Results 61 to 70 of about 6,238 (235)

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains [PDF]

Frontiers in Genetics, 2020
Recent research using chromatin conformation capture technologies, such as Hi-C, has demonstrated the importance of topologically associated domains (TADs) and smaller chromatin loops, collectively referred hereafter as "interacting domains." Many such domains change during development or disease, and exhibit cell- and condition-specific differences ...
Kellen G. Cresswell, Mikhail G. Dozmorov
openaire   +3 more sources

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

Genome Biology, 2017
Background The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns.
Kevin Van Bortle, Douglas H. Phanstiel, Michael P. Snyder   +2 more
doaj   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

Using LDpred2 to adapt polygenic risk score techniques for methylation score creation

BMC Research Notes
Objective This study sought to determine if the R package LDpred2, designed for polygenic risk score creation for genome-wide association studies using summary statistics, could be adapted for deriving DNA methylation scores from methylome-wide ...
Kristoffer Sandås, Leticia Spindola, Solveig Løkhammer, Anne-Kristin Stavrum, Ole Andreassen, Markos Tesfaye, Stéphanie Le Hellard   +6 more
doaj   +1 more source

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains

Nature Communications, 2017
Proximity-ligation methods like Hi-C map DNA-DNA interactions and reveal its organization into topologically associating domains (TADs). Here the authors describe PSYCHIC, a computational approach for analysing Hi-C data that allows the identification of
Gil Ron, Yuval Globerson, Dror Moran, Tommy Kaplan   +3 more
doaj   +1 more source

Effectiveness of rTMS on Working Memory and Inhibitory Impairments in Patients With Post‐Stroke Executive Deficits

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Considerable efforts have been dedicated to developing effective treatments for post‐stroke executive impairment (PSEI), among which repetitive transcranial magnetic stimulation (rTMS) has shown great potential. This study aimed to investigate the therapeutic effects of high‐frequency rTMS on working memory (WM) and response ...
Mengting Lao, Rongwei Du, Zhujun Wang, Yang Gao, Meiling Cheng, Xianglong Wang, Wen Wu   +6 more
wiley   +1 more source

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Nature Communications, 2018
Although topologically associating domains (TADs) have been extensively investigated, it is not clear to what extent DNA sequence contributes to their formation.
Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke   +8 more
doaj   +1 more source

Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. [PDF]

Cell Rep, 2018
Expression of vast repertoires of antigen receptors by lymphocytes, with each cell expressing a single receptor, requires stochastic activation of individual variable (V) genes for transcription and recombination. How this occurs remains unknown. Using single-cell RNA sequencing (scRNA-seq) and allelic variation, we show that individual pre-B cells ...
Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR.   +15 more
europepmc   +5 more sources

Unraveling 4‐Phenylbutyrate's Therapeutic Role in SLC6A1 Disorders: Pharmacochaperoning Over HDAC Inhibition

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Variants in SLC6A1, encoding the GABA transporter 1 (GAT‐1), cause epilepsy, autism spectrum disorder, and developmental delay via loss of GABA uptake, impaired trafficking, and ER retention. We previously found that 4‐Phenylbutyrate (PBA), an FDA‐approved drug, restores GABA uptake and reduces seizures in SLC6A1‐related disorders ...
Melissa B. DeLeeuw, Karishma Randhave, Ekta Anand, Ziang (Debbie) Song, Wangzhen Shen, Jing‐Qiong Kang   +5 more
wiley   +1 more source

Molecular basis of CTCF binding polarity in genome folding

Nature Communications, 2020
The boundaries of topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin.
Elphège P. Nora, Laura Caccianini, Geoffrey Fudenberg, Kevin So, Vasumathi Kameswaran, Abigail Nagle, Alec Uebersohn, Bassam Hajj, Agnès Le Saux, Antoine Coulon, Leonid A. Mirny, Katherine S. Pollard, Maxime Dahan, Benoit G. Bruneau   +13 more
doaj   +1 more source