Development of Oligopaint probes for chromosomes with high frequency of repetitive sequences

• Grant number: 23/14607-6
• Support Opportunities: Regular Research Grants
• Start date: February 01, 2024
• End date: January 31, 2026
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Maria Dulcetti Vibranovski
• Grantee: Maria Dulcetti Vibranovski
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Antonio Bernardo de Carvalho
• Associated scholarship(s): 24/18487-8 - In situ Validation of Oligopaint Probes for Chromosomes with High Frequency of Repetitive Sequences, BP.TT

Abstract

Cytogenetics plays a pivotal role in unraveling the complexities of chromosomal structures and dynamic protein interactions during the cell cycle. The use of fluorescence-based chromosomal labeling techniques, such as Fluorescence in situ hybridization (FISH), holds paramount significance in this context. However, comprehensive labeling of chromosomes containing highly repetitive sequences, such as the Y chromosomes and neo-sex chromosomes, poses a well-recognized challenge. This is primarily due to the lack of highly specific probes and the propensity for non-specific hybridization. This project's central objective is the development and validation of a bioinformatics pipeline that will be instrumental in creating highly specific oligopaint probes for the unique repetitive sequences found in different chromosomes. These oligopaint probes will be strategically combined with single-stranded oligonucleotides, enabling comprehensive labeling of chromosomes characterized by a high density of repetitive sequences. Initially, the focus will be on the Y chromosome of the species Drosophila melanogaster, notable for its abundance of repetitive sequences. Subsequently, the research will expand to the neo-sex chromosomes of Drosophila miranda, a species harboring sex chromosomes of distinct evolutionary ages and, therefore, varying levels of sequence differentiation. This project will not only advance genomic research but also streamline cytogenetic studies across diverse species. It will be based on a process encompassing the identification of unique genetic sequences, the design of customized oligopaint probes, including the incorporation of repetitive sequences, and the judicious application of filters to ensure probe specificity. The efficacy of labeling chromosomes with repetitive sequences will be confirmed in situ through laboratory experiments. This advancement in the ability to efficiently label chromosomes with repetitive sequences will open new avenues of research and deepen our understanding of genomic organization and chromosomal evolution, not only in Drosophila but also in other species. It has the potential to transform the way we conduct cytogenetic and genomic studies at the molecular level. (AU)