Identifying individual pseudouridine (Ψ) sites across transcripts from HIV-1 infected cells

Hannah L. Coutts; David G Courtney

doi:10.1007/978-1-0716-3862-0_16

Identifying individual pseudouridine (Ψ) sites across transcripts from HIV-1 infected cells

Hannah L. Coutts, David G Courtney^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

Abstract

The identification of RNA modifications at single nucleotide resolution has become an emerging area of interest within biology and specifically among virologists seeking to ascertain how this untapped area of RNA regulation may be altered or hijacked upon viral infection. Herein, we describe a straightforward biochemical approach modified from two original published Ψ mapping protocols, BID-seq and PRAISE, to specifically identify pseudouridine modifications on mRNA transcripts from an HIV-1 infected T cell line. This protocol could readily be adapted for other viral infected cell types and additionally for populations of purified virions from infected cells.

Original language	English
Title of host publication	HIV protocols
Editors	Vinayaka R. Prasad, Ganjam V. Kalpana
Publisher	Humana Press
Chapter	16
Pages	229-242
Edition	4th
ISBN (Electronic)	9781071638620
ISBN (Print)	9781071638613
DOIs	https://doi.org/10.1007/978-1-0716-3862-0_16
Publication status	Published - 15 May 2024

Publication series

Name	Methods in Molecular Biology
Volume	2807
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

Humans
Cell Line
Pseudouridine - metabolism - genetics
HIV-1
Modifications
Virus
RNA, Messenger - genetics - metabolism
Epitranscriptomics
HIV-1 - genetics
HIV Infections - virology - genetics
Pseudouridine
RNA
RNA, Viral - genetics
Mapping
RNA Processing, Post-Transcriptional
Bisulfite

UN SDGs

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

Access to Document

10.1007/978-1-0716-3862-0_16Licence: Unspecified

Post-transcriptional regulation of Influenza A virus mRNAs
Coutts, H. L. (Author), Courtney, D. (Supervisor), Mousnier, A. (Supervisor) & Bengoechea, J. (Supervisor), Jul 2025
Student thesis: Doctoral Thesis › Thesis with Publications

File

Cite this

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title = "Identifying individual pseudouridine (Ψ) sites across transcripts from HIV-1 infected cells",

abstract = "The identification of RNA modifications at single nucleotide resolution has become an emerging area of interest within biology and specifically among virologists seeking to ascertain how this untapped area of RNA regulation may be altered or hijacked upon viral infection. Herein, we describe a straightforward biochemical approach modified from two original published Ψ mapping protocols, BID-seq and PRAISE, to specifically identify pseudouridine modifications on mRNA transcripts from an HIV-1 infected T cell line. This protocol could readily be adapted for other viral infected cell types and additionally for populations of purified virions from infected cells. ",

keywords = "Humans, Cell Line, Pseudouridine - metabolism - genetics, HIV-1, Modifications, Virus, RNA, Messenger - genetics - metabolism, Epitranscriptomics, HIV-1 - genetics, HIV Infections - virology - genetics, Pseudouridine, RNA, RNA, Viral - genetics, Mapping, RNA Processing, Post-Transcriptional, Bisulfite",

author = "Coutts, \{Hannah L.\} and Courtney, \{David G\}",

year = "2024",

month = may,

day = "15",

doi = "10.1007/978-1-0716-3862-0\_16",

language = "English",

isbn = "9781071638613",

series = "Methods in Molecular Biology",

publisher = "Humana Press",

pages = "229--242",

editor = "Prasad, \{Vinayaka R.\} and Kalpana, \{Ganjam V.\}",

booktitle = "HIV protocols",

address = "United States",

edition = "4th",

}

Identifying individual pseudouridine (Ψ) sites across transcripts from HIV-1 infected cells. / Coutts, Hannah L.; Courtney, David G.
HIV protocols. ed. / Vinayaka R. Prasad; Ganjam V. Kalpana. 4th. ed. Humana Press, 2024. p. 229-242 (Methods in Molecular Biology; Vol. 2807).

Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

TY - CHAP

T1 - Identifying individual pseudouridine (Ψ) sites across transcripts from HIV-1 infected cells

AU - Coutts, Hannah L.

AU - Courtney, David G

PY - 2024/5/15

Y1 - 2024/5/15

N2 - The identification of RNA modifications at single nucleotide resolution has become an emerging area of interest within biology and specifically among virologists seeking to ascertain how this untapped area of RNA regulation may be altered or hijacked upon viral infection. Herein, we describe a straightforward biochemical approach modified from two original published Ψ mapping protocols, BID-seq and PRAISE, to specifically identify pseudouridine modifications on mRNA transcripts from an HIV-1 infected T cell line. This protocol could readily be adapted for other viral infected cell types and additionally for populations of purified virions from infected cells.

AB - The identification of RNA modifications at single nucleotide resolution has become an emerging area of interest within biology and specifically among virologists seeking to ascertain how this untapped area of RNA regulation may be altered or hijacked upon viral infection. Herein, we describe a straightforward biochemical approach modified from two original published Ψ mapping protocols, BID-seq and PRAISE, to specifically identify pseudouridine modifications on mRNA transcripts from an HIV-1 infected T cell line. This protocol could readily be adapted for other viral infected cell types and additionally for populations of purified virions from infected cells.

KW - Humans

KW - Cell Line

KW - Pseudouridine - metabolism - genetics

KW - HIV-1

KW - Modifications

KW - Virus

KW - RNA, Messenger - genetics - metabolism

KW - Epitranscriptomics

KW - HIV-1 - genetics

KW - HIV Infections - virology - genetics

KW - Pseudouridine

KW - RNA

KW - RNA, Viral - genetics

KW - Mapping

KW - RNA Processing, Post-Transcriptional

KW - Bisulfite

U2 - 10.1007/978-1-0716-3862-0_16

DO - 10.1007/978-1-0716-3862-0_16

M3 - Chapter (peer-reviewed)

C2 - 38743232

SN - 9781071638613

T3 - Methods in Molecular Biology

SP - 229

EP - 242

BT - HIV protocols

A2 - Prasad, Vinayaka R.

A2 - Kalpana, Ganjam V.

PB - Humana Press

ER -

Identifying individual pseudouridine (Ψ) sites across transcripts from HIV-1 infected cells

Abstract

Publication series

Keywords

UN SDGs

Access to Document

Fingerprint

Student theses

Post-transcriptional regulation of Influenza A virus mRNAs

Cite this