scholarly journals Non-B-form DNA structures mark centromeres

2017 ◽  
Author(s):  
Sivakanthan Kasinathan ◽  
Steven Henikoff
Keyword(s):  
Dna Binding ◽  
Satellite Dna ◽  
Binding Sites ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Genetic Characteristics ◽  
Dna Structures ◽  
Centromere Function ◽  
General Basis ◽  
Human And Mouse

AbstractAnimal and plant centromeres are embedded in repetitive “satellite” DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in <10-bp dyad symmetries predicted to adopt non-B-form conformations. Organisms lacking centromeric dyad symmetries had binding sites for sequence-specific DNA binding proteins with DNA bending activity. For example, human and mouse centromeres are depleted for dyad symmetries, but are enriched for non-B DNA and are associated with binding sites for the conserved DNA-binding protein CENP-B, which is required for artificial centromere function but is paradoxically non-essential. We also detected dyad symmetries and predicted non-B-form DNA structures at neocentromeres, which form at ectopic loci. We propose that centromeres form at non-B-form DNA because of dyad symmetries or are strengthened by sequence-specific DNA binding proteins. Our findings resolve the CENP-B paradox and provide a general basis for centromere specification.

scholarly journals Non-B-Form DNA Is Enriched at Centromeres

2018 ◽  
Vol 35 (4) ◽  
pp. 949-962 ◽  
Author(s):  
Sivakanthan Kasinathan ◽  
Steven Henikoff
Keyword(s):  
Dna Binding ◽  
Satellite Dna ◽  
Binding Sites ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Genetic Characteristics ◽  
Dna Structures ◽  
Centromere Function ◽  
General Basis ◽  
Human And Mouse

AbstractAnimal and plant centromeres are embedded in repetitive “satellite” DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in <10-bp dyad symmetries predicted to adopt non-B-form conformations. Organisms lacking centromeric dyad symmetries had binding sites for sequence-specific DNA-binding proteins with DNA-bending activity. For example, human and mouse centromeres are depleted for dyad symmetries, but are enriched for non-B-form DNA and are associated with binding sites for the conserved DNA-binding protein CENP-B, which is required for artificial centromere function but is paradoxically nonessential. We also detected dyad symmetries and predicted non-B-form DNA structures at neocentromeres, which form at ectopic loci. We propose that centromeres form at non-B-form DNA because of dyad symmetries or are strengthened by sequence-specific DNA binding proteins. This may resolve the CENP-B paradox and provide a general basis for centromere specification.

scholarly journals The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA

2020 ◽  
Vol 48 (19) ◽  
pp. 10820-10831
Author(s):  
Kiyoto Kamagata ◽  
Kana Ouchi ◽  
Cheng Tan ◽  
Eriko Mano ◽  
Sridhar Mandali ◽  
...  
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Binding Modes ◽  
Dna Structures ◽  
Bacterial Proteins ◽  
Associated Proteins ◽  
Diffusion Mechanisms ◽  
Dynamics Simulations

Abstract DNA binding proteins rapidly locate their specific DNA targets through a combination of 3D and 1D diffusion mechanisms, with the 1D search involving bidirectional sliding along DNA. However, even in nucleosome-free regions, chromosomes are highly decorated with associated proteins that may block sliding. Here we investigate the ability of the abundant chromatin-associated HMGB protein Nhp6A from Saccharomyces cerevisiae to travel along DNA in the presence of other architectural DNA binding proteins using single-molecule fluorescence microscopy. We observed that 1D diffusion by Nhp6A molecules is retarded by increasing densities of the bacterial proteins Fis and HU and by Nhp6A, indicating these structurally diverse proteins impede Nhp6A mobility on DNA. However, the average travel distances were larger than the average distances between neighboring proteins, implying Nhp6A is able to bypass each of these obstacles. Together with molecular dynamics simulations, our analyses suggest two binding modes: mobile molecules that can bypass barriers as they seek out DNA targets, and near stationary molecules that are associated with neighboring proteins or preferred DNA structures. The ability of mobile Nhp6A molecules to bypass different obstacles on DNA suggests they do not block 1D searches by other DNA binding proteins.

scholarly journals Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins

2007 ◽  
Vol 36 (1) ◽  
pp. e8-e8 ◽  
Author(s):  
Jue Zeng ◽  
Jizhou Yan ◽  
Ting Wang ◽  
Deborah Mosbrook-Davis ◽  
Kyle T. Dolan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Binding Proteins ◽  
Target Genes ◽  
Dna Binding Proteins ◽  
Genome Wide ◽  
Potential Binding

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 Combgap contributes to recruitment of Polycomb group proteins in Drosophila

2016 ◽  
Vol 113 (14) ◽  
pp. 3826-3831 ◽  
Author(s):  
Payal Ray ◽  
Sandip De ◽  
Apratim Mitra ◽  
Karel Bezstarosti ◽  
Jeroen A. A. Demmers ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Developmentally Regulated ◽  
Polycomb Response Elements ◽  
Protein Recruitment ◽  
Polycomb Repressive Complex 1 ◽  
Transcriptional State

Polycomb group (PcG) proteins are responsible for maintaining the silenced transcriptional state of many developmentally regulated genes. PcG proteins are organized into multiprotein complexes that are recruited to DNA via cis-acting elements known as “Polycomb response elements” (PREs). In Drosophila, PREs consist of binding sites for many different DNA-binding proteins, some known and others unknown. Identification of these DNA-binding proteins is crucial to understanding the mechanism of PcG recruitment to PREs. We report here the identification of Combgap (Cg), a sequence-specific DNA-binding protein that is involved in recruitment of PcG proteins. Cg can bind directly to PREs via GTGT motifs and colocalizes with the PcG proteins Pleiohomeotic (Pho) and Polyhomeotic (Ph) at the majority of PREs in the genome. In addition, Cg colocalizes with Ph at a number of targets independent of Pho. Loss of Cg leads to decreased recruitment of Ph at only a subset of sites; some of these sites are binding sites for other Polycomb repressive complex 1 (PRC1) components, others are not. Our data suggest that Cg can recruit Ph in the absence of PRC1 and illustrate the diversity and redundancy of PcG protein recruitment mechanisms.

DISPOM: A DISCRIMINATIVE DE-NOVO MOTIF DISCOVERY TOOL BASED ON THE JSTACS LIBRARY

2013 ◽  
Vol 11 (01) ◽  
pp. 1340006 ◽  
Author(s):  
JAN GRAU ◽  
JENS KEILWAGEN ◽  
ANDRÉ GOHR ◽  
IVAN A. PAPONOV ◽  
STEFAN POSCH ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Motif Discovery ◽  
Binding Proteins ◽  
Target Genes ◽  
De Novo ◽  
Specific Binding ◽  
Dna Binding Proteins ◽  
De Novo Motif Discovery

DNA-binding proteins are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in target regions of genomic DNA. However, de-novo discovery of these binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not yet been solved satisfactorily. Here, we present a detailed description and analysis of the de-novo motif discovery tool Dispom, which has been developed for finding binding sites of DNA-binding proteins that are differentially abundant in a set of target regions compared to a set of control regions. Two additional features of Dispom are its capability of modeling positional preferences of binding sites and adjusting the length of the motif in the learning process. Dispom yields an increased prediction accuracy compared to existing tools for de-novo motif discovery, suggesting that the combination of searching for differentially abundant motifs, inferring their positional distributions, and adjusting the motif lengths is beneficial for de-novo motif discovery. When applying Dispom to promoters of auxin-responsive genes and those of ABI3 target genes from Arabidopsis thaliana, we identify relevant binding motifs with pronounced positional distributions. These results suggest that learning motifs, their positional distributions, and their lengths by a discriminative learning principle may aid motif discovery from ChIP-chip and gene expression data. We make Dispom freely available as part of Jstacs, an open-source Java library that is tailored to statistical sequence analysis. To facilitate extensions of Dispom, we describe its implementation using Jstacs in this manuscript. In addition, we provide a stand-alone application of Dispom at http://www.jstacs.de/index.php/Dispom for instant use.

scholarly journals The modular mechanism of chromocenter formation in Drosophila

2018 ◽  
Author(s):  
Madhav Jagannathan ◽  
Ryan Cummings ◽  
Yukiko M. Yamashita
Keyword(s):  
Dna Binding ◽  
Satellite Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Dna Repeats ◽  
Satellite Dnas ◽  
Modular Network ◽  
Full Complement ◽  
Single Nucleus ◽  
Nuclear Structures

AbstractA central principle underlying the ubiquity and abundance of pericentromeric satellite DNA repeats in eukaryotes has remained poorly understood. In our previous study (Jagannathan et al., 2018), we proposed that the interchromosomal clustering of satellite DNAs into nuclear structures known as chromocenters ensures encapsulation of all chromosomes into a single nucleus. Chromocenter disruption led to micronuclei formation, resulting in cell death. Here we show that chromocenter formation is mediated by a ‘modular’ network, where interactions between two sequence-specific satellite DNA-binding proteins, D1 and Prod, bound to their cognate satellite DNAs, bring the full complement of chromosomes into the chromocenter. D1 prod double mutants die during embryogenesis, exhibiting enhanced phenotypes associated with chromocenter disruption, revealing the universal importance of satellite DNAs and chromocenters. Taken together, we propose that interactions between chromocenter modules, consisting of satellite DNA binding proteins and their cognate satellite DNA, package the Drosophila genome within a single nucleus.

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