The ruminant telomere-to-telomere (rt2t) consortium

TS Kalbfleisch, SD McKay, BM Murdoch, DL Adelson… - Nature …, 2024 - nature.com
Abstract Telomere-to-telomere (T2T) assemblies reveal new insights into the structure and
function of the previously 'invisible'parts of the genome and allow comparative analyses of …

Enhancer–promoter specificity in gene transcription: molecular mechanisms and disease associations

MJ Friedman, T Wagner, H Lee… - … & Molecular Medicine, 2024 - nature.com
Although often located at a distance from their target gene promoters, enhancers are the
primary genomic determinants of temporal and spatial transcriptional specificity in …

Engineering 3D genome organization

H Wang, M Han, LS Qi - Nature Reviews Genetics, 2021 - nature.com
Cancers and developmental disorders are associated with alterations in the 3D genome
architecture in space and time (the fourth dimension). Mammalian 3D genome organization …

Chromatin conformation in development and disease

I Boltsis, F Grosveld, G Giraud… - Frontiers in Cell and …, 2021 - frontiersin.org
Chromatin domains and loops are important elements of chromatin structure and dynamics,
but much remains to be learned about their exact biological role and nature. Topological …

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

C Anania, RD Acemel, J Jedamzick, A Bolondi… - Nature Genetics, 2022 - nature.com
Vertebrate genomes organize into topologically associating domains, delimited by
boundaries that insulate regulatory elements from nontarget genes. However, how boundary …

p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

F Serra, A Nieto-Aliseda, L Fanlo-Escudero… - Nature …, 2024 - nature.com
Activation of the p53 tumor suppressor triggers a transcriptional program to control cellular
response to stress. However, the molecular mechanisms by which p53 controls gene …

Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis

W Xu, H Zhang, W Guo, L Jiang, Y Zhao… - Briefings in …, 2024 - academic.oup.com
Nucleosomes represent hubs in chromatin organization and gene regulation and interact
with a plethora of chromatin factors through different modes. In addition, alterations in …

Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells

AR Barutcu, G Elizalde, AE Gonzalez, K Soni, JL Rinn… - Skeletal Muscle, 2022 - Springer
Background The AP-1 transcription factor, FBJ osteosarcoma oncogene (FOS), is induced in
adult muscle satellite cells (SCs) within hours following muscle damage and is required for …

Regulation of chromatin organization during animal regeneration

X Jia, W Lin, W Wang - Cell Regeneration, 2023 - Springer
Activation of regeneration upon tissue damages requires the activation of many
developmental genes responsible for cell proliferation, migration, differentiation, and tissue …

Fine mapping with epigenetic information and 3D structure

G Orozco - Seminars in Immunopathology, 2022 - Springer
Since 2005, thousands of genome-wide association studies (GWAS) have been published,
identifying hundreds of thousands of genetic variants that increase risk of complex traits …