Applications of genomic tools to decode genome function

The revolution in sequencing technologies has greatly advanced our understanding of genomes. Many regulatory elements lacking protein-coding ability, such as long non-coding RNAs have been identified and characterized in different biological contexts. However, functional interrogation of these non-coding elements remains to be challenging when it comes to resolving the relationships between genotypes and phenotypes. To elucidate the functional roles of regulatory elements encoded in the genome and further to deconvolute the evolutionary history of chromosomes, I developed new informatics tools/strategies and combined them with existing computational tools to analyse the genomic data.

In study I, a bioinformatics strategy was developed and implemented to identify sex-linked sequences and to recover the genes from a set of recently available avian genomes. The analysis of molecular signatures on sex chromosomes across species has described the unique evolutionary trajectories in avian genomes for the first time. In study II, a novel in vitro assay was applied to determine the binding specificities of human RNA binding proteins. By searching for the potential enrichment of their binding sites in the human genome with a newly implemented tool, the essential roles of RBPs involved in many RNA metabolic procedures have been reinforced. In study III, the unique molecular identifiers were incorporated into the loss-of-function study in CRISPR/Cas9 based pooled screening. I implemented the analytical tools to interpret the data, which has immensely extended the power of pooled screening by allowing to trace phenotypes of individual cell lineages. In study IV, sequence conservation information contributed by comparative genomics has been integrated to indicate the functional significance of enhancers upstream of the oncogene Myc, which, however, counter-intuitively did not show obvious physiological consequences after knockout.

In summary, four studies were conducted to dissect the functionality of the genome. Through integrating knowledge from distinct dimensions, we can eventually attempt to unveil the principles that dictate the relationships between genotypes and phenotypes.

List of scientific papers

I. Zhou, Q., Zhang, J., Bachtrog, D., An, N., Huang, Q., Jarvis, E. D., Gilbert, M. T. P., & Zhang, G. (2014). Complex evolutionary trajectories of sex chromosomes across bird taxa. Science. 346(6215), 1246338.
https://doi.org/10.1126/science.1246338

II. Jolma, A., Zhang, J., Mondragón, E., Kivioja, T., Yin, Y., Zhu, F., Morris, Q., Hughes, T. R., Maher, L. J., & Taipale, J. (2019). Binding specificities of human RNA binding proteins towards structured and linear RNA sequences. [Manuscript]

III. Schmierer, B., Botla, S. K., Zhang, J., Turunen, M., Kivioja, T., & Taipale, J. (2017). CRISPR/Cas9 screening using unique molecular identifiers. Molecular Systems Biology. 13(10), 945.
https://doi.org/10.15252/msb.20177834

IV. Dave, K., Sur, I., Yan, J., Zhang, J., Kaasinen, E., Zhong, F., Blaas, L., Li, X., Kharazi, S., Gustafsson, C., De Paepe, A., Månsson, R., & Taipale, J. (2017). Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. eLife. 6.
https://doi.org/10.7554/eLife.23382