Universität zu Köln

Arora, Ankit (2018). Development of Web-Application for High-Throughput Sequencing Data and In Silico Dissection of LINE-1 Retrotransposons in Cellular Senescence. PhD thesis, Universität zu Köln.

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Abstract

Next-generation sequencing (NGS) technologies have been remarkably advantageous in opening new paths for scientific research. The large-scale generation of data has resulted in the advancement of tools for data analysis, but the requirement to implement increasing amount of tools in a systematic way is still a vast question. In the initial analysis of distant NGS datasets, we observed the need for an efficient framework for downstream analysis of NGS data. Therefore, the web application titled "RanchNGS" was developed. This particular web-framework aims to understand the downstream and integrative analysis for various sequencing data such as RNA-Seq, Ribo-seq and additionally ChIP-seq. RanchNGS benefits from an efficient analysis in a reduced time frame and without the need of any advanced programming skills. Furthermore, the role of transposable elements (TEs) in cellular senescence was revealed by studying distinct NGS technologies. TEs are segments of DNA that have the potential to be in-motion by jumping from one location in the genome to another. Due to this reason, they are also called as "jumping genes". Long Interspersed Nuclear Element-1 (LINE-1 or L1) are the only autonomous TEs currently active in human and non-human primate genomes. Our study primarily targeted a broad extent of L1 elements. The result of excessive oncogenic stress in immortalized cells undergoing senescence were investigated. The current study focused on the transcriptional and post-transcriptional mechanisms that confer the cross-talk between L1 and host-defense machinery. It was observed that the transcriptional and post-transcriptional regulation of L1 elements are diminished as cells undergo senescence that takes precedence to the response activation of L1 elements at RNA and protein level. Moreover, we hypothesized that excessive oncogenic stress in immortalized cells could be related to L1 retrotransposition, triggering double- strand breaks and enabling cells to enter permanent cell cycle arrest.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Arora, Ankit UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-89242
Date:	25 October 2018
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Cologne Center for Genomics
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Transposons English Web-development English LINE-1 elements English
Date of oral exam:	24 July 2018
Referee:	Name Academic Title Nürnberg, Peter Prof.Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/8924