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(Epi)genomics and transcriptomics of euchromatic satellite DNAs in embryogenesis and development

Project type
Znanstveno-istraživački projekti
Research Projects
Croatian Science Foundation
Start date
Feb 15th 2020
End date
Feb 14th 2024
Total cost
997600 HRK

Satellite DNAs (satDNAs) are abundant tandemly repeated, non-coding DNAs largely located in (peri)centromeric heterochromatin which have an essential role in centromere function. There are evidences that these regions are actively transcribed, and transcripts are engaged in heterochromatin formation, stress and malignant transformation. However, recent data revealed the existence of different satDNAs in euchromatin of many species but information on their biological role is completely missing. In the beetle model Tribolium castaneum we previously identified nine abundant satDNAs (Cast1-Cast9) located exclusively in euchromatic regions. Although Cast1-Cas9 satDNAs are strongly underrepresented in T. castaneum reference genome, quantitative analysis disclosed that these satDNAs comprise significant 5% of the genome. Our unpublished results indicate transcription potential and epigenetic status which speak in favour of their “euchromatic” nature. Genome abundance, their transcription potential and putative distribution in the vicinity of genes make euchromatic satDNAs attractive for investigation. To gain insight into evolutionary trends and the biological relevance of euchromatic satDNAs in T. castaneum two main goals will be addressed: 1) to discover the evolutionary dynamics of euchromatic satDNAs and detect genes in the vicinity of satDNA arrays, we will sequence the genome using a long read nanopore approach and Cast1-Cast9 will be assembled in the reference genome, and 2) to reveal their functional role, we will investigate their transcription potential, epigenetic regulation and possible impact on expression of genes in the vicinity during embryogenesis and development. T. castaneum represents an excellent model to achieve the proposed aims because it has annotated genome, clearly defined developmental stages, thoroughly explored embryogenesis and brain development which enable functional evaluation of the euchromatic satDNA transcriptome.

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