Nucleolar transcription and its connections to nucleolar homeostasis and mitochondrial stress responses

R-loop is a specific nucleic acid structure, and that forms during RNA transcription. It comprises an RNA:DNA hybrid and displaced ssDNA. R-loops are prevalent and dynamic in the mammalian genome occupying up to 5%. R-loops are known to act as modulators of genome dynamics. They regulate a variety of gene transcription mechanisms and influence genomic stability. Dysregulation of R-loop is linked to a variety of human diseases. For this reason, protein factors involved in DNA and RNA metabolism are known to mediate R-loop resolution. Dysfunction of these factors resulted in aberrant R-loop accumulation, often resulting in transcription disruption and genomic instability as reported in tumorigenesis and a number of genetic disorders, including trinucleotide repeat-associated diseases and neurological disorders. Here I describe the roles of Senataxin (SETX) and Replication protein A (RPA) complex in nucleolar R-loop resolution. I demonstrate their function in nucleolar homeostasis and in particular in RNA polymerase I mediated rRNA transcription and the maintenance of nucleolar structure.This dissertation is composed of three sessions. Section 1: I review nucleolar transcription that generate a complex network of RNAs, and their contribution to nucleolar R-loops formation, with multiple roles in maintaining nucleolar homeostasis. Section 2: I describe novel roles of Replication Protein A in nucleolar homeostasis. Senataxin (SETX) mutations are linked to two different neurological disease: Amyotrophic Lateral Sclerosis (ALS4) and Ataxia Oculomotor Apraxia (AOA2) both defective in R-loop resolution. We show that loss of SETX promotes RPA translocation into nucleolus in an R-loop dependent manner where it associates with rDNA. The same nucleolar RPA phenotype is evident in SETX- deficient AOA2 patient cells. We further explored this phenotype under conditions of CPT- induced genotoxic stress, which is coupled with accumulation of nucleolar R loops. Additionally, we show that loss of RPA decreased 47S pre-rRNA levels, but increased “promoter and pre-rRNA antisense” RNA (PAPAS) and promoter RNA (pRNA). Meanwhile, we also showed loss of RPA disrupted nucleolar structure. Section 3: I describe the identification and characterization of nucleolar lncRNA (PAPAS) which encodes a short polypeptide RIEP that plays a role in combating genomic instability and mitochondrial stress. We show that this novel peptide encoded by PAPAS is localized to the nucleolus and mitochondria but is translocated to the peri-nucleolus and peri-nucleus region upon heat shock induced cellular stresses. We also showed that RIEP facilitates SETX protein stability and plays a role in restricting genomic instability possibly through its association with H3K9me3 which maintains a heterochromatin state. Finally, we show that RIEP interacts with CHCHD2 and C1QBP(P32) and may consequently function in mitochondrial stress responses.