Supervision team information
Computational Biology & Gene Regulation group, Norwegian Centre for Molecular Biosciences and Medicine (NCMBM)
Supervisor: Anthony Mathelier; e-mail address: anthony.mathelier@ncmbm.uio.no
IBV supervisor: Pierre Chymkovitch
Internship place: NCMBM, Oslo, Norway
Keywords: transcription factor activity, CAGE, ATAC-seq, histone modifications, computational biology, breast cancer, epigenetic reprogramming
Project description
Transcription factors (TFs) regulate gene expression through binding at specific DNA sequences known as transcription factor binding sites (TFBSs). Understanding TF activity from omics data is crucial for deciphering regulatory mechanisms involved in complex biological processes such as cancer progression and epigenetic reprogramming. Inspired by methods such as MAYA [1], this Master's project aims to develop a software to quantify multi-modal TF activities at pre-defined TFBSs from omics data (including Cap Analysis of Gene Expression (CAGE), ATAC-seq, and histone modification profiles). Leveraging our expertise and databases, notably JASPAR [2] and UniBind [3], the candidate will build the computational software to decompose TF activity from omics data. This approach will be applied to in-house datasets to investigate regulatory dynamics underlying breast cancer and cellular reprogramming, providing insights into transcriptional regulation with potential clinical and biological implications.
[1] Multi-modal quantification of pathway activity with MAYA. Y. Landais and C. Vallot. Nature Communications (2023)
[2] JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. I. Rauluseviciute, R.R. Puig, et al. Nucleic Acids Research (2024)
[3] UniBind: maps of high-confidence direct TF-DNA interactions across nine species. R.R. Puig, P. Boddie, A. Khan, J.A.C. Mondragon, A. Mathelier. BMC Genomics (2021)