Utilizing data from a new, quantitative ChIP-sequencing method to investigate the dynamics of histone H3.3

Sammanfattning: DNA is a key component of almost all cells, but it is not the sole determinant of the cellular functions and features. A great number of histones, transcription factors and other proteins interact with the DNA, regulating fundamental processes such as DNA accessibility and gene expression. Perturbations of these interactions are associated to a wide range of diseases. An example is the histone variant H3.3, which is normally involved in prevention of genomic rearrangements during mammalian development. Mutations in the H3.3 gene have been shown to be related to pediatric brain cancer forms. Studying this histone variant and other protein-DNA interactions is important in order to understand cellular processes as well as causes of diseases. This has commonly been done through a sequencing method called ChIP-seq, which however does not normally capture the dynamics of the interactions. Therefore a new method called MINUTE-ChIP has been developed, which in combination with a special type of pulse-chase experiment adds a time dimension to the analyses. In this project, data from this new method has been analyzed in order to investigate the dynamics of histone H3.3. In addition to calculating the rates of incorporation and release from the DNA, tools for visualizing the data in interactive plots have also been developed. These calculations and tools facilitate the interpretation of the histone H3.3 data and can in the future be used for analyzing data generated by similar experiments for other chromatin factors.