Long non-coding RNAs identification and annotation in Schistosoma mansoni and Schistosoma japonicum

Author(s)

Lucas Ferreira Maciel

• Document type: Master's Dissertation
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI)
• Defense date: 2020-03-23

Examining board members

Sergio Verjovski de Almeida; Júlia Pinheiro Chagas da Cunha; Eduardo Moraes Rego Reis; Thiago Motta Venancio

• Advisor: Sergio Verjovski de Almeida

Abstract

Long non-coding RNAs (lncRNAs) (>200 nt) are expressed at levels lower than those of the messenger RNAs (mRNAs), and in all eukaryotic model species where they have been characterized, they are transcribed from thousands of different genomic loci. In humans, some four dozen lncRNAs have been studied in detail, and they have been shown to play important roles in transcriptional regulation, acting in conjunction with transcription factors and epigenetic marks to modulate the tissue-type specific programs of transcriptional gene activation and repression. Previous works have identified around 10,000 and 3,000 lncRNAs in Schistosoma mansoni and Schistosoma japonicum, respectively. These are flatworms that cause schistosomiasis, an important neglected tropical disease. The limited number of RNA- sequencing (RNA-seq) libraries that had been previously assessed, together with the use of old and incomplete versions of S. mansoni and S. japonicum genomes and their protein- coding transcriptome annotations, have hampered the identification of all lncRNAs expressed in these parasites. Here 66 S. japonicum RNA-seq libraries from whole worms at different life-cycle stages and 633 S. mansoni RNA-seq libraries from whole worms at different stages, from isolated tissues, from cell-populations, and from single-cells were used to identify lncRNAs. All libraries were obtained from the public domain. A pipeline was developed and used for transcripts mapping to the genomes and gene assembly. A set of 16,583 S. mansoni and 12,291 S. japonicum lncRNA transcripts were identified and annotated; gene sequences identity and synteny analyses between the species demonstrate that some lncRNAs have synteny conservation even when there is a lack of sequence conservation. Weighted gene co- expression network analyses were performed for both species and lncRNAs with dynamic expression through parasite development were identified. These lncRNAs are co-expressed with protein-coding genes associated with several important biological pathways such as reproduction, replication, drug metabolism, and nervous system development. This work paves the way towards future functional characterization of the role of lncRNAs in schistosomes. (AU)

• FAPESP's process: 18/19591-2 - Long non-coding RNAs annotation and identification of potential therapeutic targets in Schistosoma mansoni
• Grantee: Lucas Ferreira Maciel
• Support Opportunities: Scholarships in Brazil - Master