◽

1993 ◽

Vol 268 (31) ◽

pp. 23409-23416

Author(s):

T.A. Chen-Cleland ◽

L.C. Boffa ◽

E.M. Carpaneto ◽

M.R. Mariani ◽

E Valentin ◽

...

Keyword(s):

Chromatin Structure ◽

Magnetic Beads ◽

Gene Activation ◽

Higher Order ◽

Active Chromatin ◽

Restriction Fragments ◽

Sensitive Method

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Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

International Journal of Molecular Sciences ◽

10.3390/ijms22010076 ◽

2020 ◽

Vol 22 (1) ◽

pp. 76

Author(s):

Aaron Morgan ◽

Sarah LeGresley ◽

Christopher Fischer

Keyword(s):

Free Energy ◽

Dna Replication ◽

Recent Work ◽

Chromatin Remodeling ◽

Chromatin Structure ◽

Genetic Information ◽

Molecular Machines ◽

Mechanical Work ◽

Eukaryotic Genome ◽

Hydrolysis Of

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.

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The salt dependence of chicken and yeast chromatin structure. Effects on internucleosomal organization and relation to active chromatin.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)67602-1 ◽

1986 ◽

Vol 261 (21) ◽

pp. 9904-9914

Author(s):

D Lohr

Keyword(s):

Chromatin Structure ◽

Active Chromatin ◽

Salt Dependence

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An active chromatin structure acquired by translocated c-myc genes

Molecular and Cellular Biology ◽

10.1128/mcb.6.4.1357-1361.1986 ◽

1986 ◽

Vol 6 (4) ◽

pp. 1357-1361

Author(s):

E Kakkis ◽

J Prehn ◽

K Calame

Keyword(s):

Chromatin Structure ◽

Gene Segment ◽

Dnase I ◽

Regulatory Sequences ◽

Active Chromatin ◽

Alpha Gene

We used general sensitivity to DNase I digestion to analyze the chromatin structure of c-myc genes in seven murine plasmacytomas. In every case, the 3' portion of c-myc juxtaposed with C alpha displayed a much more DNase I-sensitive chromatin structure than untranslocated c-myc or, in one case analyzed, the reciprocally translocated 5' portion. Our data suggest the presence of regulatory sequences near the C alpha gene segment.

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Dispersed Mutations in Histone H3 That Affect Transcriptional Repression and Chromatin Structure of the CHA1 Promoter in Saccharomyces cerevisiae

Eukaryotic Cell ◽

10.1128/ec.00233-08 ◽

2008 ◽

Vol 7 (10) ◽

pp. 1649-1660 ◽

Cited By ~ 7

Author(s):

Qiye He ◽

Cailin Yu ◽

Randall H. Morse

Keyword(s):

Saccharomyces Cerevisiae ◽

Chromatin Structure ◽

Transcriptional Repression ◽

Histone H3 ◽

Temperature Sensitive ◽

Active Chromatin ◽

Temperature Sensitive Mutants ◽

Nucleosome Structure ◽

Lysine Residues ◽

Chromatin Configuration

ABSTRACT The histone H3 amino terminus, but not that of H4, is required to prevent the constitutively bound activator Cha4 from remodeling chromatin and activating transcription at the CHA1 gene in Saccharomyces cerevisiae. Here we show that neither the modifiable lysine residues nor any specific region of the H3 tail is required for repression of CHA1. We then screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, three of which are also temperature-sensitive mutants and four of which exhibit a sin − phenotype. Histone mutant levels were similar to that of wild-type H3, and the mutations did not cause gross alterations in nucleosome structure. One specific and strongly derepressing mutation, H3 A111G, was examined in depth and found to cause a constitutively active chromatin configuration at the uninduced CHA1 promoter as well as at the ADH2 promoter. Transcriptional derepression and altered chromatin structure of the CHA1 promoter depend on the activator Cha4. These results indicate that modest perturbations in distinct regions of the nucleosome can substantially affect the repressive function of chromatin, allowing activation in the absence of a normal inducing signal (at CHA1) or of Swi/Snf (resulting in a sin − phenotype).

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Drosophila UTX Is a Histone H3 Lys27 Demethylase That Colocalizes with the Elongating Form of RNA Polymerase II

Molecular and Cellular Biology ◽

10.1128/mcb.01504-07 ◽

2007 ◽

Vol 28 (3) ◽

pp. 1041-1046 ◽

Cited By ~ 79

Author(s):

Edwin R. Smith ◽

Min Gyu Lee ◽

Benjamin Winter ◽

Nathan M. Droz ◽

Joel C. Eissenberg ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Histone H3 ◽

Silent Chromatin ◽

H3k4 Methylation ◽

Active Chromatin ◽

Pol Ii ◽

H3k27 Methylation ◽

Histone H3 Methylation ◽

Heat Shock Induction

ABSTRACT Histone H3 methylation at Lys27 (H3K27 methylation) is a hallmark of silent chromatin, while H3K4 methylation is associated with active chromatin regions. Here we report that a Drosophila JmjC family member, dUTX, specifically demethylates di- and trimethylated but not monomethylated H3K27. dUTX localization on chromatin correlates with the elongating form of RNA polymerase II (Pol II), and dUTX can associate with Pol II. Furthermore, heat shock induction results in the recruitment of dUTX to the hsp70 gene, like that of several other Pol II elongation factors. Our data indicate that dUTX is intimately associated with actively transcribed genes and may provide a paradigm for how H3K27 demethylation is required for the activation of preinitiated Pol II on transcriptionally poised genes.

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Chromatin organization in the homogeneously staining regions of a methotrexate-resistant mouse cell line: interspersion of inactive and active chromatin domains distinguished by acetylation of histone H4

Journal of Cell Science ◽

10.1242/jcs.109.9.2221 ◽

1996 ◽

Vol 109 (9) ◽

pp. 2221-2228 ◽

Cited By ~ 2

Author(s):

L. Nicol ◽

P. Jeppesen

Keyword(s):

Cell Line ◽

Dna Sequences ◽

Satellite Dna ◽

Mouse Cell ◽

Histone H4 ◽

Active Chromatin ◽

Chromatin Domains ◽

Resistant Mouse ◽

Major Satellite ◽

Drosophila Heterochromatin

We have analyzed the organization of the homogeneously staining regions (HSRs) in chromosomes from a methotrexate-resistant mouse melanoma cell line. Fluorescence in situ hybridization techniques were used to localize satellite DNA sequences and the amplified copies of the dihydrofolate reductase (DHFR) gene that confer drug-resistance, in combination with immunofluorescence using antibody probes to differentiate chromatin structure. We show that the major DNA species contained in the HSRs is mouse major satellite, confirming previous reports, and that this is interspersed with DHFR DNA in an alternating tandem array that can be resolved at the cytological level. Mouse minor satellite DNA, which is normally located at centromeres, is also distributed along the HSRs, but does not appear to interfere with centromere function. The blocks of major satellite DNA are coincident with chromatin domains that are labelled by an autoantibody that recognizes a mammalian homologue of Drosophila heterochromatin-associated protein 1, shown previously to be confined to centric heterochromatin in mouse. An antiserum that specifically recognizes acetylated histone H4, a marker for active chromatin, fails to bind to the satellite DNA domains, but labels the intervening segments containing DHFR DNA. We can find no evidence for the spreading of the inactive chromatin domains into adjacent active chromatin, even after extended passaging of cells in the absence of methotrexate selection.

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