ChIPseq analysis of transcription factors network of cold-tolerant bacteria Lactococcus carnosus

Abstract

This study was completed for the University of Helsinki. It is part of the project which focuses on analysing transcription factor networks in the cold-tolerant bacterium Lactococcus carnosus using chromatin immunoprecipitation followed by sequencing (ChIP-seq). The main project focuses on transcription factors (CcpA, SigA, SigE, SigL, SigW, Rex, and MngR) that regulate metabolic pathways in the bacterium, and the work’s goal was to identify where these transcription factors bind on the bacterial genome, helping to understand how L. carnosus adapts to cold and regulates its metabolism. In this thesis study, as a part of the main project, the quality of the sequencing reads was assessed to determine which samples could be used for further analysis. The work involved bacterial culture preparation, cross-linking, sonication, immunoprecipitation, and DNA purification, with following sequencing and data analysis. After sample preparation, sequencing results were analyzed to determine the quality of the reads. Eight samples had a read count above value of 100,000, which was the goal for reliable data. These samples were considered suitable for further analysis. However, most samples had low read counts, potentially because of insufficient DNA input concentrations or possible sample degradation during handling and storage. Next steps include rerunning samples with low read counts in optimised conditions and continuing the analysis. The findings may have applications in food preservation and biotechnology.