GC content strongly influences the role of poly(dA) in the intrinsic nucleosome positioning in Saccharomyces cerevisiae.
Sign Up to like & getrecommendations! Published in 2022 at "Yeast"
DOI: 10.1002/yea.3701
Abstract: The nucleosome is the basic structural element of genomic DNA packaging and plays a role in transcription, replication, and recombination. Poly(dA) tracts are considered major sequence determinants of nucleosome positioning, although their role is not… read more here.
Keywords: nucleosome positioning; saccharomyces cerevisiae; intrinsic nucleosome; role ... See more keywords
Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8657-6_21
Abstract: The precise positioning of nucleosomes along the underlying DNA is critical for a variety of biological processes, especially in regulating transcription. The interplay between nucleosomes and transcription factors for accessing the underlying DNA sequences is… read more here.
Keywords: mnase seq; mapping nucleosome; nucleosome positioning; mnase ... See more keywords
Chd1p recognizes H3K36Ac to maintain nucleosome positioning near the transcription start site.
Sign Up to like & getrecommendations! Published in 2018 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2018.07.025
Abstract: In Saccharomyces cerevisiae, the ATP-dependent chromatin remodeler, Chd1p, globally affects nucleosome positioning at coding regions, where nucleosomes are specifically and directionally aligned with respect to the transcription start site (TSS). Various auxiliary domains of remodelers… read more here.
Keywords: start site; chd1p; h3k36ac; transcription start ... See more keywords
Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation.
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DOI: 10.1038/s41422-022-00652-8
Abstract: Chromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using… read more here.
Keywords: genome; nucleosome positioning; fertilization; genome activation ... See more keywords
Nucleosomal organization and DNA base composition patterns
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DOI: 10.1080/19491034.2017.1337611
Abstract: ABSTRACT Nucleosomes are the basic units of chromatin. They compact the genome inside the nucleus and regulate the access of proteins to DNA. In the yeast genome, most nucleosomes occupy well-defined positions, which are maintained… read more here.
Keywords: nucleosomal organization; base composition; nucleosome positioning; dna ... See more keywords
LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks
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DOI: 10.1093/bioinformatics/bty003
Abstract: Motivation: Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome‐wide nucleosome occupancy profiles… read more here.
Keywords: dna sequences; positioning; convolutional neural; lenup learning ... See more keywords
The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac826
Abstract: Abstract Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically… read more here.
Keywords: positioning transcription; swi snf; transcription; nucleosome positioning ... See more keywords
Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms
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DOI: 10.1186/s12859-021-04006-w
Abstract: Background Nucleosome plays an important role in the process of genome expression, DNA replication, DNA repair and transcription. Therefore, the research of nucleosome positioning has invariably received extensive attention. Considering the diversity of DNA sequence… read more here.
Keywords: machine; feature; analysis; nucleosome positioning ... See more keywords
DeepNup: Prediction of Nucleosome Positioning from DNA Sequences Using Deep Neural Network
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DOI: 10.3390/genes13111983
Abstract: Nucleosome positioning is involved in diverse cellular biological processes by regulating the accessibility of DNA sequences to DNA-binding proteins and plays a vital role. Previous studies have manifested that the intrinsic preference of nucleosomes for… read more here.
Keywords: dna sequences; nucleosome positioning; positioning dna; prediction nucleosome ... See more keywords
Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome
Sign Up to like & getrecommendations! Published in 2022 at "Life"
DOI: 10.3390/life12040541
Abstract: Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of… read more here.
Keywords: positioning; genome; chromosome; nucleosome positioning ... See more keywords