Parental Chromosome-specific Chromatin Conformation in the ImprintedU2af1-rs1Gene in the Mouse

Abstract Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a-priori. So far however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes. Results We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimise phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data. Availability GAMIBHEAR is available as an R package under the open source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear Maintainer [email protected] Supplementary information Supplementary information is available at Bioinformatics online.

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Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

Nature Genetics ◽

10.1038/s41588-021-00842-x ◽

2021 ◽

Vol 53 (5) ◽

pp. 650-662 ◽

Cited By ~ 1

Author(s):

Stephanie Sungalee ◽

Yuanlong Liu ◽

Ruxandra A. Lambuta ◽

Natalya Katanayeva ◽

Maria Donaldson Collier ◽

...

Keyword(s):

Histone Acetylation ◽

Chromatin Conformation ◽

Specific Interactions ◽

Allele Specific

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Distribution of X-ray-induced G2 chromatid damage among Chinese hamster chromosomes: influence of chromatin conformation

Mutation Research Letters ◽

10.1016/0165-7992(94)90084-1 ◽

1994 ◽

Vol 323 (3) ◽

pp. 113-119 ◽

Cited By ~ 35

Author(s):

P. Slijepcevic ◽

A.T. Natarajan

Keyword(s):

Chinese Hamster ◽

Chromatin Conformation ◽

X Ray

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Long-Distance Control of Origin Choice and Replication Timing in the Human β-Globin Locus Are Independent of the Locus Control Region

Molecular and Cellular Biology ◽

10.1128/mcb.20.15.5581-5591.2000 ◽

2000 ◽

Vol 20 (15) ◽

pp. 5581-5591 ◽

Cited By ~ 75

Author(s):

Daniel M. Cimbora ◽

Dirk Schübeler ◽

Andreas Reik ◽

Joan Hamilton ◽

Claire Francastel ◽

...

Keyword(s):

Gene Expression ◽

Control Region ◽

Globin Gene ◽

Replication Timing ◽

S Phase ◽

Chromatin Conformation ◽

Erythroid Cells ◽

Long Distance ◽

Targeted Deletion ◽

Globin Gene Expression

ABSTRACT DNA replication in the human β-globin locus is subject to long-distance regulation. In murine and human erythroid cells, the human locus replicates in early S phase from a bidirectional origin located near the β-globin gene. This Hispanic thalassemia deletion removes regulatory sequences located over 52 kb from the origin, resulting in replication of the locus from a different origin, a shift in replication timing to late S phase, adoption of a closed chromatin conformation, and silencing of globin gene expression in murine erythroid cells. The sequences deleted include nuclease-hypersensitive sites 2 to 5 (5′HS2-5) of the locus control region (LCR) plus an additional 27-kb upstream region. We tested a targeted deletion of 5′HS2-5 in the normal chromosomal context of the human β-globin locus to determine the role of these elements in replication origin choice and replication timing. We demonstrate that the 5′HS2-5-deleted locus initiates replication at the appropriate origin and with normal timing in murine erythroid cells, and therefore we conclude that 5′HS2-5 in the classically defined LCR do not control replication in the human β-globin locus. Recent studies also show that targeted deletion of 5′HS2-5 results in a locus that lacks globin gene expression yet retains an open chromatin conformation. Thus, the replication timing of the locus is closely correlated with nuclease sensitivity but not globin gene expression.

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Altered chromatin conformation of the higher plant gene phaseolin

Biochemistry ◽

10.1021/bi00313a032 ◽

1984 ◽

Vol 23 (18) ◽

pp. 4225-4232 ◽

Cited By ~ 44

Author(s):

Michael G. Murray ◽

Wayne C. Kennard

Keyword(s):

Chromatin Conformation ◽

Higher Plant ◽

Plant Gene

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Pea–Fusarium solani Interactions Contributions of a System Toward Understanding Disease Resistance

Phytopathology ◽

10.1094/phyto-98-4-0372 ◽

2008 ◽

Vol 98 (4) ◽

pp. 372-379 ◽

Cited By ~ 42

Author(s):

Lee A. Hadwiger

Keyword(s):

Immune Response ◽

Transcription Factor ◽

Disease Resistance ◽

Fusarium Solani ◽

Nonhost Resistance ◽

Chromatin Conformation ◽

Resistance Response ◽

Resistance Components ◽

Pathogenesis Related ◽

Molecular Aspects

This mini-review points to the usefulness of the pea–Fusarium solani interaction in researching the biochemical and molecular aspects of the nonhost resistance components of peas. This interaction has been researched to evaluate the resistance roles of the phytoalexin, pisatin, the cuticle barrier, and the activation of the nonhost resistance response. Concurrently, evaluations of associated signaling processes and the tools possessed by the pathogen to contend with host obstacles were included. The properties of some pathogenesis-related genes of pea and their regulation and contribution to resistance are discussed. A proposed action of two biotic elicitors on both chromatin conformation and the architectural transcription factor, HMG A, is presented and includes time lines of events within the host immune response.

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Functional annotation of human long noncoding RNAs using chromatin conformation data

10.1101/2021.01.13.426305 ◽

2021 ◽

Author(s):

Saumya Agrawal ◽

Tanvir Alam ◽

Masaru Koido ◽

Ivan V. Kulakovskiy ◽

Jessica Severin ◽

...

Keyword(s):

Functional Annotation ◽

Rna Binding ◽

Functional Characterization ◽

Cell Types ◽

Chromatin Interaction ◽

Spatial Proximity ◽

Chromatin Conformation ◽

Cell Type ◽

Cell Type Specific ◽

Rna Domains

AbstractTranscription of the human genome yields mostly long non-coding RNAs (lncRNAs). Systematic functional annotation of lncRNAs is challenging due to their low expression level, cell type-specific occurrence, poor sequence conservation between orthologs, and lack of information about RNA domains. Currently, 95% of human lncRNAs have no functional characterization. Using chromatin conformation and Cap Analysis of Gene Expression (CAGE) data in 18 human cell types, we systematically located genomic regions in spatial proximity to lncRNA genes and identified functional clusters of interacting protein-coding genes, lncRNAs and enhancers. Using these clusters we provide a cell type-specific functional annotation for 7,651 out of 14,198 (53.88%) lncRNAs. LncRNAs tend to have specialized roles in the cell type in which it is first expressed, and to incorporate more general functions as its expression is acquired by multiple cell types during evolution. By analyzing RNA-binding protein and RNA-chromatin interaction data in the context of the spatial genomic interaction map, we explored mechanisms by which these lncRNAs can act.

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