A TAD skeptic: is 3D genome topology conserved?
IE Eres, Y Gilad - Trends in Genetics, 2021 - cell.com
The notion that topologically associating domains (TADs) are highly conserved across
species is prevalent in the field of 3D genomics. However, what exactly is meant by 'highly …
species is prevalent in the field of 3D genomics. However, what exactly is meant by 'highly …
Vertebrate chromosome evolution
The study of chromosome evolution is undergoing a resurgence of interest owing to
advances in DNA sequencing technology that facilitate the production of chromosome-scale …
advances in DNA sequencing technology that facilitate the production of chromosome-scale …
Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability
E McArthur, JA Capra - The American Journal of Human Genetics, 2021 - cell.com
Topologically associating domains (TADs) are fundamental units of three-dimensional (3D)
nuclear organization. The regions bordering TADs—TAD boundaries—contribute to the …
nuclear organization. The regions bordering TADs—TAD boundaries—contribute to the …
Multi-species annotation of transcriptome and chromatin structure in domesticated animals
Background Comparative genomics studies are central in identifying the coding and non-
coding elements associated with complex traits, and the functional annotation of genomes is …
coding elements associated with complex traits, and the functional annotation of genomes is …
Comparative 3D genome architecture in vertebrates
Background The three-dimensional (3D) architecture of the genome has a highly ordered
and hierarchical nature, which influences the regulation of essential nuclear processes at …
and hierarchical nature, which influences the regulation of essential nuclear processes at …
A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Background Although considerable progress has been made towards annotating the
noncoding portion of the human and mouse genomes, regulatory elements in other species …
noncoding portion of the human and mouse genomes, regulatory elements in other species …
TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
M Okhovat, J VanCampen, KA Nevonen… - Nature …, 2023 - nature.com
Topological associating domains (TADs) are self-interacting genomic units crucial for
sha** gene regulation patterns. Despite their importance, the extent of their evolutionary …
sha** gene regulation patterns. Despite their importance, the extent of their evolutionary …
Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
Topologically associating domains (TADs) were recently identified as fundamental units of
three-dimensional eukaryotic genomic organization, although our knowledge of the …
three-dimensional eukaryotic genomic organization, although our knowledge of the …
CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction
S Galan, N Machnik, K Kruse, N Díaz… - Nature …, 2020 - nature.com
Dynamic changes in the three-dimensional (3D) organization of chromatin are associated
with central biological processes, such as transcription, replication and development …
with central biological processes, such as transcription, replication and development …
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
DI Lee, S Roy - Genome biology, 2021 - Springer
High-throughput chromosome conformation capture assays, such as Hi-C, have shown that
the genome is organized into organizational units such as topologically associating domains …
the genome is organized into organizational units such as topologically associating domains …