scholarly journals Yeast heterochromatin is a dynamic structure that requires silencers continuously

2000 ◽  
Vol 14 (4) ◽  
pp. 452-463 ◽  
Author(s):  
Tzu-Hao Cheng ◽  
Marc R. Gartenberg
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Transcriptional Silencing ◽  
Dynamic Structure ◽  
Regulatory Elements ◽  
S Phase ◽  
Silent Chromatin ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Silent State

Transcriptional silencing of the HM loci in yeast requirescis-acting elements, termed silencers, that function during S-phase passage to establish the silent state. To study the role of the regulatory elements in maintenance of repression, site-specific recombination was used to uncouple preassembled silent chromatin fragments from silencers. DNA rings excised from HMR were initially silent but ultimately reactivated, even in G1- or G2/M-arrested cells. In contrast, DNA rings bearing HML-derived sequence were stably repressed due to the presence of a protosilencing element. These data show that silencers (or protosilencers) are required continuously for maintenance of silent chromatin. Reactivation of unstably repressed rings was blocked by overexpression of silencing proteins Sir3p and Sir4p, and chromatin immunoprecipitation studies showed that overexpressed Sir3p was incorporated into silent chromatin. Importantly, the protein was incorporated even when expressed outside of S phase, during G1 arrest. That silencing factors can associate with and stabilize preassembled silent chromatin in non-S-phase cells demonstrates that heterochromatin in yeast is dynamic.

scholarly journals Involvement of a Short Interspersed Element in Epigenetic Transcriptional Silencing of the Amoebapore Gene in Entamoeba histolytica

2005 ◽  
Vol 4 (11) ◽  
pp. 1775-1784 ◽  
Author(s):  
Michael Anbar ◽  
Rivka Bracha ◽  
Yael Nuchamowitz ◽  
Yan Li ◽  
Anat Florentin ◽  
...  
Keyword(s):  
Entamoeba Histolytica ◽  
Chromatin Immunoprecipitation ◽  
Promoter Region ◽  
Histone H3 ◽  
Transcriptional Silencing ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Antisense Strand ◽  
Interfering Rna

ABSTRACT Transcriptional silencing of an amoebapore (ap-a) gene occurred in Entamoeba histolytica following the transfection of plasmids containing a DNA segment (473 bp) homologous to the 5′ upstream region of the gene (R. Bracha, Y. Nuchamowitz, and D. Mirelman, Eukaryot. Cell 2:295-305, 2003). This segment contains the promoter region of the ap-a gene, a T-rich stretch, followed by a truncated SINE1 (short interspersed element 1) that is transcribed from the antisense strand. Transfection of plasmids containing truncated SINE1 sequences which lack their 3′ regulatory elements upstream of the ap-a gene was essential for the downstream silencing of the ap-a gene while transfection with plasmids containing the entire SINE1 sequence or without the T-rich stretch promoted the overexpression of the ap-a gene. Both the T-rich stretch and sequences of the 5′ SINE1 were essential for the transcription of SINE1. RNA extracts from gene-silenced cultures showed small amounts of short (∼140-nucleotide), single-stranded molecules with homology to SINE1 but no short interfering RNA. Chromatin immunoprecipitation analysis with an antibody against methylated K4 of histone H3 showed a demethylation of K4 at the domain of the ap-a gene, indicating transcriptional inactivation. These results suggest the involvement of SINE1 in triggering the gene silencing and the role of histone modification in its epigenetic maintenance.

scholarly journals Role of attP in Integrase-Mediated Integration of the Shigella Resistance Locus Pathogenicity Island of Shigella flexneri

2004 ◽  
Vol 48 (3) ◽  
pp. 1028-1031 ◽  
Author(s):  
Sally A. Turner ◽  
Shelley N. Luck ◽  
Harry Sakellaris ◽  
Kumar Rajakumar ◽  
Ben Adler
Keyword(s):  
Shigella Flexneri ◽  
Pathogenicity Island ◽  
Resistance Locus ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Independent Site

ABSTRACT The Shigella resistance locus (SRL) pathogenicity island (PAI) in Shigella spp. mediates resistance to streptomycin, ampicillin, chloramphenicol, and tetracycline. It can be excised from the chromosome via site-specific recombination mediated by the P4-related int gene. Here, we show that SRL PAI attP is capable of RecA-independent, site-specific, int-mediated integration into two bacterial tRNA attB sites.

The role of himA and xis in lambda site-specific recombination

1980 ◽  
Vol 138 (3) ◽  
pp. 503-512 ◽  
Author(s):  
Susan Gottesman ◽  
Ken Abremski
Keyword(s):  
Site Specific ◽  
Site Specific Recombination

Site-specific Recombination of Bacteriophage  : The Role of Host Gene Products

1979 ◽  
Vol 43 (0) ◽  
pp. 1121-1126 ◽  
Author(s):  
H. I. Miller ◽  
A. Kikuchi ◽  
H. A. Nash ◽  
R. A. Weisberg ◽  
D. I. Friedman
Keyword(s):  
Host Gene ◽  
Gene Products ◽  
Site Specific ◽  
Site Specific Recombination

Role of Gin and FIS in Site-specific Recombination

1993 ◽  
Vol 58 (0) ◽  
pp. 505-513 ◽  
Author(s):  
P. Merker ◽  
G. Muskhelishvili ◽  
A. Deufel ◽  
K. Rusch ◽  
R. Kahmann
Keyword(s):  
Site Specific ◽  
Site Specific Recombination

scholarly journals Enhancer Blocking Activity of the Insulator at H19-ICR Is Independent of Chromatin Barrier Establishment

2008 ◽  
Vol 28 (11) ◽  
pp. 3767-3775 ◽  
Author(s):  
Vikrant Singh ◽  
Madhulika Srivastava
Keyword(s):  
Histone Modifications ◽  
Regulatory Elements ◽  
Barrier Formation ◽  
Insulator Activity ◽  
Allele Specific ◽  
Chromatin Boundary ◽  
Specific Association ◽  
Silent State ◽  
Inactive Chromatin

ABSTRACT Transcriptional insulators are cis regulatory elements that organize chromatin into independently regulated domains. At the imprinted murine Igf2/H19 locus, the H19-ICR insulator prevents the activation of the Igf2 promoter on the maternal allele by enhancers that activate H19 on the same chromosome. Given the well-demonstrated role of H19-ICR as an enhancer blocker, we investigated its ability to define a chromatin barrier, as the two activities are coincident on several insulators and may act in concert to define a functional chromatin boundary between adjacent genes with distinct transcriptional profiles. Allele-specific association of posttranslationally modified histones, reflecting the presence of active or inactive chromatin, was analyzed in the region encompassing H19-ICR using chromatin immunoprecipitation. The existence of differential histone modifications upstream and downstream of H19-ICR specifically on the maternal chromosome was observed, which is suggestive of a chromatin barrier formation. However, H19-ICR deletion analysis indicated that distinct chromatin states exist despite the absence of an intervening “barrier.” Also, the enhancers can activate the Igf2 promoter despite some parts of the intervening chromatin being in the silent state. Hence, H19-ICR insulator activity is not dependent on preventing the enhancer-mediated alteration of the histone modifications in the region between the Igf2 promoter and the cognate enhancers.

scholarly journals Quantitative analysis of Histone modifications in gene silencing

2020 ◽  
Author(s):  
Kenneth Wu ◽  
Namrita Dhillon ◽  
Kelvin Du ◽  
Rohinton T. Kamakaka
Keyword(s):  
Quantitative Analysis ◽  
Gene Silencing ◽  
Transcriptional Silencing ◽  
High Fidelity ◽  
Promoter Strength ◽  
Silent Chromatin ◽  
Large Domain ◽  
Functional Consequences ◽  
Silent State ◽  
Silent Region

AbstractGene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. This transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown and we developed a method to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state. We show that loss of silencing required between 50% and 75% of the unacetylated histones to be replaced with acetylated histone mimics. The precise levels of unacetylated nucleosomes required varied from locus to locus and was influenced by both silencer strength and UAS enhancer/promoter strength. Simple calculations suggest that an approximately 50% reduction in the ability of acetylases to acetylate individual nucleosomes across a large domain may be sufficient to generate a transcriptionally silent region in the nucleus.

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