SUPR
Expression of the zebra finch germline-restricted chromosome
Dnr:

NAISS 2024/22-164

Type:

NAISS Small Compute

Principal Investigator:

Niki Vontzou

Affiliation:

Uppsala universitet

Start Date:

2024-02-02

End Date:

2025-03-01

Primary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Webpage:

Allocation

Abstract

The germline-restricted chromosome (GRC) constitutes the largest chromosome of the zebra finch genome. It was initially cytogenetically detected back in 90’s, yet each genetic content has been thoroughly examined in the last five years. There are considerable oddities surrounding this chromosome. Firstly, its genomic content is based on the amplification of hundreds of gene copies found in autosomal and sex chromosomes (A-chromosomes). Secondly, it is an understudied case of programmed DNA elimination at an unknown embryonic stage of the zebra finch development. Thirdly, whether the GRC has a beneficial function for the zebra finch genome or a more parasitic, B chromosome-like behavior, is to be elucidated. In this project, we collected transcriptomic data from different stages of the zebra finch development and we are interrogating the function of this peculiar chromosome. Specifically, we are using different RNA technologies, including RNA-seq, small-RNA-seq and Spatial Transcriptomics to identify the GRC expression in the course of zebra finch development. In total we have 27 and 25 RNA-seq and small-RNA- seq libraries respectively, and we are expecting the data of two 10x Visium slides as well. These data will enable differential expression analyses between key developmental stages and the spatial identification of the GRC expression in the representative tissues.