scholarly journals CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes

Cell Reports ◽  
2020 ◽  
Vol 33 (4) ◽  
pp. 108302
Author(s):  
Keerthivasan Raanin Chandradoss ◽  
Bindia Chawla ◽  
Shivnarayan Dhuppar ◽  
Rakhee Nayak ◽  
Rajesh Ramachandran ◽  
...  
Keyword(s):  
Allelic Expression ◽  
Genome Architecture ◽  
Stable Mono

Methods for mapping three-dimensional genome architecture

Methods ◽  
2020 ◽  
Vol 170 ◽  
pp. 1-3
Author(s):  
Surabhi Chowdhary ◽  
Amoldeep S. Kainth ◽  
David S. Gross
Keyword(s):  
Three Dimensional ◽  
Genome Architecture

scholarly journals Allelic expression imbalance of human mu opioid receptor (OPRM1) caused by variant A118G. VOLUME 280 (2005) PAGES 32618-32624

2005 ◽  
Vol 280 (46) ◽  
pp. 38888
Author(s):  
Ying Zhang ◽  
Danxin Wang ◽  
Andrew D. Johnson ◽  
Audrey C. Papp ◽  
Wolfgang Sadée
Keyword(s):  
Opioid Receptor ◽  
Mu Opioid Receptor ◽  
Allelic Expression ◽  
Allelic Expression Imbalance ◽  
Mu Opioid

Allelic expression imbalance refined genome-wide association signals in osteoarthritis

2021 ◽  
Vol 29 ◽  
pp. S313
Author(s):  
R.C. de Almeida ◽  
W. Den Hollander ◽  
R.R. Nelissen ◽  
L. Mei ◽  
I. Meulenbelt
Keyword(s):  
Genome Wide Association ◽  
Allelic Expression ◽  
Allelic Expression Imbalance ◽  
Genome Wide

scholarly journals GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

2021 ◽  
Author(s):  
Julia Markowski ◽  
Rieke Kempfer ◽  
Alexander Kukalev ◽  
Ibai Irastorza-Azcarate ◽  
Gesa Loof ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Embryonic Stem Cell Line ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Supplementary Information ◽  
Model Organisms ◽  
Genome Architecture ◽  
Chromatin Conformation ◽  
Haplotype Reconstruction ◽  
Allele Specific

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.

The role of Polycomb in stem cell genome architecture

2016 ◽  
Vol 43 ◽  
pp. 87-95 ◽  
Author(s):  
Gloria Mas ◽  
Luciano Di Croce
Keyword(s):  
Stem Cell ◽  
Genome Architecture ◽  
Cell Genome

scholarly journals Allelic expression imbalance of the human CYP3A4 gene and individual phenotypic status

2004 ◽  
Vol 13 (23) ◽  
pp. 2959-2969 ◽  
Author(s):  
Takeshi Hirota ◽  
Ichiro Ieiri ◽  
Hiroshi Takane ◽  
Shinji Maegawa ◽  
Masakiyo Hosokawa ◽  
...  
Keyword(s):  
Allelic Expression ◽  
Allelic Expression Imbalance ◽  
Cyp3a4 Gene
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