Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

Alexander L. Cope; Sangeevan Vellappan; John S. Favate; Kyle S. Skalenko; Srujana S. Yadavalli; Premal Shah

doi:10.1007/978-1-0716-1851-6_5

Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

Alexander L. Cope, Sangeevan Vellappan, John S. Favate, Kyle S. Skalenko, Srujana S. Yadavalli, Premal Shah

Rutgers, The State University

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218–223, 2009), ribosome profiling measurements and subsequent data analysis remain challenging. Here, we describe our lab’s protocol for performing ribosome profiling in bacteria, yeast, and mammalian cells. This protocol has integrated elements from three published ribosome profiling methods. In addition, we describe a tool called RiboViz (Carja et al., BMC Bioinformatics 18:461, 2017) (https://github.com/riboviz/riboviz ) for the analysis and visualization of ribosome profiling data. Given raw sequencing reads and transcriptome information (e.g., FASTA, GFF) for a species, RiboViz performs the necessary pre-processing and mapping of the raw sequencing reads. RiboViz also provides the user with various quality control visualizations.

Original language	American English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	83-110
Number of pages	28
DOIs	https://doi.org/10.1007/978-1-0716-1851-6_5
State	Published - 2022

Publication series

Name	Methods in Molecular Biology
Volume	2404

ASJC Scopus subject areas

Molecular Biology
Genetics

Keywords

Antibiotic inhibitors
Footprinting
RNA
Ribo-seq
Ribosome profiling
Translation initiation

Access to Document

10.1007/978-1-0716-1851-6_5

Cite this

@inbook{903c50708af5442d9244f1f4bb1aa0a6,

title = "Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling",

abstract = "The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218–223, 2009), ribosome profiling measurements and subsequent data analysis remain challenging. Here, we describe our lab{\textquoteright}s protocol for performing ribosome profiling in bacteria, yeast, and mammalian cells. This protocol has integrated elements from three published ribosome profiling methods. In addition, we describe a tool called RiboViz (Carja et al., BMC Bioinformatics 18:461, 2017) (https://github.com/riboviz/riboviz ) for the analysis and visualization of ribosome profiling data. Given raw sequencing reads and transcriptome information (e.g., FASTA, GFF) for a species, RiboViz performs the necessary pre-processing and mapping of the raw sequencing reads. RiboViz also provides the user with various quality control visualizations.",

keywords = "Antibiotic inhibitors, Footprinting, RNA, Ribo-seq, Ribosome profiling, Translation initiation",

author = "Cope, {Alexander L.} and Sangeevan Vellappan and Favate, {John S.} and Skalenko, {Kyle S.} and Yadavalli, {Srujana S.} and Premal Shah",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

year = "2022",

doi = "10.1007/978-1-0716-1851-6_5",

language = "American English",

series = "Methods in Molecular Biology",

publisher = "Humana Press Inc.",

pages = "83--110",

booktitle = "Methods in Molecular Biology",

}

TY - CHAP

T1 - Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

AU - Cope, Alexander L.

AU - Vellappan, Sangeevan

AU - Favate, John S.

AU - Skalenko, Kyle S.

AU - Yadavalli, Srujana S.

AU - Shah, Premal

PY - 2022

Y1 - 2022

N2 - The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218–223, 2009), ribosome profiling measurements and subsequent data analysis remain challenging. Here, we describe our lab’s protocol for performing ribosome profiling in bacteria, yeast, and mammalian cells. This protocol has integrated elements from three published ribosome profiling methods. In addition, we describe a tool called RiboViz (Carja et al., BMC Bioinformatics 18:461, 2017) (https://github.com/riboviz/riboviz ) for the analysis and visualization of ribosome profiling data. Given raw sequencing reads and transcriptome information (e.g., FASTA, GFF) for a species, RiboViz performs the necessary pre-processing and mapping of the raw sequencing reads. RiboViz also provides the user with various quality control visualizations.

AB - The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218–223, 2009), ribosome profiling measurements and subsequent data analysis remain challenging. Here, we describe our lab’s protocol for performing ribosome profiling in bacteria, yeast, and mammalian cells. This protocol has integrated elements from three published ribosome profiling methods. In addition, we describe a tool called RiboViz (Carja et al., BMC Bioinformatics 18:461, 2017) (https://github.com/riboviz/riboviz ) for the analysis and visualization of ribosome profiling data. Given raw sequencing reads and transcriptome information (e.g., FASTA, GFF) for a species, RiboViz performs the necessary pre-processing and mapping of the raw sequencing reads. RiboViz also provides the user with various quality control visualizations.

KW - Antibiotic inhibitors

KW - Footprinting

KW - RNA

KW - Ribo-seq

KW - Ribosome profiling

KW - Translation initiation

UR - http://www.scopus.com/inward/record.url?scp=85118459957&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85118459957&partnerID=8YFLogxK

U2 - 10.1007/978-1-0716-1851-6_5

DO - 10.1007/978-1-0716-1851-6_5

M3 - Chapter

C2 - 34694605

T3 - Methods in Molecular Biology

SP - 83

EP - 110

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

Abstract

Publication series

ASJC Scopus subject areas

Keywords

Access to Document

Other files and links

Fingerprint

Cite this