Results 31 to 40 of about 1,018,957 (214)

Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation. [PDF]

Nucleic Acids Res
Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative ...
Mulero-Hernández J, Mironov V, Miñarro-Giménez JA, Kuiper M, Fernández-Breis JT.   +4 more
europepmc   +2 more sources

A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. [PDF]

Nat Commun
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy.
Xu J, Xu X, Huang D, Luo Y, Lin L, Bai X, Zheng Y, Yang Q, Cheng Y, Huang A, Shi J, Bo X, Gu J, Chen H.   +13 more
europepmc   +2 more sources

Three‐dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development

Clinical and Translational Medicine, 2022
Background During meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three‐dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood.
Geng G. Tian, Changliang Hou, Jing Li, Ji Wu   +3 more
doaj   +1 more source

Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk

, 2023
<p>Codes for reproducing results in the manuscript "Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk".</p ...
Honda, Kurara, Takata, Atsushi, Kazuno, An-a, Nakamura, Takumi, Mizuno, Shota, Ueda, Junko, Hara, Tomonori, Yamamoto, Hirona   +7 more
core   +1 more source

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

Stem Cell Reports, 2019
Summary: During mammalian embryogenesis, changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the preimplantation blastocyst (naive) and postimplantation epiblast (primed ...
Stephanie L. Battle, Naresh Doni Jayavelu, Robert N. Azad, Jennifer Hesson, Faria N. Ahmed, Eliah G. Overbey, Joseph A. Zoller, Julie Mathieu, Hannele Ruohola-Baker, Carol B. Ware, R. David Hawkins   +10 more
doaj   +1 more source

Utilization of Host Cell Chromosome Conformation by Viral Pathogens: Knowing When to Hold and When to Fold

Frontiers in Immunology, 2021
Though viruses have their own genomes, many depend on the nuclear environment of their hosts for replication and survival. A substantial body of work has therefore been devoted to understanding how viral and eukaryotic genomes interact.
Kinjal Majumder, Abigail J. Morales
doaj   +1 more source

Mapping chromosome neighborhoods

BioTechniques, 2015
The discovery of topologically associating domains (TADs) changed the way researchers think about gene expression and chromosome structure. Jeffrey Perkel takes a closer look into these “chromosome neighborhoods.”
Jeffrey Perkel
doaj   +1 more source

HiCmapTools: a tool to access HiC contact maps

BMC Bioinformatics, 2022
Background With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to
Jia-Ming Chang, Yi-Fu Weng, Wei-Ting Chang, Fu-An Lin, Giacomo Cavalli   +4 more
doaj   +1 more source

Methods for the Analysis of Topologically Associating Domains (TADs)

, 2021
Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus ...
Giovanni Ciriello, Tavernari, D., Zufferey, M., Ciriello, G., Marie Zufferey, Daniele Tavernari   +5 more
core   +1 more source

Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers

Nature Communications, 2022
Identifying structural variants (SVs) under positive selection in cancer is challenging. Here, the authors develop CSVDriver, a method that computes SV breakpoint proximity and the contribution of elements such as topologically associating domains, and ...
Alexander Martinez-Fundichely, Austin Dixon, Ekta Khurana   +2 more
doaj   +1 more source