TADs and their borders: free movement or building a wall?

LH Chang, S Ghosh, D Noordermeer - Journal of molecular biology, 2020 - Elsevier
The tridimensional (3D) organization of mammalian genomes combines structures from
different length scales. Within this organization, Topologically Associating Domains (TADs) …

Function and evolution of the loop extrusion machinery in animals

E Kabirova, A Nurislamov, A Shadskiy… - International Journal of …, 2023 - mdpi.com
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in
genomes of all cellular organisms. Essential functions of these proteins, such as mitotic …

A map of cis-regulatory elements and 3D genome structures in zebrafish

H Yang, Y Luan, T Liu, HJ Lee, L Fang, Y Wang… - Nature, 2020 - nature.com
The zebrafish (Danio rerio) has been widely used in the study of human disease and
development, and about 70% of the protein-coding genes are conserved between the two …

The 3D architecture of the pepper genome and its relationship to function and evolution

Y Liao, J Wang, Z Zhu, Y Liu, J Chen, Y Zhou… - Nature …, 2022 - nature.com
The organization of chromatin into self-interacting domains is universal among eukaryotic
genomes, though how and why they form varies considerably. Here we report a …

RNA polymerase II pausing regulates chromatin organization in erythrocytes

A Penagos-Puig, S Claudio-Galeana… - Nature Structural & …, 2023 - nature.com
Chicken erythrocytes are nucleated cells often considered to be transcriptionally inactive,
although the epigenetic changes and chromatin remodeling that would mediate …

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

S Foissac, S Djebali, K Munyard, N Vialaneix, A Rau… - BMC biology, 2019 - Springer
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 …

Comparative 3D genome architecture in vertebrates

D Li, M He, Q Tang, S Tian, J Zhang, Y Li, D Wang… - BMC biology, 2022 - Springer
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 …

Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

D Li, C Ning, J Zhang, Y Wang, Q Tang, H Kui… - Nature …, 2022 - nature.com
Folliculogenesis is a complex biological process involving a central oocyte and its
surrounding somatic cells. Three-dimensional chromatin architecture is an important …

[HTML][HTML] Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

L Álvarez-González, C Arias-Sardá, L Montes-Espuña… - Cell reports, 2022 - cell.com
Studying the similarities and differences in genomic interactions between species provides
fertile grounds for determining the evolutionary dynamics underpinning genome function …

Why do some vertebrates have microchromosomes?

K Srikulnath, SF Ahmad, W Singchat, T Panthum - Cells, 2021 - mdpi.com
With more than 70,000 living species, vertebrates have a huge impact on the field of biology
and research, including karyotype evolution. One prominent aspect of many vertebrate …