Molecular and Epigenetic Characterization of Ring Chromosomes: Investigation of Formation Mechanisms and Position Effect through DNA Methylation Profile and Gene Expression

• Grant number: 25/05729-6
• Support Opportunities: Scholarships in Brazil - Master
• Start date: August 01, 2025
• End date: March 31, 2027
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Principal Investigator: Maria Isabel de Souza Aranha Melaragno
• Grantee: Gabriella Rodrigues dos Santos
• Host Institution: Escola Paulista de Medicina (EPM). Universidade Federal de São Paulo (UNIFESP). Campus São Paulo. São Paulo , SP, Brazil
• Associated research grant: 19/21644-0 - Impact of genetic variants on genomic stability and their effects on the phenotype, AP.TEM

Abstract

Ring chromosomes generally form due to breaks and fusions of chromosomal arms, leading to the loss of genetic material at both ends. These breaks and fusions predominantly occur in highly repetitive regions, making it challenging to precisely identify the junction points and formation mechanisms, as well as the functional impact of the rings on the genome. The replication of ring chromosomes can result in secondary alterations, contributing to dynamic mosaicism. Additionally, the circular structure of the ring chromosome may have a position effect, influencing epigenetic regulation through changes in DNA methylation and gene expression, both near the breakpoints and in more distant regions. This project proposes the study of approximately eight patients with autosomal ring chromosomes. Karyotyping will be performed to confirm the presence of the ring chromosome and assess its instability in lymphocyte cultures. Innovative investigative approaches, including whole-genome sequencing using long-read sequencing (LRS) and bioinformatics tools, will be applied to characterize the ring chromosomes in terms of genomic content, define the breakpoints, and infer their formation mechanisms. This technique also enables the investigation of allele-specific DNA methylation, comparing the ring chromosome with its normal homolog. Genes found to be differentially methylated will be analyzed for gene expression using RT-qPCR. This study aims to enhance the understanding of the genome's responses to structural alterations, with scientific and clinical implications, particularly for prognosis and genetic counseling.