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   Articles with "chromatin state" as a keyword



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Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch.

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recommendations! Published in 2018 at "Journal of molecular biology"

DOI: 10.1016/j.jmb.2018.08.021

Abstract: Polycomb group proteins play essential roles in transcriptional gene repression during both animal and plant development. Polycomb repression complex 1 (PRC1) is one of the key functional modules in polycomb group silencing. It acts as… read more here.

Keywords: al2; chromatin state; chromatin; state switch ... See more keywords
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A Homeostatic Arid1a-Dependent Permissive Chromatin State Licenses Hepatocyte Responsiveness to Liver-Injury-Associated YAP Signaling.

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recommendations! Published in 2019 at "Cell stem cell"

DOI: 10.1016/j.stem.2019.06.008

Abstract: Following injury, differentiated epithelial cells can serve as a stem cell-independent source for tissue regeneration by undergoing reprogramming into other cell types. The intrinsic molecular basis underlying plasticity of differentiated cells remains largely unaddressed. Here… read more here.

Keywords: chromatin state; regeneration; liver injury; permissive chromatin ... See more keywords
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Multi-scale chromatin state annotation using a hierarchical hidden Markov model

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recommendations! Published in 2017 at "Nature Communications"

DOI: 10.1038/ncomms15011

Abstract: Chromatin-state analysis is widely applied in the studies of development and diseases. However, existing methods operate at a single length scale, and therefore cannot distinguish large domains from isolated elements of the same type. To… read more here.

Keywords: state; hidden markov; chromatin state; markov model ... See more keywords
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Computational methods to explore chromatin state dynamics

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recommendations! Published in 2022 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbac439

Abstract: Abstract The human genome is marked by several singular and combinatorial histone modifications that shape the different states of chromatin and its three-dimensional organization. Genome-wide mapping of these marks as well as histone variants and… read more here.

Keywords: explore chromatin; chromatin state; computational methods; methods explore ... See more keywords
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Continuous chromatin state feature annotation of the human epigenome.

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac283

Abstract: MOTIVATION Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These methods take as input a set of sequencing-based assays of epigenomic activity, such as ChIP-seq measurements of… read more here.

Keywords: chromatin state; epigenome ssm; state features; annotation ... See more keywords
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A framework for group-wise summarization and comparison of chromatin state annotations

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac722

Abstract: Abstract Motivation Genome-wide maps of epigenetic modifications are powerful resources for non-coding genome annotation. Maps of multiple epigenetics marks have been integrated into cell or tissue type-specific chromatin state annotations for many cell or tissue… read more here.

Keywords: state; chromatin state; state maps; group ... See more keywords
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Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation

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recommendations! Published in 2017 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkx884

Abstract: Abstract Transposable elements, including endogenous retroviruses (ERVs), constitute a large fraction of the mammalian genome. They are transcriptionally silenced during early development to protect genome integrity and aberrant transcription. However, the mechanisms that control their… read more here.

Keywords: rif1; chromatin state; promotes repressive; activation ... See more keywords
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EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences

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recommendations! Published in 2019 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkz287

Abstract: Abstract The availability of genome-wide epigenomic datasets enables in-depth studies of epigenetic modifications and their relationships with chromatin structures and gene expression. Various alignment tools have been developed to align nucleotide or protein sequences in… read more here.

Keywords: state sequences; chromatin state; chromatin; alignment ... See more keywords
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Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster

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recommendations! Published in 2022 at "PLOS Genetics"

DOI: 10.1101/2022.09.26.509449

Abstract: We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred… read more here.

Keywords: atac seq; chromatin state; chromatin; tissues drosophila ... See more keywords
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Chromatin state dictates drug response.

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recommendations! Published in 2017 at "Science"

DOI: 10.1126/science.355.6331.1277-p

Abstract: Cancer Therapy Drugs inhibiting the phosphoinositide-(3)-kinase (PI3K) signaling pathway are effective in a subset of breast cancer patients. Tumors become resistant to these drugs, however, and this transition is often accompanied by increased transcription of… read more here.

Keywords: drug; state dictates; estrogen receptor; chromatin state ... See more keywords
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Abstract IA20: Chromatin state and scRNA-seq analysis defines a common differentiation trajectory towards T-cell exhaustion

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recommendations! Published in 2020 at "Cancer immunology research"

DOI: 10.1158/2326-6074.tumimm19-ia20

Abstract: We will describe a unified chromatin state and single cell expression analysis underlying T-cell differentiation to “exhaustion.” Numerous studies in chronic viral infection and tumor models have shown that most T cells progress to a… read more here.

Keywords: state; chromatin state; analysis; differentiation ... See more keywords