ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells

Bo Wang; Grace Tin Yun Chung; Yi Shuai; Man Wu; Danyang Ji; Raymond Wai Ming Lung; Yuk Yu Chan; Ming Ting Liu; Ee Ling Kong; Shin Yee Hui; Hei Man Leung; Qian Wu; Melissa Sue Ann Chan; Xin Wang; Guang Zhu; Kevin Y. Yip; Chun Kit Kwok; Kwok Wai Lo; Chi Man Tsang

doi:10.1186/s13578-025-01437-3

ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells

Bo Wang
, Grace Tin Yun Chung
, Yi Shuai
, Man Wu
, Danyang Ji
, Raymond Wai Ming Lung
, Yuk Yu Chan
, Ming Ting Liu
, Ee Ling Kong
, Shin Yee Hui
, Hei Man Leung
, Qian Wu
, Melissa Sue Ann Chan
, Xin Wang
, Guang Zhu
, Kevin Y. Yip
, Chun Kit Kwok
, Kwok Wai Lo^*
, Chi Man Tsang^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

2 Citations (Scopus)

28 Downloads (CityUHK Scholars)

Abstract

Background In EBV-associated epithelial cancers, only a limited number of viral proteins are translated, while multiple EBV-encoded non-coding RNAs are expressed to minimize activation of the host’s immune response. These non-coding RNAs have been shown to play regulatory roles in maintaining latency and promoting cancer progression while many aspects of them remain to be elucidated.
Results Here we revealed abundant expression of ebv-sisRNA-3, a novel EBV transcript in nasopharyngeal carcinoma and EBV-associated gastric cancer. This 5–7 kb non-polyA transcript is derived from RPMS1 intron and is partially complementary to LF3. We observed high expression level of ebv-sisRNA-3 in multiple EBV-positive cancer cells and clinical specimens, with accumulation in the cell nucleus. Notably, ebv-sisRNA-3 invades the double-strand DNA in trans upstream of lytic replication origin in EBV genome and leads to the formation of R-loop and G-quadruplex simultaneously in the latently EBV-infected epithelial cells. Additionally, we revealed the locations of R-loops within the EBV genome and identified endogenous G-quadruplexes near the EBER1 and EBNA1 promoters.
Conclusions In this study, we revealed and characterized a novel EBV transcript ebv-sisRNA-3 widely expressed in latently infected cells. The unique ebv-sisRNA-3-binding R-loop and G-quadruplex structures near lytic replication origin may play a significant role in EBV lytic replication.
© The Author(s) 2025.

Original language	English
Article number	91
Journal	Cell & Bioscience
Volume	15
Online published	27 Jun 2025
DOIs	https://doi.org/10.1186/s13578-025-01437-3
Publication status	Published - 2025

Funding

Research Grants Council-General Research Fund (GRF): 14116124, 14113620, 14114523; Early Career Scheme (ECS): 24114922; Health and Medical Research Fund: 09203176; and Faculty Innovation Award: FIA2020/A/01 to T.C.M. The Innovation and Technology Fund (Midstream Research Programme for Universities-MRP/036/21X); Research Grant Council, Hong Kong (Areas of Excellence Scheme-AoE/M-401/20; General Research Fund-14101721) and Health and Medical Research Fund (08191046) to K.W.L. National Natural Science Foundation of China Project [32471343, 32222089]; Research Grants Council (RGC) of the Hong Kong Special Administrative Region (RFS2425-1S02, CityU 11100123, CityU 11100222, CityU 11100421); Croucher Foundation Project (9509003); State Key Laboratory of Marine Pollution Seed Collaborative Research Fund (SCRF/0037, SCRF/0040, SCRF0070); City University of Hong Kong projects (7030001, 9678302 and 6000827) to C.K.K.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Research Keywords

Epstein-barr virus
Nasopharyngeal carcinoma
ncRNA
sisRNA
R-loop
G-quadruplex

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

RGC Funding Information

RGC-funded

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10.1186/s13578-025-01437-3

305323261.pdfFinal Published version, 4.85 MBLicence: CC BY

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Wang, B., Chung, G. T. Y., Shuai, Y., Wu, M., Ji, D., Lung, R. W. M., Chan, Y. Y., Liu, M. T., Kong, E. L., Hui, S. Y., Leung, H. M., Wu, Q., Chan, M. S. A., Wang, X., Zhu, G., Yip, K. Y., Kwok, C. K., Lo, K. W., & Tsang, C. M. (2025). ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells. Cell & Bioscience, 15, Article 91. https://doi.org/10.1186/s13578-025-01437-3

@article{99eb247bc6fe4feebadcf8a61928fcb2,

title = "ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells",

abstract = "Background In EBV-associated epithelial cancers, only a limited number of viral proteins are translated, while multiple EBV-encoded non-coding RNAs are expressed to minimize activation of the host{\textquoteright}s immune response. These non-coding RNAs have been shown to play regulatory roles in maintaining latency and promoting cancer progression while many aspects of them remain to be elucidated. Results Here we revealed abundant expression of ebv-sisRNA-3, a novel EBV transcript in nasopharyngeal carcinoma and EBV-associated gastric cancer. This 5–7 kb non-polyA transcript is derived from RPMS1 intron and is partially complementary to LF3. We observed high expression level of ebv-sisRNA-3 in multiple EBV-positive cancer cells and clinical specimens, with accumulation in the cell nucleus. Notably, ebv-sisRNA-3 invades the double-strand DNA in trans upstream of lytic replication origin in EBV genome and leads to the formation of R-loop and G-quadruplex simultaneously in the latently EBV-infected epithelial cells. Additionally, we revealed the locations of R-loops within the EBV genome and identified endogenous G-quadruplexes near the EBER1 and EBNA1 promoters. Conclusions In this study, we revealed and characterized a novel EBV transcript ebv-sisRNA-3 widely expressed in latently infected cells. The unique ebv-sisRNA-3-binding R-loop and G-quadruplex structures near lytic replication origin may play a significant role in EBV lytic replication. {\textcopyright} The Author(s) 2025.",

keywords = "Epstein-barr virus, Nasopharyngeal carcinoma, ncRNA, sisRNA, R-loop, G-quadruplex",

author = "Bo Wang and Chung, \{Grace Tin Yun\} and Yi Shuai and Man Wu and Danyang Ji and Lung, \{Raymond Wai Ming\} and Chan, \{Yuk Yu\} and Liu, \{Ming Ting\} and Kong, \{Ee Ling\} and Hui, \{Shin Yee\} and Leung, \{Hei Man\} and Qian Wu and Chan, \{Melissa Sue Ann\} and Xin Wang and Guang Zhu and Yip, \{Kevin Y.\} and Kwok, \{Chun Kit\} and Lo, \{Kwok Wai\} and Tsang, \{Chi Man\}",

year = "2025",

doi = "10.1186/s13578-025-01437-3",

language = "English",

volume = "15",

journal = "Cell \& Bioscience",

issn = "2045-3701",

publisher = "Society of Chinese Bioscientists in America",

}

Wang, B, Chung, GTY, Shuai, Y, Wu, M, Ji, D, Lung, RWM, Chan, YY, Liu, MT, Kong, EL, Hui, SY, Leung, HM, Wu, Q, Chan, MSA, Wang, X, Zhu, G, Yip, KY, Kwok, CK, Lo, KW & Tsang, CM 2025, 'ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells', Cell & Bioscience, vol. 15, 91. https://doi.org/10.1186/s13578-025-01437-3

TY - JOUR

T1 - ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells

AU - Wang, Bo

AU - Chung, Grace Tin Yun

AU - Shuai, Yi

AU - Wu, Man

AU - Ji, Danyang

AU - Lung, Raymond Wai Ming

AU - Chan, Yuk Yu

AU - Liu, Ming Ting

AU - Kong, Ee Ling

AU - Hui, Shin Yee

AU - Leung, Hei Man

AU - Wu, Qian

AU - Chan, Melissa Sue Ann

AU - Wang, Xin

AU - Zhu, Guang

AU - Yip, Kevin Y.

AU - Kwok, Chun Kit

AU - Lo, Kwok Wai

AU - Tsang, Chi Man

PY - 2025

Y1 - 2025

N2 - Background In EBV-associated epithelial cancers, only a limited number of viral proteins are translated, while multiple EBV-encoded non-coding RNAs are expressed to minimize activation of the host’s immune response. These non-coding RNAs have been shown to play regulatory roles in maintaining latency and promoting cancer progression while many aspects of them remain to be elucidated. Results Here we revealed abundant expression of ebv-sisRNA-3, a novel EBV transcript in nasopharyngeal carcinoma and EBV-associated gastric cancer. This 5–7 kb non-polyA transcript is derived from RPMS1 intron and is partially complementary to LF3. We observed high expression level of ebv-sisRNA-3 in multiple EBV-positive cancer cells and clinical specimens, with accumulation in the cell nucleus. Notably, ebv-sisRNA-3 invades the double-strand DNA in trans upstream of lytic replication origin in EBV genome and leads to the formation of R-loop and G-quadruplex simultaneously in the latently EBV-infected epithelial cells. Additionally, we revealed the locations of R-loops within the EBV genome and identified endogenous G-quadruplexes near the EBER1 and EBNA1 promoters. Conclusions In this study, we revealed and characterized a novel EBV transcript ebv-sisRNA-3 widely expressed in latently infected cells. The unique ebv-sisRNA-3-binding R-loop and G-quadruplex structures near lytic replication origin may play a significant role in EBV lytic replication. © The Author(s) 2025.

AB - Background In EBV-associated epithelial cancers, only a limited number of viral proteins are translated, while multiple EBV-encoded non-coding RNAs are expressed to minimize activation of the host’s immune response. These non-coding RNAs have been shown to play regulatory roles in maintaining latency and promoting cancer progression while many aspects of them remain to be elucidated. Results Here we revealed abundant expression of ebv-sisRNA-3, a novel EBV transcript in nasopharyngeal carcinoma and EBV-associated gastric cancer. This 5–7 kb non-polyA transcript is derived from RPMS1 intron and is partially complementary to LF3. We observed high expression level of ebv-sisRNA-3 in multiple EBV-positive cancer cells and clinical specimens, with accumulation in the cell nucleus. Notably, ebv-sisRNA-3 invades the double-strand DNA in trans upstream of lytic replication origin in EBV genome and leads to the formation of R-loop and G-quadruplex simultaneously in the latently EBV-infected epithelial cells. Additionally, we revealed the locations of R-loops within the EBV genome and identified endogenous G-quadruplexes near the EBER1 and EBNA1 promoters. Conclusions In this study, we revealed and characterized a novel EBV transcript ebv-sisRNA-3 widely expressed in latently infected cells. The unique ebv-sisRNA-3-binding R-loop and G-quadruplex structures near lytic replication origin may play a significant role in EBV lytic replication. © The Author(s) 2025.

KW - Epstein-barr virus

KW - Nasopharyngeal carcinoma

KW - ncRNA

KW - sisRNA

KW - R-loop

KW - G-quadruplex

UR - https://www.webofscience.com/wos/woscc/full-record/WOS:001518386900002

UR - https://www.scopus.com/pages/publications/105009325501

UR - https://www.scopus.com/pages/publications/105009325501#tab=impact

U2 - 10.1186/s13578-025-01437-3

DO - 10.1186/s13578-025-01437-3

M3 - RGC 21 - Publication in refereed journal

C2 - 40579704

SN - 2045-3701

VL - 15

JO - Cell & Bioscience

JF - Cell & Bioscience

M1 - 91

ER -

ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells

Abstract

Funding

UN SDGs

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

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RFS: Developing RNA Structure-Targeting Bi-/Multi-Functional Laptamer-Based Chimeras for Gene Regulation

GRF: Developing Novel Short Peptides to Target G-quadruplex Structure and Modulate Gene Function

GRF: Evolving New L-RNA Aptamers and Developing L-RNA aptamer-peptide Conjugates to Control G-quadruplex Structure-associated Gene Activity

Cite this

ebv-sisRNA-3 contributes to the formation of G4-associated R-loop upstream of EBV lytic replication origin in latently infected cells

Abstract

Funding

UN SDGs

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

Access Output

Other Access Options

Permanent Link

Other Files and Links

Fingerprint

Projects

RFS: Developing RNA Structure-Targeting Bi-/Multi-Functional Laptamer-Based Chimeras for Gene Regulation

GRF: Developing Novel Short Peptides to Target G-quadruplex Structure and Modulate Gene Function

GRF: Evolving New L-RNA Aptamers and Developing L-RNA aptamer-peptide Conjugates to Control G-quadruplex Structure-associated Gene Activity

Cite this