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Abstract(s)
Long tandem repeats (LTRs) sequences, namely satellite DNA (satDNA), play a critical role in
genome organization and stability. Their detection and characterization still represent a challenge, which
long-read Nanopore sequencing is helping to simplify. Thus, there is a growing interest in developing
bioinformatic tools for the analysis of LTRs and in understanding their role in genome evolution. The main
aim of this work was the characterization of LTRs in mammalian genomes, using WGS data from two model
organisms: Peromyscus genus and Homo sapiens. In the first case, the focus was to characterize PMSat, an
evolutionarily conserved satDNA. In the second case, the key objective was to perform a comparative
assessment of LTRs between different human long-read genome datasets, to characterize in detail the human
satellite HSat1A and its transcripts, and to establish methods to analyze satDNA involvement in
Robertsonian translocations (specifically the t(14;21)).
The analysis performed identified PMSat as the most abundant LTR of the Peromyscus genus, in
accordance with previous cytogenetic studies, with GC-content, monomer and array length exhibiting little
variation. Moreover, a tendency in the positioning in Peromyscus genus chromosomes was identified. In the
study of the three WGS Nanopore human datasets, the LTRs ALR, BSR, HSat2 and HSat1A were identified
as the most abundant. It was possible to demonstrate the potential of chromosome sorting to facilitate the
analysis of translocated chromosomes. However, low sequencing yield and DNA fragmentation did not
allow for characterization of the target region. Finally, LTRs of HSat1A were shown to have a predominance
of 9-mer monomers, and to express polyadenylated transcripts of varying lengths, probably resulting from
alternative polyadenylation.
This study represents a relevant contribution to understanding the role of LTRs in genome
organization and evolution.
Description
Tese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de Ciências
Keywords
LTR DNA satélite Sequenciação Nanopore PMSat HSat1A Teses de mestrado - 2023