Maintenance of genome integrity via activities of the cohesin network

Correct segregation of sister chromatids is an important mechanism for keeping the genome intact. The cohesin complex holds the sister chromatids together from the time of their formation during replication, until separation at anaphase and is thereby mediating cohesion between the sister chromatids, essential for correct chromatid segregation. Members of the cohesin network in addition play essential roles in the repair of double strand breaks (DSBs), and have been shown to be involved in regulation of transcription. Thus, cohesin is a master regulator of a majority of the cellular processes required for transfer of the correct genetic information from one cell generation to the next.

The aim with this thesis was to further elucidate the function(s) of the cohesin network in genome integrity. In doing so, either budding yeast or human cell cultures were used. In budding yeast, cohesin is recruited to the vicinity of an induced DSB and cohesion is established genome wide. This phenomenon of re-establishment of cohesion is called Damage induced (DI-) cohesion. By investigating the function of Polymerase η in DI-cohesion, we found that it is differentially regulated at the break site and genome-wide. We also suggested that the function of break proximal DI-cohesion is to support DSB repair, while the genome wide DI-cohesion is important for correct chromosomal segregation and for survival following repeated break induction. A gene regulatory role of cohesin and its loading complex Scc2/4 has been described in several organisms, but not investigated thoroughly in yeast. Thus, we investigated the gene transcription profiles in Scc2-deficient cells in the absence and presence of DNA damage. We conclude that Scc2 is indeed instrumental for gene regulation also in budding yeast, both globally in an undamaged situation, and in response to DSB induction. Our data also indicate that the difference in gene response between WT and Scc2-deficient cells is not based on overt changes in cohesin binding. Mutations in NIPBL (human ortholog of SCC2), are frequent in Cornelia de Lange syndrome (CdLS) patients. By studying the DSB repair in B-cells originated from CdLS patient, we found a shift towards the alternative, microhomology-based, end joining pathway during class switch recombination, implicating that NIPBL is important for classical NonHomologous End Joining (NHEJ).

Our results suggest that NIPBL plays an important and conserved role for NHEJ, in addition to its previously known function in homologous recombination. Altogether I have with this thesis highlighted the importance of the cohesin network in DI-cohesion and DNA DSB repair, as well as in the transcriptional regulation, all important components of the systems used for maintenance of genome integrity.

List of scientific papers

I. Enervald, E., Lindgren, E., Katou, Y., Shirahige, K., Ström, L. Importance of Polη for Damage-Induced Cohesion Reveals Differential Regulation of Cohesion Establishment at the Break Site and Genome-Wide. PLoS Genet. (2013) 9:e1003158.
https://doi.org/10.1371/journal.pgen.1003158

II. Lindgren, E., Hägg, S., Giordano, F., Björkegren, J., Ström, L. Inactivation of the Cohesin Loader Scc2 alters Gene Expression Both Globally and in Response to a Singel DNA Double Strand Break. [Manuscript]

III. Enervald, E., Du, L., Visnes, T., Björkman, A., Lindgren, E., Wincent, J., Borck, J., Colleaux, L., Cormier-­Daire, V., C. van Gent, D., Pie, J., Puisac, B., de Miranda, N., Kracker, S., Hammarström, L., Villartay, J.P., Durandy, A., Schoumans, J., Ström, L., Pan-­Hammarström, Q. A regulatory role for the cohesin loader NIPBL in nonhomologous end joining during immunoglobulin class switch recombination. J Exp Med. (2013) 210:2503-­13.
https://doi.org/10.1084/jem.20130168.