Analysis of repetitive elements transcription during embryogenesis of sea urchin Strongylocentrotus purpuratus

Okorokova Larisa, student of the Bioinformatics Institute, St. Petersburg, Nikolay Panyushev, research adviser, Leonid Adonin, PI

Introduction

Repetitive elements (RE) occupy significant part of eukaryotic genomes and some of them are shown to play diverse roles in genome regulation. For example, they are implied to be the origins of non-coding RNA. During embryogenesis of the sea urchin, a significant number of RE are expressed (up to 80%). The role of these elements in the regulation of biological processes remains unknown.

Aim

The aim of this study was to identify the RE in the genome of the purple sea urchin and analyze their expression at different stages of embryogenesis.

Project steps and methods

1. Identifing and classification RE in the genome S. purpuratus (Spur 5.0) using RepeatModeler
2. Quantify RE abundance in genome.
3. Reference transcriptome assembling which includes RE and previously annotated genes.
4. Quantification of transcripts abundances using Kallisto.
5. Statistical analysis in Sleuth.
6. Identifing active RE
7. Primary analysis of scRNAseq (including RE expression)
8. Secondary analysis of scRNAseq in R (see scrnaseq directory)

Detailed description of steps 1-4, 6-7 can be found in lab notebook Step 5 description can be found in sleuth_script

RNA-seq data

RNA-seq data of S. purpuratus embryos on different stages were obtained from SRA database (Project PRJNA531297)

System requirements

• RepeatModeler and RepeatMasker can be found here
• R version 3.5.3
• kallisto version 0.46.0 can be found here
• sleuth R package v0.30.0 (conda package)