scholarly journals Interferon Stimulated Binding of ISRE Is Cell Type Specific and Is Predicted by Homeostatic Chromatin State

Cytokine X ◽  
2021 ◽  
pp. 100056
Author(s):  
Sivan Leviyang
Keyword(s):  
Chromatin State ◽  
Cell Type ◽  
Cell Type Specific

scholarly journals Global Mapping of H3K4me1 and H3K4me3 Reveals the Chromatin State-Based Cell Type-Specific Gene Regulation in Human Treg Cells

PLoS ONE ◽  
2011 ◽  
Vol 6 (11) ◽  
pp. e27770 ◽  
Author(s):  
Yi Tian ◽  
Zhengcai Jia ◽  
Jun Wang ◽  
Zemin Huang ◽  
Jun Tang ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Treg Cells ◽  
Chromatin State ◽  
Specific Gene ◽  
Cell Type ◽  
Global Mapping ◽  
Cell Type Specific

scholarly journals Multi-scale annotations of chromatin states in 127 human cell-types

2020 ◽  
Author(s):  
Yan Kai ◽  
Stephanos Tsoucas ◽  
Shengbao Suo ◽  
Guo-Cheng Yuan
Keyword(s):  
Human Cell ◽  
Biological Function ◽  
Cell Types ◽  
Chromatin State ◽  
Cell Type ◽  
Chromatin States ◽  
Multi Scale ◽  
Public Data ◽  
Domain State ◽  
Cell Type Specific

AbstractGenome-wide profiling of chromatin states has been widely used to characterize the biological function of non-coding genomic sequences in a cell-type specific manner. However, the systematic, comprehensive annotations of chromatin states from experimental data are challenging and require not just extensive biological knowledge but also sophisticated computational modeling. Previously we developed a hierarchical hidden Markov model, named diHMM, to systematically annotate chromatin states at multiple scales based on the combination of histone mark and chromatin regulator binding profiles. Here, we have improved the method by optimizing computational efficiency and using an ensemble-clustering approach to achieve a unified annotation by integrating information from cell-type-specific models. We then applied this improved method to generate a unified multi-scale chromatin state map in 127 human cell types, based on public data generated by the Epigenome Roadmap and ENCODE consortia. We found cell types with similar origin are typically associated with similar chromatin states, but cultured cell lines have distinct structures than primary cells. The contribution of enhancer elements to gene regulation is mediated by the broader context of domain-state organization. Distinct domain-state patterns are associated with various 3D chromatin structures. As such, we have demonstrated the utility of the multi-scale chromatin state map in characterizing the biological function of the human genome.

scholarly journals Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

2015 ◽  
Vol 25 (4) ◽  
pp. 544-557 ◽  
Author(s):  
Maxwell W. Libbrecht ◽  
Ferhat Ay ◽  
Michael M. Hoffman ◽  
David M. Gilbert ◽  
Jeffrey A. Bilmes ◽  
...  
Keyword(s):  
Chromatin State ◽  
Chromatin Conformation ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

scholarly journals Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns

2014 ◽  
Vol 111 (3) ◽  
pp. E344-E353 ◽  
Author(s):  
L. Pinello ◽  
J. Xu ◽  
S. H. Orkin ◽  
G.-C. Yuan
Keyword(s):  
Chromatin State ◽  
Cell Type ◽  
Cell Type Specific

scholarly journals Single cell epigenomic atlas of the developing human brain and organoids

2019 ◽  
Author(s):  
Ryan S. Ziffra ◽  
Chang N. Kim ◽  
Amy Wilfert ◽  
Tychele N. Turner ◽  
Maximilian Haeussler ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Cell Fate ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Chromatin State ◽  
Cell Type ◽  
Fate Specification ◽  
Cell Type Specific

AbstractDynamic changes in chromatin accessibility coincide with important aspects of neuronal differentiation, such as fate specification and arealization and confer cell type-specific associations to neurodevelopmental disorders. However, studies of the epigenomic landscape of the developing human brain have yet to be performed at single-cell resolution. Here, we profiled chromatin accessibility of >75,000 cells from eight distinct areas of developing human forebrain using single cell ATAC-seq (scATACseq). We identified thousands of loci that undergo extensive cell type-specific changes in accessibility during corticogenesis. Chromatin state profiling also reveals novel distinctions between neural progenitor cells from different cortical areas not seen in transcriptomic profiles and suggests a role for retinoic acid signaling in cortical arealization. Comparison of the cell type-specific chromatin landscape of cerebral organoids to primary developing cortex found that organoids establish broad cell type-specific enhancer accessibility patterns similar to the developing cortex, but lack many putative regulatory elements identified in homologous primary cell types. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

scholarly journals Universal annotation of the human genome through integration of over a thousand epigenomic datasets

2020 ◽  
Author(s):  
Ha Vu ◽  
Jason Ernst
Keyword(s):  
Human Genome ◽  
Large Scale ◽  
Cell Types ◽  
Chromatin State ◽  
Open Chromatin ◽  
Cell Type ◽  
Chromatin States ◽  
Modeling Approach ◽  
Cell Type Specific ◽  
Stack Model

AbstractGenome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative ‘stacked modeling’ approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges. In this paper, using a version of ChromHMM enhanced for large-scale applications, we applied the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, denoted the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we used in characterizing each state. Compared to cell-type-specific annotations, the full-stack annotation directly differentiates constitutive from cell-type-specific activity and is more predictive of locations of external genomic annotations. Overall, the full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing cell-type-specific annotations for studying the non-coding human genome.

scholarly journals Single-cell epigenomics reveals mechanisms of human cortical development

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 205-213
Author(s):  
Ryan S. Ziffra ◽  
Chang N. Kim ◽  
Jayden M. Ross ◽  
Amy Wilfert ◽  
Tychele N. Turner ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Cortical Development ◽  
Chromatin Accessibility ◽  
Chromatin State ◽  
Open Chromatin ◽  
Cell Fate Specification ◽  
Cell Type ◽  
Fate Specification ◽  
Cell Type Specific

AbstractDuring mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscape1. In the developing brain, cell fate specification and topographic identity are important for defining cell identity2 and confer selective vulnerabilities to neurodevelopmental disorders3. Here, to identify cell-type-specific chromatin accessibility patterns in the developing human brain, we used a single-cell assay for transposase accessibility by sequencing (scATAC-seq) in primary tissue samples from the human forebrain. We applied unbiased analyses to identify genomic loci that undergo extensive cell-type- and brain-region-specific changes in accessibility during neurogenesis, and an integrative analysis to predict cell-type-specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell-type-specific enhancer accessibility patterns but lack many cell-type-specific open chromatin regions that are found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells in the cerebral cortex and implicated retinoic acid signalling in the specification of neuronal lineage identity in the prefrontal cortex. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

IFIH1-deficiency results in a cell-type specific alteration of autophagic activity in response to S. typhimurium

2017 ◽  
Vol 55 (05) ◽  
pp. e28-e56
Author(s):  
S Macheiner ◽  
R Gerner ◽  
A Pfister ◽  
A Moschen ◽  
H Tilg
Keyword(s):  
Cell Type ◽  
A Cell ◽  
Cell Type Specific ◽  
Autophagic Activity ◽  
Specific Alteration
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