Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation DOI Creative Commons
Simon Zhongyuan Tian, Yang Yang, Duo Ning

и другие.

The EMBO Journal, Год журнала: 2025, Номер unknown

Опубликована: Май 27, 2025

Abstract The three-dimensional (3D) chromatin structure of Epstein–Barr virus (EBV) within host cells and the underlying mechanisms interaction gene regulation, particularly those involving EBV’s noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques 3D genome mapping, including protein-associated analysis with paired-end tag sequencing (ChIA-PET), RNA-associated technique (RDD), super-resolution microscopy, to delineate spatial architecture EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E–E), EBV-to-host (E–H), host-to-host (H–H) interactions linked proteins RNAs. Our findings reveal that utilizes CCCTC-binding factor (CTCF) RNA polymerase II (RNAPII) form distinct contact domains (CCDs) RNAPII-associated (RAIDs). anchors these serve as platforms for extensive chromatin, thus modulating expression. Notably, ncRNAs, especially Epstein–Barr-encoded (EBERs), target interact less accessible regions repress a subset genes via inhibition loops. This process involves cofactor nucleolin (NCL) its recognition motifs, depletion either NCL or EBERs alters expression crucial infection control, immune response, cell cycle regulation. These unveil sophisticated interplay between chromatin.

Язык: Английский

Tn5-Labeled DNA-FISH: An Optimized Probe Preparation Method for Probing Genome Architecture DOI Open Access
Yang Yang,

Gengzhan Chen,

Tong Gao

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(5), С. 2224 - 2224

Опубликована: Фев. 28, 2025

Three-dimensional genome organization reveals that gene regulatory elements, which are linearly distant on the genome, can spatially interact with target genes to regulate their expression. DNA fluorescence in situ hybridization (DNA-FISH) is an efficient method for studying spatial proximity of genomic loci. In this study, we developed optimized Tn5 transposome-based DNA-FISH method, termed Tn5-labeled DNA-FISH. This approach amplifies region and uses a self-assembled transposome simultaneously fragment into ~100 bp segments label it fluorescent oligonucleotides single step. enables preparation probes regions as small 4 kb visualizes both endogenous exogenous loci at resolution. provides streamlined cost-effective tool probe generation, facilitating investigation chromatin conformations, interactions, architecture.

Язык: Английский

Процитировано

0
Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation DOI Creative Commons
Simon Zhongyuan Tian, Yang Yang, Duo Ning

и другие.

The EMBO Journal, Год журнала: 2025, Номер unknown

Опубликована: Май 27, 2025

Abstract The three-dimensional (3D) chromatin structure of Epstein–Barr virus (EBV) within host cells and the underlying mechanisms interaction gene regulation, particularly those involving EBV’s noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques 3D genome mapping, including protein-associated analysis with paired-end tag sequencing (ChIA-PET), RNA-associated technique (RDD), super-resolution microscopy, to delineate spatial architecture EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E–E), EBV-to-host (E–H), host-to-host (H–H) interactions linked proteins RNAs. Our findings reveal that utilizes CCCTC-binding factor (CTCF) RNA polymerase II (RNAPII) form distinct contact domains (CCDs) RNAPII-associated (RAIDs). anchors these serve as platforms for extensive chromatin, thus modulating expression. Notably, ncRNAs, especially Epstein–Barr-encoded (EBERs), target interact less accessible regions repress a subset genes via inhibition loops. This process involves cofactor nucleolin (NCL) its recognition motifs, depletion either NCL or EBERs alters expression crucial infection control, immune response, cell cycle regulation. These unveil sophisticated interplay between chromatin.

Язык: Английский

Процитировано

0