Lindsay Shopland Institute for Molecular Biophysics

1. Visualizing chromosome organization in the cell nucleus May be used to thinking of genome organization in terms of linear map of genes along primary sequence. But those genes and that sequence are active within the nucleus, and in their active state have a 3-D organization. Long-standing and fundamental question in biology is how ~1 Gb DNA folds up to fit in 10 um nucleus and successfully manage all the information in primary sequence???May be used to thinking of genome organization in terms of linear map of genes along primary sequence. But those genes and that sequence are active within the nucleus, and in their active state have a 3-D organization. Long-standing and fundamental question in biology is how ~1 Gb DNA folds up to fit in 10 um nucleus and successfully manage all the information in primary sequence???

2. Technology Wish List

3. 100-year-old view of chromosomes Scientists have been looking at chromosomes for well over 100 years now. From views such as this that it was inferred that chromosomes contain heritable information. Now we think in terms of chromosomes as making up the genome. But how do these structures work to use that genomic information in the right cells and at the right time? Actually, chromosomes don�t take on this rod-like structure when genome is expressed. These are chromosomes in mitosis, when cell is dividing.Scientists have been looking at chromosomes for well over 100 years now. From views such as this that it was inferred that chromosomes contain heritable information. Now we think in terms of chromosomes as making up the genome. But how do these structures work to use that genomic information in the right cells and at the right time? Actually, chromosomes don�t take on this rod-like structure when genome is expressed. These are chromosomes in mitosis, when cell is dividing.

4. Chromosomes during the cell cycle

5. Interphase chromosomes form �territories�, not rods Genome partitioned into chromosomes. Form territories, not just mixed up spagetti. However, each chromosome looks differentGenome partitioned into chromosomes. Form territories, not just mixed up spagetti. However, each chromosome looks different

6. Probing chromosome structure in the nucleus

7. Interphase chromosome structure Genome partitioned into chromosomes. Form territories, not just mixed up spagetti. However, each chromosome looks differentGenome partitioned into chromosomes. Form territories, not just mixed up spagetti. However, each chromosome looks different

8. DNA folding: a long-standing mystery Know a lot about primary sequence folding around histones, folds then into 30 nm fiber, then additional levels of folding. In interphase, can resolve sequences 200 kb apart, on mitotic chroms, >3 Mb. Know a lot about primary sequence folding around histones, folds then into 30 nm fiber, then additional levels of folding. In interphase, can resolve sequences 200 kb apart, on mitotic chroms, >3 Mb.

9. Model:the �piebald� region of chromosome 14 Mention Kevin and CarolMention Kevin and Carol

10. Bar-coding 5 Mb of chromosome What I�ve done to begin addressing this issue of a more global view of organization within the nuclear chromosome is to start with a relatively simple sequence feature, namely to examine where genes are versus sequences that are not genes. And to do this, I chose a relatively large but manageable chromosome subregion. The model system . . . What I�ve done to begin addressing this issue of a more global view of organization within the nuclear chromosome is to start with a relatively simple sequence feature, namely to examine where genes are versus sequences that are not genes. And to do this, I chose a relatively large but manageable chromosome subregion. The model system . . .

11. Predominant 3-D patterns in the nucleus

12. Model of chromosome region folding and organization Turn to the sequence again to figure out why we might be getting gene cluster hubsTurn to the sequence again to figure out why we might be getting gene cluster hubs

13. Modeling randomized chromosomes Probablistic associations between individual clusters and deserts Collaboration with ChristophProbablistic associations between individual clusters and deserts Collaboration with Christoph

14. Summary

15. Technology Wish List

16. Technology Wish List

17. Acknowledgements