Identification of target genes mediated by two-component regulators of staphylococcus aureus using RNA-seq technology

Ting Lei; Junshu Yang; Aaron Becker; Yinduo Ji

doi:10.1007/978-1-4939-9849-4_10

Identification of target genes mediated by two-component regulators of staphylococcus aureus using RNA-seq technology

Ting Lei, Junshu Yang, Aaron Becker, Yinduo Ji

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

4 Scopus citations

Abstract

Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.

Original language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	125-138
Number of pages	14
Volume	2069
DOIs	https://doi.org/10.1007/978-1-4939-9849-4_10
State	Published - 2020

Publication series

Name	Methods in molecular biology (Clifton, N.J.)
Publisher	Humana Press
ISSN (Print)	1064-3745

Bibliographical note

Funding Information:
We thank Dr. Juan E Abrahante Llorens at the University of Minnesota Informatics Institute (UMII) and Lisa Fazzino for the assistance with data analysis. This work was supported by grant AI057451 from the National Institute of Allergy and Infectious Disease and partially supported by grant MIN-63-082 and MIN-63-113 from CVM research Office UMN Ag Experimental Station General Agricultural Research Funds.

Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2020.

Keywords

Gene expression profile
RNA sequencing technologies (RNA-seq)
Real-time reverse transcription polymerase chain reaction
Staphylococcus aureus
Two-component system (TCS)
RNA-Seq
Regulatory Sequences, Nucleic Acid
Transcriptome
Staphylococcus aureus/genetics
Gene Expression Regulation, Bacterial
Reverse Transcriptase Polymerase Chain Reaction
Real-Time Polymerase Chain Reaction

PubMed: MeSH publication types

Research Support, Non-U.S. Gov't
Journal Article
Research Support, N.I.H., Extramural

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10.1007/978-1-4939-9849-4_10

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title = "Identification of target genes mediated by two-component regulators of staphylococcus aureus using RNA-seq technology",

abstract = "Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.",

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author = "Ting Lei and Junshu Yang and Aaron Becker and Yinduo Ji",

note = "Funding Information: We thank Dr. Juan E Abrahante Llorens at the University of Minnesota Informatics Institute (UMII) and Lisa Fazzino for the assistance with data analysis. This work was supported by grant AI057451 from the National Institute of Allergy and Infectious Disease and partially supported by grant MIN-63-082 and MIN-63-113 from CVM research Office UMN Ag Experimental Station General Agricultural Research Funds. Publisher Copyright: {\textcopyright} Springer Science+Business Media, LLC, part of Springer Nature 2020.",

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AU - Yang, Junshu

AU - Becker, Aaron

AU - Ji, Yinduo

N1 - Funding Information: We thank Dr. Juan E Abrahante Llorens at the University of Minnesota Informatics Institute (UMII) and Lisa Fazzino for the assistance with data analysis. This work was supported by grant AI057451 from the National Institute of Allergy and Infectious Disease and partially supported by grant MIN-63-082 and MIN-63-113 from CVM research Office UMN Ag Experimental Station General Agricultural Research Funds. Publisher Copyright: © Springer Science+Business Media, LLC, part of Springer Nature 2020.

PY - 2020

Y1 - 2020

N2 - Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.

AB - Transcriptomics enables us to elucidate comprehensive gene expression profiles in given experimental conditions. Global regulators, which include transcriptional regulators and two-component regulatory systems, have evolved in a variety of bacterial systems. They play important roles in bacterial fitness and pathogenesis by regulating target gene expression. Advanced next-generation RNA sequencing technology (RNA-seq) provides a powerful and effective tool to analyze the transcriptome of bacterial cells. In this chapter, we provide a detailed procedure for the investigation of gene expression profiles and identification of target genes, regulons, and/or pathways that are mediated by a regulator. This procedure is done using RNA-seq analysis, which involves RNA purification, mRNA enrichment, decontamination, RNA-seq data analysis, and quantitative real-time reverse transcription PCR.

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KW - RNA sequencing technologies (RNA-seq)

KW - Real-time reverse transcription polymerase chain reaction

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KW - Regulatory Sequences, Nucleic Acid

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KW - Staphylococcus aureus/genetics

KW - Gene Expression Regulation, Bacterial

KW - Reverse Transcriptase Polymerase Chain Reaction

KW - Real-Time Polymerase Chain Reaction

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PB - Humana Press Inc.

ER -

Identification of target genes mediated by two-component regulators of staphylococcus aureus using RNA-seq technology

Abstract

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Keywords

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