Comparison of computational methods for the identification of topologically associating domains [PDF]
Genome Biology, 2018 Background Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs).
Marie Zufferey +3 more
doaj +6 more sources
Evolutionary stability of topologically associating domains is associated with conserved gene regulation [PDF]
BMC Biology, 2017 BackgroundThe human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts.
Miguel A. Andrade-Navarro +2 more
core +4 more sources
KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin [PDF]
Journal of Virology, 2022 Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 bp resolution and constructed a
Izumiya, Yoshihiro +19 more
core +5 more sources
Form and function of topologically associating genomic domains in budding yeast [PDF]
Proceedings of the National Academy of Sciences, 2017 Significance In metazoans, topological domains are regions in the genome that more frequently associate with themselves than with neighboring regions. These domains are important for regulating transcription and replication.
Devon Chandler-Brown +6 more
core +3 more sources
Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency [PDF]
Genome Biology, 2021 Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and
Yongzheng Li +13 more
doaj +2 more sources
Identifying topologically associating domains using differential kernels [PDF]
PLOS Computational Biology, 2023 Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication.
King, Megan C. +5 more
core +5 more sources
Finding Topologically Associating Domains [PDF]
, 2015 In this thesis, we propose a new method for finding Topologically Associating Domains, which are contiguous segments of chromatin, ranging in size from thousands to millions of base pairs.
Grytten, Ivar
core +2 more sources
Pattern recognition of topologically associating domains using deep learning
BMC Bioinformatics, 2022 Background Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal ...
Jhen Yuan Yang, Jia-Ming Chang
doaj +5 more sources
An Investigation of Segmental Duplications across Topologically Associating Domains [PDF]
, 2022 High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data.
Bell, Sara
core +2 more sources
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 +5 more
core +4 more sources