Integrative single-cell and multi-omic analysis resolves granulosa-cell programs during chicken follicle selection. [PDF]
Poult SciQu M +6 more
europepmc +1 more source
Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease [PDF]
Frontiers in Cell and Developmental Biology, 2021 Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as
Juan J Tena, José M Santos-Pereira
exaly +7 more sources
Emerging Regulatory Mechanisms of Noncoding RNAs in Topologically Associating Domains
Trends in Genetics, 2023 Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of ...
Vinay Tergaonkar, Melissa J Fullwood
exaly +5 more sources
On the Existence and Functionality of Topologically Associating Domains
Nature Genetics, 2020 Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin domains. Topologically associating domains (TADs) were originally discovered empirically in low-resolution Hi-C heat maps representing ensemble average interaction frequencies from millions of cells. Here, we discuss recent advances in high-resolution Hi-C, single-cell
Jennifer E Phillips-Cremins +1 more
exaly +4 more sources
Structural and Functional Diversity of Topologically Associating Domains [PDF]
FEBS Letters, 2015 Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the ...
Job Dekker, Edith Heard
exaly +4 more sources
HPTAD: A Computational Method to Identify Topologically Associating Domains From HiChIP and PLAC-Seq Datasets [PDF]
Computational and Structural Biotechnology Journal, 2023 High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization.
Armen Abnousi, Jia Wen
exaly +3 more sources
Chromatin-Driven Behavior of Topologically Associating Domains
Journal of Molecular Biology, 2015 Metazoan genomes are highly organized inside the cell nucleus. Topologically associating domains (TADs) represent the building blocks of genome organization, but their linear modularity does not explain alone their spatial organization. Indeed, the chromatin type adorning a TAD can shape its structure and drives its nuclear positioning and its function.
Filippo Ciabrelli, Giacomo Cavalli
exaly +4 more sources
Topologically Associating Domains Are Stable Units of Replication-Timing Regulation [PDF]
Nature, 2014 Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types ...
James Taylor +2 more
exaly +3 more sources
Topologically Associating Domains and the Evolution of Three-Dimensional Genome Architecture in Rice
Plant JournalSUMMARYWe examined the nature and evolution of three‐dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within the genus Oryza. These included three varieties from subspecies within domesticated Asian rice O. sativa as well as their closely related wild relatives O. rufipogon and O.
Amina Kurbidaeva +2 more
exaly +6 more sources
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Gene regulation during development in the light of topologically associating domains
WIREs Developmental Biology, 2015During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis‐regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous ...
Silvia Remeseiro +2 more
openaire +2 more sources