Post-graduate theses
Current Record: 26 of 802
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Identifier |
000460509 |
Title |
The role of the nascent RNA in chromatin conformation and genome regulation |
Alternative Title |
Ο ρόλος του νεοσυντιθέμενου RNA στη ρύθμιση της διαμόρφωσης της χρωματίνης και της γονιδιακής έκφρασης |
Author
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Κυδωνάκης, Κωνσταντίνος Ε.
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Thesis advisor
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Lavigne, Matthieu
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Reviewer
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Σπηλιανάκης, Χαράλαμπος
Γιακουντής, Αντώνιος
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Abstract |
Nascent RNA has for long time been considered as a passive molecule of transcription and co-transcriptional processes. However, recently published studies demonstrate and establish its role in transcription progression, splicing and chromatin architecture. In line with these studies, we tried to standardize and optimize two molecular methods to address the issue of RNA organization. Our aim was to elaborate on its implication in various nuclear function, such as 3D chromatin conformation maintenance and gene expression regulation. We apply Global RNA Interaction with DNA by deep sequencing (GRID-seq) is an “all to all” genomic approach to study RNA-chromatin interaction and CRISPR-dCas9 system-based chromatin precipitation (CRISPR pull down) as a molecular approach to targeting specific chromatin regions and co-precipitate every factor that interacts with it. Regarding GRID-seq, we managed to perform double fixation in our cells, but further optimization is necessary, particularly in improving the efficiency of nuclei isolation. In parallel, for CRISPR pull down, we worked with the in vitro approach, and attempted to isolate the target chromatin and evaluate if our assay was specific calculating fold enrichment ratio between expected vs non-specific loci via qPCR. Although we only reached low efficiency in our first attempts, we propose several optimizations that will improve our approach.
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Language |
English |
Issue date |
2023-11-24 |
Collection
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School/Department--School of Sciences and Engineering--Department of Biology--Post-graduate theses
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Type of Work--Post-graduate theses
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Permanent Link |
https://elocus.lib.uoc.gr//dlib/6/6/a/metadata-dlib-1700653279-903492-11457.tkl
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Views |
988 |