MIT CompBio Lecture 09 - Three Dimensional Genome

MIT Computational Biology: Genomes, Networks, Evolution, Health Prof. Manolis Kellis http://compbio.mit.edu/6.047/ Fall 2018 Lecture 09 - Three Dimensional Genome 1. Methods for studying nuclear genome organization - Measuring locus-landmark interactions: ChIP, DamID - Measuring locus-locus interactions: 3C, 4C, 5C, Hi-C, ChIA-PET 2. Processing and normalization of Hi-C datasets - Correcting for biases and issues with Hi-C data - Normalization, sources of bias and bias correction 3. Interpretation of data and functional characterization - Lamina Associated Domains (LADs) - Topologically Associated Domains (TADs) and other compartments 4. Conservation of nuclear genome organization - Across species, across cell types - Sequence basis for conservation? 5. Towards a mechanistic understanding - Nuclear genome organization through the (single) cell cycle - (Limitations of) 3D modeling of nuclear genome organization - Loop extrusion as a potential mechanism for nuclear organization Slides for Lecture 9: https://stellar.mit.edu/S/course/6/fa18/6.047/courseMaterial/topics/topic2/lectureNotes/Lecture09_ThreeDimensionalGenome/Lecture09_ThreeDimensionalGenome_6up.pdf