Quorum Sensing

Chapter 14

Global Expression Analysis of Quorum Sensing-Controlled

Genes by RNAseq

Charlotte D. Majerczyk

Abstract

RNA sequencing (RNAseq) enables transcriptional profiling of many organisms. This chapter describes the
use of RNAseq in prokaryotes to identify quorum sensing (QS)-controlled transcripts by comparing
samples from QS-induced and -uninduced conditions. Briefly, each RNA sample is converted to ds-
cDNA in a method that limits amplification of ribosomal RNA species. The ds-cDNA contains adapters
that enable sequencing and quantification by next-generation sequencing (NGS).

KeywordsRNA sequencing (RNAseq), Next-generation sequencing (NGS), Quorum sensing, Not-

so-random (NSR) primers, Transcriptomics

1 Introduction

RNA sequencing (RNAseq) uses next-generation sequencing (NGS)

to provide information on the presence and quantity of RNA in a

biological sample. For many purposes, RNAseq technology is repla-

cing microarray technology to analyze transcript profiles. The first

step in obtaining RNAseq data is preparing high-quality RNA sam-

ples. The RNA in the sample is then converted to ds-cDNA, and the

ds-cDNA fragments are sequenced on a next-generation sequencer,

such as the Illumina platform. During sequencing, information on

the identity and quantity of each transcript is determined as the

machine records the sequence and abundance of each molecule.

The transcriptional profile of each sample can then be compared

with another sample, in the same way that microarray analysis can

compare transcriptional profiles. Advantages of RNAseq include: no

requirement for a pre-synthesized microarray chip, analysis can be

done on sequenced and unsequenced organisms (as there is potential

to use NGS to sequence your organism of interest), data is generated

for small and/or previously unidentified RNA species (including

noncoding RNAs), and RNAseq provides detailed transcript infor-

mation (such as the transcriptional start and stop sites). That being

Livia Leoni and Giordano Rampioni (eds.),Quorum Sensing: Methods and Protocols, Methods in Molecular Biology,
vol. 1673,https://doi.org/10.1007/978-1-4939-7309-5_14,©Springer Science+Business Media LLC 2018

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