scholarly journals Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

Science ◽  
2013 ◽  
Vol 342 (6159) ◽  
pp. 744-747 ◽  
Author(s):  
H. Kilpinen ◽  
S. M. Waszak ◽  
A. R. Gschwind ◽  
S. K. Raghav ◽  
R. M. Witwicki ◽  
...  
Keyword(s):  
Dna Binding ◽  
Chromatin Structure ◽  
Sequence Variation ◽  
Coordinated Effects

Methylated DNA-binding proteins and chromatin structure

1993 ◽  
pp. 377-389
Author(s):  
R. Meehan ◽  
P. Jeppesen ◽  
J. Lewis ◽  
A. Bird
Keyword(s):  
Dna Binding ◽  
Chromatin Structure ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Methylated Dna

scholarly journals Genetic and epigenetic control of the spatial organization of the genome

2017 ◽  
Vol 28 (3) ◽  
pp. 364-369 ◽  
Author(s):  
Jason Brickner
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Chromatin Structure ◽  
Binding Sites ◽  
Spatial Organization ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Adaptive Function ◽  
Nuclear Structures ◽  
Eukaryotic Genomes

Eukaryotic genomes are spatially organized within the nucleus by chromosome folding, interchromosomal contacts, and interaction with nuclear structures. This spatial organization is observed in diverse organisms and both reflects and contributes to gene expression and differentiation. This leads to the notion that the arrangement of the genome within the nucleus has been shaped and conserved through evolutionary processes and likely plays an adaptive function. Both DNA-binding proteins and changes in chromatin structure influence the positioning of genes and larger domains within the nucleus. This suggests that the spatial organization of the genome can be genetically encoded by binding sites for DNA-binding proteins and can also involve changes in chromatin structure, potentially through nongenetic mechanisms. Here I briefly discuss the results that support these ideas and their implications for how genomes encode spatial organization.

scholarly journals The DNA Binding and Catalytic Domains of Poly(ADP-Ribose) Polymerase 1 Cooperate in the Regulation of Chromatin Structure and Transcription

2007 ◽  
Vol 27 (21) ◽  
pp. 7475-7485 ◽  
Author(s):  
David A. Wacker ◽  
Donald D. Ruhl ◽  
Ehsan H. Balagamwala ◽  
Kristine M. Hope ◽  
Tong Zhang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Enzymatic Activity ◽  
Chromatin Structure ◽  
Transcriptional Repression ◽  
Catalytic Domain ◽  
Vitro Assay ◽  
Chromatin Compaction ◽  
Amino Terminal ◽  
Nucleosome Binding ◽  
Parp 1

ABSTRACT We explored the mechanisms of chromatin compaction and transcriptional regulation by poly(ADP-ribose) polymerase 1 (PARP-1), a nucleosome-binding protein with an NAD+-dependent enzymatic activity. By using atomic force microscopy and a complementary set of biochemical assays with reconstituted chromatin, we showed that PARP-1 promotes the localized compaction of chromatin into supranucleosomal structures in a manner independent of the amino-terminal tails of core histones. In addition, we defined the domains of PARP-1 required for nucleosome binding, chromatin compaction, and transcriptional repression. Our results indicate that the DNA binding domain (DBD) of PARP-1 is necessary and sufficient for binding to nucleosomes, yet the DBD alone is unable to promote chromatin compaction and only partially represses RNA polymerase II-dependent transcription in an in vitro assay with chromatin templates (∼50% of the repression observed with wild-type PARP-1). Furthermore, our results show that the catalytic domain of PARP-1, which does not bind nucleosomes on its own, cooperates with the DBD to promote chromatin compaction and efficient transcriptional repression in a manner independent of its enzymatic activity. Collectively, our results have revealed a novel function for the catalytic domain in chromatin compaction. In addition, they show that the DBD and catalytic domain cooperate to regulate chromatin structure and chromatin-dependent transcription, providing mechanistic insights into how these domains contribute to the chromatin-dependent functions of PARP-1.

scholarly journals Targeted Recruitment of the Sin3-Rpd3 Histone Deacetylase Complex Generates a Highly Localized Domain of Repressed Chromatin In Vivo

1998 ◽  
Vol 18 (9) ◽  
pp. 5121-5127 ◽  
Author(s):  
David Kadosh ◽  
Kevin Struhl
Keyword(s):  
Dna Binding ◽  
Histone Deacetylase ◽  
Chromatin Structure ◽  
Transcriptional Repression ◽  
Dna Binding Proteins ◽  
Histone Deacetylation ◽  
Yeast Cells ◽  
Multiprotein Complex ◽  
Eukaryotic Organisms

ABSTRACT Eukaryotic organisms contain a multiprotein complex that includes Rpd3 histone deacetylase and the Sin3 corepressor. The Sin3-Rpd3 complex is recruited to promoters by specific DNA-binding proteins, whereupon it represses transcription. By directly analyzing the chromatin structure of a repressed promoter in yeast cells, we demonstrate that transcriptional repression is associated with localized histone deacetylation. Specifically, we observe decreased acetylation of histones H3 and H4 (preferentially lysines 5 and 12) that depends on the DNA-binding repressor (Ume6), Sin3, and Rpd3. Mapping experiments indicate that the domain of histone deacetylation is highly localized, occurring over a range of one to two nucleosomes. Taken together with previous observations, these results define a novel mechanism of transcriptional repression which involves targeted recruitment of a histone-modifying activity and localized perturbation of chromatin structure.

Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro

2004 ◽  
Vol 322 (1) ◽  
pp. 110-118 ◽  
Author(s):  
Andrea K. Robertson ◽  
Theresa M. Geiman ◽  
Umesh T. Sankpal ◽  
Gordon L. Hager ◽  
Keith D. Robertson
Keyword(s):  
Dna Binding ◽  
Chromatin Structure ◽  
Dna Methyltransferases

scholarly journals Probing the Functional Impact of Sequence Variation on p53-DNA Interactions Using a Novel Microsphere Assay for Protein-DNA Binding with Human Cell Extracts

PLoS Genetics ◽  
2009 ◽  
Vol 5 (5) ◽  
pp. e1000462 ◽  
Author(s):  
Maher A. Noureddine ◽  
Daniel Menendez ◽  
Michelle R. Campbell ◽  
Omari J. Bandele ◽  
Monica M. Horvath ◽  
...  
Keyword(s):  
Dna Binding ◽  
Human Cell ◽  
Sequence Variation ◽  
Dna Interactions ◽  
Functional Impact ◽  
Cell Extracts

scholarly journals Transcriptional re-wiring by mutation of the yeast Hsf1 oligomerization domain

2020 ◽  
Author(s):  
Elizabeth A. Morton ◽  
Michael W. Dorrity ◽  
Wei Zhou ◽  
Stanley Fields ◽  
Christine Queitsch
Keyword(s):  
Heat Stress ◽  
Dna Binding ◽  
Sequence Variation ◽  
Heat Shock Transcription Factors ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Specificity ◽  
Evolutionarily Conserved ◽  
Oligomerization Domain

AbstractResponse to heat stress is mediated by heat shock transcription factors (HSFs), which possess conserved DNA-binding and oligomerization domains. The oligomerization domain is required for HSF1 to transition under heat stress from a monomer to a homotrimer, which alters DNA-binding specificity and affinity. Sequence variation in the oligomerization domain affects HSF1 activity, although this link is poorly understood. We performed a deep mutational scan of >400,000 variants of the oligomerization domain of Saccharomyces cerevisiae Hsf1 and measured fitness under stress and non-stress conditions. We identify mutations that confer temperature-specific phenotypes; some exceptional Hsf1variants lead to enhanced growth under heat stress and changes to in vivo DNA-binding and transcriptional programs. The link between Hsf1 oligomerization and DNA-binding domain is evolutionarily conserved, with co-evolving residues between these domains found among fungi. Mutation of transcription factor oligomerization domains may represent a path toward re-wiring transcriptional programs without mutation of DNA-binding domains.

scholarly journals PO-464 Influence of natural DNA-binding compounds with cancer preventive activity on chromatin structure

2018 ◽  
Author(s):  
O Vlasova ◽  
V Maksimova ◽  
A Safina ◽  
G Belitsky ◽  
K Gurova ◽  
...  
Keyword(s):  
Dna Binding ◽  
Chromatin Structure ◽  
Preventive Activity
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