CLIP-seq to identify KSHV ORF57-binding RNA in host B cells

Yanping Ma; Poching Liu; Vladimir Majerciak; Jun Zhu; Zhi Ming Zheng

doi:10.1002/cpmc.3

CLIP-seq to identify KSHV ORF57-binding RNA in host B cells

Yanping Ma, Poching Liu, Vladimir Majerciak, Jun Zhu, Zhi Ming Zheng

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Kaposi’s sarcoma-associated herpesvirus (KSHV), a human gammaherpesvirus, is etiologically linked to the development of several malignancies, mainly Kaposi’s sarcoma. Expressed as an early viral protein, KSHV ORF57 is essential for lytic replication and virion production. ORF57 selectively binds to a subset of viral RNA and affects nearly all aspects of viral RNA processing. To globally identify all viral and host RNA associated with KSHV ORF57 in the infected cells, we have utilized UV cross-linking and immunoprecipitation (CLIP) of KSHV ORF57 combined with high-throughput RNA sequencing (CLIP-seq) to identify ORF57-binding RNA in BCBL-1 cells at genome-wide level. This unit provides step-by-step details on this new method that is applicable for any pathogen or host RNA-binding proteins by slight modification.

Original language	English
Pages (from-to)	1E.11.1-1E.11.18
Journal	Current Protocols in Microbiology
Volume	2016
DOIs	https://doi.org/10.1002/cpmc.3
State	Published - 2016
Externally published	Yes

Keywords

High throughput sequencing
KSHV
ORF57
RNA
UV cross-linking

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10.1002/cpmc.3

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title = "CLIP-seq to identify KSHV ORF57-binding RNA in host B cells",

abstract = "Kaposi{\textquoteright}s sarcoma-associated herpesvirus (KSHV), a human gammaherpesvirus, is etiologically linked to the development of several malignancies, mainly Kaposi{\textquoteright}s sarcoma. Expressed as an early viral protein, KSHV ORF57 is essential for lytic replication and virion production. ORF57 selectively binds to a subset of viral RNA and affects nearly all aspects of viral RNA processing. To globally identify all viral and host RNA associated with KSHV ORF57 in the infected cells, we have utilized UV cross-linking and immunoprecipitation (CLIP) of KSHV ORF57 combined with high-throughput RNA sequencing (CLIP-seq) to identify ORF57-binding RNA in BCBL-1 cells at genome-wide level. This unit provides step-by-step details on this new method that is applicable for any pathogen or host RNA-binding proteins by slight modification.",

keywords = "High throughput sequencing, KSHV, ORF57, RNA, UV cross-linking",

author = "Yanping Ma and Poching Liu and Vladimir Majerciak and Jun Zhu and Zheng, {Zhi Ming}",

note = "Publisher Copyright: {\textcopyright} 2016 by John Wiley & Sons, Inc.",

year = "2016",

doi = "10.1002/cpmc.3",

language = "English",

volume = "2016",

pages = "1E.11.1--1E.11.18",

journal = "Current Protocols in Microbiology",

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TY - JOUR

T1 - CLIP-seq to identify KSHV ORF57-binding RNA in host B cells

AU - Ma, Yanping

AU - Liu, Poching

AU - Majerciak, Vladimir

AU - Zhu, Jun

AU - Zheng, Zhi Ming

PY - 2016

Y1 - 2016

N2 - Kaposi’s sarcoma-associated herpesvirus (KSHV), a human gammaherpesvirus, is etiologically linked to the development of several malignancies, mainly Kaposi’s sarcoma. Expressed as an early viral protein, KSHV ORF57 is essential for lytic replication and virion production. ORF57 selectively binds to a subset of viral RNA and affects nearly all aspects of viral RNA processing. To globally identify all viral and host RNA associated with KSHV ORF57 in the infected cells, we have utilized UV cross-linking and immunoprecipitation (CLIP) of KSHV ORF57 combined with high-throughput RNA sequencing (CLIP-seq) to identify ORF57-binding RNA in BCBL-1 cells at genome-wide level. This unit provides step-by-step details on this new method that is applicable for any pathogen or host RNA-binding proteins by slight modification.

AB - Kaposi’s sarcoma-associated herpesvirus (KSHV), a human gammaherpesvirus, is etiologically linked to the development of several malignancies, mainly Kaposi’s sarcoma. Expressed as an early viral protein, KSHV ORF57 is essential for lytic replication and virion production. ORF57 selectively binds to a subset of viral RNA and affects nearly all aspects of viral RNA processing. To globally identify all viral and host RNA associated with KSHV ORF57 in the infected cells, we have utilized UV cross-linking and immunoprecipitation (CLIP) of KSHV ORF57 combined with high-throughput RNA sequencing (CLIP-seq) to identify ORF57-binding RNA in BCBL-1 cells at genome-wide level. This unit provides step-by-step details on this new method that is applicable for any pathogen or host RNA-binding proteins by slight modification.

KW - High throughput sequencing

KW - KSHV

KW - ORF57

KW - RNA

KW - UV cross-linking

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U2 - 10.1002/cpmc.3

DO - 10.1002/cpmc.3

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SN - 1934-8525

VL - 2016

SP - 1E.11.1-1E.11.18

JO - Current Protocols in Microbiology

JF - Current Protocols in Microbiology

ER -

CLIP-seq to identify KSHV ORF57-binding RNA in host B cells

Abstract

Keywords

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