How does GG-NER complex-dependent chromatin remodeling initiate DNA damage recognition in chromatin by the Rad4-Rad23 damage recognition complex

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All forms of life contain within their cells the encrypted information necessary for coordinating the function of individual cells and the organism as a whole. The information is stored in the nucleus of the cell within a large molecule called deoxyribonucleic acid [DNA], sometimes referred to as the double helix. This information is divided into units called genes, and the sum of all the genetic material of an organism is referred to as its genome. DNA might be expected to be extremely stable and resistant to change, since altering the coded message could cause genes to malfunction. On the other hand, organisms are able to adapt to changes in their environment by virtue of the genetic variation within the population caused by acquired differences in the genetic material of each individual - a process is known as evolution. Much of the genetic variation within the human population is the result of 'reshuffling' the genes during sexual reproduction - this is called recombination. However, changes in the genetic material can occur by other means. DNA can be damaged by the normal events occuring within the cell, as well as physical or chemical damage from the environment, including ultraviolet radiation from sunlight. Each of our cells receives thousands of DNA lesions each day. The vast majority of this damage, if left unchecked, would result in the rapid loss of the information contained in the genetic material, since replication of damaged DNA during normal cell division can permanently alter the genetic code. These heritable changes are called mutations. During evolution mechanisms that can repair DNA have been encoded in the genome of all organisms and these are fundamental to maintaining the stability of the genome. People with defects in the genes controlling these DNA repair pathways suffer serious diseases, but it is now understood that collectively these repair mechanisms are fundamental to normal DNA function.Our research aims to understand how one of these processes, nucleotide excision repair [NER] operates. Much of our knowledge has come from the study of NER in a variety of different organisms including yeast. The process is remarkably similar in yeast and human cells, and studying NER in yeast continues to inform on the mechanism of this process. DNA repair is integrated with other cellular process including the ubiquitin proteasome pathway [UPP]. Our laboratory has made important discoveries into how these pathways interact, uncovering a new E3 ubiquitin ligase, a part of the UPP, which connects the activity of the proteasome to NER. This ubiquitin ligase controls how cells respond to DNA damage. We recently uncovered an unanticipated regulatory mechanism that integrates the ubiquitination of DNA repair factors with the regulation of gene transcription. We showed that DNA damage recognition factors involved in NER, can also bind to the promoters of certain genes in the absence of damage. In this context, the repair factors can switch off gene transcription. In response to DNA damage, and in a manner dependent on ubiquitination of Rad4, the damage recognition factors are released from these promoters and this allows the damage-induced transcription of these genes. In this application, we plan to investigate how the GG-NER chromatin remodelling complex regulates the activity of the DNA damage recognition complex, promoting efficient recognition of UV induced lesions in chromatin. Understanding how DNA damage is recognised in chromatin is of central importance, because recently it has been reported that many novel cancer causing genes that have been identified from cancer genome sequencing projects turn out to be involved in the chromatin remodelling process. It is likely that defective chromatin remodelling will cause genomic instability, possibly in specific regions of the genome, giving rise to tumourigenesis. This project seeks to understand how UV damage recognition occurs throughout the genome.