Evolutionary analysis of gene ages across TADs associates chromatin topology with whole-genome duplications

Evolutionary analysis of gene ages across TADs associates chromatin topology with whole-genome duplications

Summary: Topologically associated domains (TADs) are interaction subnetworks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We sh...

Full description

Bibliographic Details
Main Authors:	Caelinn James, Marco Trevisan-Herraz, David Juan, Daniel Rico
Format:	Article
Language:	English
Published:	Elsevier 2024-04-01
Series:	Cell Reports
Subjects:	CP: Molecular biology CP: Genomics
Online Access:	http://www.sciencedirect.com/science/article/pii/S2211124724002237

Similar Items

Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids
by: Sian M. Bray, et al.
Published: (2024-08-01)

Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana
by: Agustín L. Arce, et al.
Published: (2023-01-01)

Uncoupling programmed DNA cleavage and repair scrambles the Paramecium somatic genome
by: Julien Bischerour, et al.
Published: (2024-04-01)

Haplotype mapping of H3K27me3-associated chromatin interactions defines topological regulation of gene silencing in rice
by: Weizhi Ouyang, et al.
Published: (2023-04-01)

Heterogeneous force response of chromatin in isolated nuclei
by: Giulia Bergamaschi, et al.
Published: (2024-10-01)

TONSOKU is required for the maintenance of repressive chromatin modifications in Arabidopsis
by: Lin Wang, et al.
Published: (2023-07-01)

The mTOR chromatin-bound interactome in prostate cancer
by: Catherine R. Dufour, et al.
Published: (2022-03-01)

Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5
by: Yanran Chen, et al.
Published: (2023-09-01)

Twist2-driven chromatin remodeling governs the postnatal maturation of dermal fibroblasts
by: Jin Yong Kim, et al.
Published: (2022-05-01)

PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility
by: Zihan Xu, et al.
Published: (2023-08-01)

Parent-of-origin-specific DNA replication timing is confined to large imprinted regions
by: Matthew M. Edwards, et al.
Published: (2024-09-01)

Interface-guided phenotyping of coding variants in the transcription factor RUNX1
by: Kivilcim Ozturk, et al.
Published: (2024-07-01)

Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4
by: Kiranmayi Vemuri, et al.
Published: (2024-06-01)

Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptional regulation
by: Jacqueline F. Pelham, et al.
Published: (2023-04-01)

Condensate cooperativity underlies transgenerational gene silencing
by: Zhenzhen Du, et al.
Published: (2023-08-01)

Deciphering the functional landscape of phosphosites with deep neural network
by: Zhongjie Liang, et al.
Published: (2023-09-01)

Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2
by: Jonathan Lerner, et al.
Published: (2023-07-01)

SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites
by: Bao Wang, et al.
Published: (2023-04-01)

Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation
by: Alexander Hall Hickman, et al.
Published: (2024-03-01)

The genomic and evolutionary landscapes of anaplastic thyroid carcinoma
by: Peter Y.F. Zeng, et al.
Published: (2024-03-01)

Identification of the main barriers to Ku accumulation in chromatin
by: Madeleine Bossaert, et al.
Published: (2024-08-01)

SWI/SNF chromatin remodeling factor BAF60b restrains inflammatory diseases by affecting regulatory T cell migration
by: Xiaoqian Liu, et al.
Published: (2024-07-01)

A unified mechanism for PARP inhibitor-induced PARP1 chromatin retention at DNA damage sites in living cells
by: Petar-Bogomil Kanev, et al.
Published: (2024-05-01)

The male pachynema-specific protein MAPS drives phase separation in vitro and regulates sex body formation and chromatin behaviors in vivo
by: Zexiong Lin, et al.
Published: (2024-01-01)

Increased nuclear factor I-mediated chromatin access drives transition to androgen receptor splice variant dependence in prostate cancer
by: Larysa Poluben, et al.
Published: (2025-01-01)

SWI/SNF-dependent genes are defined by their chromatin landscape
by: Laura Basurto-Cayuela, et al.
Published: (2024-03-01)

YAP1 maintains active chromatin state in head and neck squamous cell carcinomas that promotes tumorigenesis through cooperation with BRD4
by: Nana Chen, et al.
Published: (2022-06-01)

Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer
by: Parik Kakani, et al.
Published: (2025-02-01)

Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains
by: Mona Rheinberger, et al.
Published: (2023-02-01)

RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin
by: Jérémy Lebreton, et al.
Published: (2024-03-01)

The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion
by: Evan Healy, et al.
Published: (2024-03-01)

METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells
by: Mu, M, et al.
Published: (2023)

METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells
by: Mandi Mu, et al.
Published: (2023-06-01)

CEBPA phase separation links transcriptional activity and 3D chromatin hubs
by: Marie Christou-Kent, et al.
Published: (2023-08-01)

Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication
by: Vanesa Alvarez, et al.
Published: (2023-01-01)

Phosphorylation by ATR triggers FANCD2 chromatin loading and activates the Fanconi anemia pathway
by: Marian Kupculak, et al.
Published: (2023-07-01)

Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq
by: Caterina Carraro, et al.
Published: (2023-10-01)

Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA biogenesis in mosquitoes
by: Jieqiong Qu, et al.
Published: (2023-03-01)

Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis
by: Zhaoying Shi, et al.
Published: (2023-03-01)

Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes
by: Julian Gurgo, et al.
Published: (2024-05-01)