Contents

**Preface XI**


Vahap Eldem, Gokmen Zararsiz, Tunahan Taşçi, Izzet Parug Duru, Yakup Bakir and Melike Erkan


#### **X** Contents



Preface

This book is an overview about transcriptome analysis and how other "omics" could be ap‐ plied in different fields, from microorganisms to precision medicine. The content of each chapter was designed to encourage three types of readers. First, this book will benefit those interested in learning about the most powerful and cost-efficient methods applied for a broad analysis of gene expression regulation of a single cell, a tissue, or the whole living organisms. We aim to offer a wide view of these applications in distinct areas, from agricul‐ ture to human diseases, introducing and revising advanced concepts of RNA-Seq technolo‐ gy. In addition, some particularities of the vast world of RNAs were investigated. Most researchers would agree that the memorable event in the RNA area over the last 20 years has been the discovery of the driver functions of noncoding RNAs, such as siRNA and miR‐ NA. These new findings allowed new extensive researches on the control of RNA levels. Besides the contribution to uncover the multitude of small RNAs regulating gene expres‐ sion, the development of high-throughput sequencing technologies also allowed the investi‐ gation of mechanisms related to RNA modifications. Unlike the well-established role of DNA modifications in gene regulation, little is known about modifications in RNA and their influence on gene expression. Mechanisms of RNA modification were addressed here, dis‐ cussing future challenges and perspectives of studies that attempt to unravel the processes related to the regulation of several stages of the biological system. In spite of the numerous initiatives with animal model investigation, the study of gene expression in plants was also assessed in this book. We point out tools and methodologies for those who are interested in transcriptome analysis in this area, considering the most diverse aspects involved in this challenge. Some points discussed were the influence of transcriptome regulation and mecha‐ nisms associated to the responses of environmental stresses, plant-pathogen interactions, and resistance, which in many aspects are closely related to studies performed in the agri‐

Second, this book will also benefit those who are interested in developing an RNA-Seq study, from the experimental design to the exploration of the most varied algorithms availa‐ ble, following the best practices currently recommended. We present an overview of stateof-the-art methods including experimental design, library preparation, quality check, and preprocessing of raw reads. The particularities involved in differential expression analysis and an accurate investigation of data for specific biological questions aims to show the dif‐ ferent approaches that could be found by researchers during the development of the most varied experiments using this technology. Besides presenting a description of concepts and tools, the chapters also offer *in silico* mechanisms to initiate an experiment and to perform a good quality data analysis. Numerous options of bioinformatics tools were presented con‐ sidering users with limited access for computational resources or little experience with com‐

culture field to improve, for example, the productivity.

