Gene expression lab, Instituto de Biomedicina de Sevilla
September 2017 - October 2018
Master's thesis student and research assistant
In the context of the master’s thesis (MSc in Molecular Genetics & Biotechnology), under the supervision of Dr. Sebastián Chávez de Diego and Dr. Gabriel Gutierrez Pozo and within Dr. Victoria Begley’s PhD project, I started studying Xrn1, a protein involved in the degradation of mRNA, and it’s role in the nucleosome localization and transcription in Saccharomyces cerevisiae. Using MNase-seq and following a DANPOS-based analysis, we found that the Xrn1 knockout mutant strains had higher nucleosome occupancy around TSS, which we related with a lower transcription initiation compared to WT strains, whereas in the gene body, the nucleosome occupancy was diminished as a consequence of RNA pol II backtracking. Results were validated using MNase-qPCR of two selected genes in Xrn1 conditional mutants.
Tasks:
- Pre-processing and analysis of MNase-seq data.
- MNase-qPCR validation: yeast culture, MNase-driven DNA digestion, design of MNase-qPCR primers, performing qPCR.
- Scientific writting.
Related works
Research papers:
- Begley et al (2020). Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration. RNA Biology. doi: 10.1080/15476286.2020.1845504.
Master’s thesis:
- Mitjavila-Ventura (2018). Influence of Xrn1 in nucleosome positioning across Saccharomyces cerevisiae genome and its effects in transcription. Universidad de Sevilla (US).