Genome-Wide Identification and Functional Characterization of Noncoding RNAs (ncRNAs) Differentially Expressed During Insect Development

Yue Wang; Minsheng You; Weiyi He

doi:10.1007/978-1-0716-1633-8_1

Genome-Wide Identification and Functional Characterization of Noncoding RNAs (ncRNAs) Differentially Expressed During Insect Development

Methods Mol Biol. 2022:2360:1-8. doi: 10.1007/978-1-0716-1633-8_1.

Authors

Yue Wang^{1

2

3}, Minsheng You^{1

2

3}, Weiyi He^{4

5

6}

Affiliations

¹ State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.
² International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
³ Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China.
⁴ State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China. wy.he@fafu.edu.cn.
⁵ International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. wy.he@fafu.edu.cn.
⁶ Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China. wy.he@fafu.edu.cn.

PMID: 34495502
DOI: 10.1007/978-1-0716-1633-8_1

Abstract

MicroRNAs (miRNAs) are important regulatory noncoding RNAs (ncRNAs) at the posttranscriptional level of gene expression. Linear long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) can function as competing endogenous RNAs (ceRNAs) of miRNAs and regulate the expression of protein-coding genes. This chapter presents a procedure for the bioinformatic analysis of these three ncRNAs that are differentially expressed during insect development. In the first step, lncRNAs and circRNAs are identified based on RNA-sequencing data. In the second step, miRNAs are identified based on small RNA-sequencing data and combined with the two ncRNAs from the previous step for functional characterization.

Keywords: Noncoding RNAs; Target gene prediction; Transcriptome analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genome
Insecta / genetics
MicroRNAs / genetics
RNA, Circular
RNA, Long Noncoding / genetics*
RNA, Untranslated / genetics

Substances

MicroRNAs
RNA, Circular
RNA, Long Noncoding
RNA, Untranslated