FÁTIMA MANZANO NÚÑEZ Next step Elucidation of the cellular organization of genomes and its impact on genome regulation and activity How is the genome organized in 3D space? What are the fundamental principles of organization? What are the molecular mechanisms that give rise to the organization patterns? What are the physiological consequences of spatial genome organization? Loops LADs Fig.1 T. Cremer and C. Cremer. Nature reviews . Vo. 2. 2001 LADs Only structural properties? Low gene expression levels Nearly 40% of human genome consist on LADs Lars Guelen et al. Nature. Vo. 453. 2008. LADs Study the association of chromatin to any protein Dam (DNA adenine methyltansferase) + Protein Methylated regions are amplified (PCR) and analyzed by high-throughput techniques (microarrays or sequencing). Alejandro Rodriguez et al. Biochemical Society Transactions . Vo. 41, p. 6, 2013. LADs Dam - Lamin B1 Interaction map a)High levels of LADs alternate with low levels. Sharp transitions. b) and c) LADs vary in size and are frequently 1 megabase (Mb) in size or larger Fig. 1. Lars Guelen et al. Nature. Vo. 453. 2008. LADs Fig. 4. Lars Guelen et al. Nature. Vo. 453. 2008. Loops Structural elements with regulatory functions MHC II cluster Fig. 2. Tom Misteli. Cell. 128, 787–800, 2007 Fig.4. Emanuela V. Volpi1 et al. Journal of Cell Science 113, 1565-1576 . 2000. Internal vs. peripherial Relative positions Translocations Changes in transcriptional activity and gene density Change the position of genes during differentiation Fig.2 Masahiko Kuroda et al. Journal of Cell Science. 117, 5897-5903, 2004. Functional consequences of Global chromatin organization Relative position important determinant of function Separate chromosomes into Separate chromosomes into physical interaction physical proximity sharing corregulating gene loci. transcription sites. Trans-regulation. Fig. 3. Tom Misteli. Cell. 128, 787–800, 2007 Tissue-specific proximity of chromosomes correlates with tissuespecific translocation frequency Tissue specific chromosomes organization Fig. 3. Tom Misteli. Cell. 128, 787–800, 2007 Fig.1. Luis A Parada et al. Genome Biology, Vo. 5, 7, R44. 2004 Such areas that are nearly the lamina have low gene density and transcription. Loops are structural elements with regulatory functions. The organization of the genome is related with its regulation. The organization of the genome depends of the genes that are active or inactive, so also of the kind of cell and its differentiation level. The organization can follow the internal vs. peripheral pattern or the relative position model. Translocations have tissue-specific frequency. 1. 2. 3. 4. 5. 6. 7. 8. Alejandro Rodriguez et al. The links between chromatin spatial organization and biological function. Biochemical Society Transactions . Vo. 41, p. 6, 2013. Emanuela V. Volpi1 et al. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. Journal of Cell Science 113, 1565-1576 . 2000. Lars Guelen et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. Vo. 453. 2008. Luis A Parada et al. Tissue-specific spatial organization of genomes. Genome Biology, Vo. 5, 7, R44. 2004. Masahiko Kuroda et al. Alteration of chromosome positioning during adipocyte differentiation. Journal of Cell Science. 117, 5897-5903, 2004. Shlomit Farkash-Amar et al. Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization. Plos one. Vo. 7 , 11, 2012. T. Cremer and C. Cremer. Chromosome territories nuclear architecture and gene regulation in mammalian cells. Nature reviews . Vo. 2. 2001. Tom Misteli. Beyond the Sequence: Cellular Organization of Genome Function. Cell. 128, 787–800, 2007.