3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

CM Uyehara, E Apostolou - Cell reports, 2023 - cell.com
The spatiotemporal control of gene expression is dependent on the activity of cis-acting
regulatory sequences, called enhancers, which regulate target genes over variable genomic …

Meningioma: International Consortium on Meningiomas consensus review on scientific advances and treatment paradigms for clinicians, researchers, and patients

JZ Wang, AP Landry, DR Raleigh, F Sahm… - Neuro …, 2024 - academic.oup.com
Meningiomas are the most common primary intracranial tumors in adults and are increasing
in incidence due to the aging population and increased access to neuroimaging. While most …

Transcriptional coupling of distant regulatory genes in living embryos

M Levo, J Raimundo, XY Bing, Z Sisco, PJ Batut… - Nature, 2022 - nature.com
The prevailing view of metazoan gene regulation is that individual genes are independently
regulated by their own dedicated sets of transcriptional enhancers. Past studies have …

Resolving the 3D landscape of transcription-linked mammalian chromatin folding

THS Hsieh, C Cattoglio, E Slobodyanyuk, AS Hansen… - Molecular cell, 2020 - cell.com
Whereas folding of genomes at the large scale of epigenomic compartments and
topologically associating domains (TADs) is now relatively well understood, how chromatin …

Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging

S Ma, S Sun, L Geng, M Song, W Wang, Y Ye, Q Ji… - Cell, 2020 - cell.com
Aging causes a functional decline in tissues throughout the body that may be delayed by
caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as …

Aging disrupts circadian gene regulation and function in macrophages

E Blacher, C Tsai, L Litichevskiy, Z Shipony… - Nature …, 2022 - nature.com
Aging is characterized by an increased vulnerability to infection and the development of
inflammatory diseases, such as atherosclerosis, frailty, cancer and neurodegeneration …

Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes

BK Wolf, Y Zhao, A McCray, WH Hawk… - Nature structural & …, 2023 - nature.com
The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to
be coordinated by transcription factors (TFs), yet demonstrating a specific TF influence has …

MyoD is a 3D genome structure organizer for muscle cell identity

R Wang, F Chen, Q Chen, X Wan, M Shi… - Nature …, 2022 - nature.com
The genome exists as an organized, three-dimensional (3D) dynamic architecture, and each
cell type has a unique 3D genome organization that determines its cell identity. An …

DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution

S Zhang, D Plummer, L Lu, J Cui, W Xu, M Wang… - Nature …, 2022 - nature.com
Map** chromatin loops from noisy Hi-C heatmaps remains a major challenge. Here we
present DeepLoop, which performs rigorous bias correction followed by deep-learning …

Generation and characterization of stable pig pregastrulation epiblast stem cell lines

M Zhi, J Zhang, Q Tang, D Yu, S Gao, D Gao, P Liu… - Cell Research, 2022 - nature.com
Pig epiblast-derived pluripotent stem cells are considered to have great potential and broad
prospects for human therapeutic model development and livestock breeding. Despite …