Regulation of 3D genome organization during T cell activation DOI Open Access
Bao Wang, Qian Bian

FEBS Journal, Journal Year: 2024, Volume and Issue: unknown

Published: June 29, 2024

Within the three-dimensional (3D) nuclear space, genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation specific effector and memory cell subsets. Recent evidence suggests activation is accompanied by dynamic changes architecture at multiple levels, providing unique biological context explore functional relevance molecular mechanisms 3D organization. Here, we summarize recent advances link reorganization programs conversion fates during differentiation. We further discuss how various chromatin regulators, including CCCTC-binding factor several transcription factors, collectively modulate this process.

Language: Английский

ParSite is a multicolor DNA labeling system that allows for simultaneous imaging of triple genomic loci in living cells DOI Creative Commons

Xiaohui He,

Yadong Sun, Hanhui Ma

et al.

PLoS Biology, Journal Year: 2025, Volume and Issue: 23(1), P. e3003009 - e3003009

Published: Jan. 24, 2025

The organization of the human genome in space and time is critical for transcriptional regulation cell fate determination. However, robust methods tracking or genomic interactions over living cells are lacking. Here, we developed a multicolor DNA labeling system, ParSite, to simultaneously track triple loci U2OS cells. tricolor ParSite system derived from T . thermophilus ParB/ParSc ( Tt ParB/ParSc) by rational design. We mutated interface between ParB ParSc generated new pair ParBm ParSm labeling. insertions 16 base-pair palindromic into allow dual-color imaging A labeled could be colocalized with p53-binding protein 1 (53BP1) response CRISPR/Cas9-mediated double-strand breaks (DSBs). permits promoter terminator dynamics APP gene, which spans 290 kilobases length. Intriguingly, hybrid ParS (ParSh) half-ParSc half-ParSm enables visualization third locus independent ParSm. 3 distance 36, 89, 352 downstream C3 repeat locus, respectively. In sum, multiple

Language: Английский

Citations

0
Deciphering the Role of Epigenetics in Plant Pathogen Resistance: Strategies for Sustainable Sugarcane Management DOI Creative Commons

Faisal Mehdi,

Yuan-li Wu,

Shuzhen Zhang

et al.

Plant Stress, Journal Year: 2025, Volume and Issue: unknown, P. 100754 - 100754

Published: Jan. 1, 2025

Language: Английский

Citations

0
Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales DOI Creative Commons
Hisashi Miura, Ichiro Hiratani

Current Opinion in Genetics & Development, Journal Year: 2022, Volume and Issue: 73, P. 101898 - 101898

Published: Jan. 10, 2022

In the mammalian cell nucleus, chromosomes are folded differently in interphase and mitosis. Interphase relatively decondensed display at least two unique layers of higher-order organization: topologically associating domains (TADs) cell-type-specific A/B compartments, which correlate well with early/late DNA replication timing (RT). mitosis, these structures rapidly disappear but gradually reconstructed during G1 phase, coincident establishment RT program. However, also change dynamically differentiation reprogramming, yet we surprisingly ignorant about relationship between their cycle dynamics developmental dynamics. this review, summarize recent findings on topic, discuss how processes might be coordinated each other its potential significance.

Language: Английский

Citations

16
CRISPR/Pepper‐tDeg: A Live Imaging System Enables Non‐Repetitive Genomic Locus Analysis with One Single‐Guide RNA DOI Creative Commons
Meng Chen,

Xing Huang,

Yakun Shi

et al.

Advanced Science, Journal Year: 2024, Volume and Issue: 11(32)

Published: June 26, 2024

Abstract CRISPR‐based genomic‐imaging systems have been utilized for spatiotemporal imaging of the repetitive genomic loci in living cells, but they are still challenged by limited signal‐to‐noise ratio (SNR) at a non‐repetitive locus. Here, an efficient system is proposed, termed CRISPR/Pepper‐tDeg, engineering CRISPR sgRNA scaffolds with degron‐binding Pepper aptamers binding fluorogenic proteins fused Tat peptide derived degron domain (tDeg). The target‐dependent stability switches both and protein allow this to image telomeres sensitively 5‐fold higher SNR than conventional CRISPR/MS2‐MCP using “always‐on” fluorescent tag. Subsequently, CRISPR/Pepper‐tDeg applied simultaneously label track two different loci, centromeres, cells combining systems. Given further improved split design, extended sequence only one aptamer insertions. Neither complex design nor difficult plasmid construction required, greatly reducing technical barriers define organization dynamics thus demonstrating large application potential biological research, clinical diagnosis therapy.

Language: Английский

Citations

3
Regulation of 3D genome organization during T cell activation DOI Open Access
Bao Wang, Qian Bian

FEBS Journal, Journal Year: 2024, Volume and Issue: unknown

Published: June 29, 2024

Within the three-dimensional (3D) nuclear space, genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation specific effector and memory cell subsets. Recent evidence suggests activation is accompanied by dynamic changes architecture at multiple levels, providing unique biological context explore functional relevance molecular mechanisms 3D organization. Here, we summarize recent advances link reorganization programs conversion fates during differentiation. We further discuss how various chromatin regulators, including CCCTC-binding factor several transcription factors, collectively modulate this process.

Language: Английский

Citations

3