# The evolutionary and functional genomics of satellite DNA

> **NIH NIH R35** · UNIVERSITY OF ROCHESTER · 2020 · $383,843

## Abstract

Project summary
Eukaryotic genomes contain arrays of tandemly repeated non-coding sequences that we currently know little
about—satellite DNAs. Typically found near centromeres, telomeres and on Y chromosomes, satellite DNAs
can comprise over 50% of some eukaryotic genomes. They are known to change rapidly in sequence and
genomic location, which can cause genetic incompatibilities between closely related species. The
misregulation of satellite DNA can have serious consequences for genomic stability and cancer formation.
Despite being a ubiquitous part of genomes and having important functional consequences, we know little
about satellite DNA. The lack of genetic, genomic and molecular tools to study tandemly repeated sequences
has stymied progress towards understanding satellite DNA evolution and function. For example, satellite DNAs
are particularly challenging to sequence and assemble. Recent developments in next-generation sequencing
technologies circumvent some of these problems. This proposal integrates genomic, molecular and cytological
methods to study the evolutionary and functional genomics of satellite DNA in Drosophila genomes. The PI has
developed new genomic and cytological methods to study the evolutionary dynamics, genomic structure and
expression of satellite DNA with unprecedented resolution. The PI will use these methods to study changes in
satellite DNA sequence, abundance and organization over evolutionary time and to determine the evolutionary
forces responsible for these changes. This proposal aims to develop comprehensive models of satellite DNA
evolution that take into consideration different types of natural selection based on the functional aspects of
satellite DNAs. Little is currently known of satellite DNA function: the precise genetic manipulation of satellite
DNAs with site-specific approaches had not been possible in the past due to a lack of unique target sites. The
new genomic methods developed in this proposal provide an opportunity to discover unique sites flanking
satellite DNAs that may serve as targets for genome editing techniques. The proposal will create precise
genomic deletions of satellite DNA in Drosophila melanogaster to test specific hypotheses about the regulation,
fitness effects and selfish genetic behavior of satellite DNA. This proposal will also use new molecular genetic
techniques to manipulate the expression of satellite DNAs in the germline to ask questions about their
functions in chromosome segregation and chromatin organization. These experiments will have broad
implications not only for genome evolution, but also for understanding the regulation of satellite DNA in cancer
and aging.

## Key facts

- **NIH application ID:** 9941099
- **Project number:** 5R35GM119515-05
- **Recipient organization:** UNIVERSITY OF ROCHESTER
- **Principal Investigator:** Amanda Marie Larracuente
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $383,843
- **Award type:** 5
- **Project period:** 2016-08-01 → 2021-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9941099

## Citation

> US National Institutes of Health, RePORTER application 9941099, The evolutionary and functional genomics of satellite DNA (5R35GM119515-05). Retrieved via AI Analytics 2026-05-29 from https://api.ai-analytics.org/grant/nih/9941099. Licensed CC0.

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