RNAs as Sensors of Oxidative Stress in Bacteria

Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.

Influenza Virus NS1 Protein-RNA Interactome Reveals Intron Targeting

The NS1 protein of influenza A virus is a multifunctional virulence factor that inhibits cellular processes to facilitate viral gene expression. While NS1 is known to interact with RNA and proteins to execute these functions, the cellular RNAs that physically interact with NS1 have not been systematically identified. Here we reveal a NS1 protein-RNA interactome and show that NS1 primarily binds intronic sequences. Among this subset of pre-mRNAs is the RIG-I pre-mRNA, which encodes the main cytoplasmic antiviral sensor of influenza virus infection. This suggested that NS1 interferes with the antiviral response at a posttranscriptional level by virtue of its RNA binding properties. Indeed, we show that NS1 is necessary in the context of viral infection and sufficient upon transfection to decrease the rate of RIG-I intron removal. This NS1 function requires a functional RNA binding domain and is independent of the NS1 interaction with the cleavage and polyadenylation specificity factor CPSF30. NS1 has been previously shown to abrogate RIG-I-mediated antiviral immunity by inhibiting its protein function. Our data further suggest that NS1 also posttranscriptionally alters RIG-I pre-mRNA processing by binding to the RIG-I pre-mRNA.IMPORTANCE A key virulence factor of influenza A virus is the NS1 protein, which inhibits various cellular processes to facilitate viral gene expression. The NS1 protein is localized in the nucleus and in the cytoplasm during infection. In the nucleus, NS1 has functions related to inhibition of gene expression that involve protein-protein and protein-RNA interactions. While several studies have elucidated the protein interactome of NS1, we still lack a clear and systematic understanding of the NS1-RNA interactome. Here we reveal a nuclear NS1-RNA interactome and show that NS1 primarily binds intronic sequences within a subset of pre-mRNAs, including the RIG-I pre-mRNA that encodes the main cytoplasmic antiviral sensor of influenza virus infection. Our data here further suggest that NS1 is necessary and sufficient to impair intron processing of the RIG-I pre-mRNA. These findings support a posttranscriptional role for NS1 in the inhibition of RIG-I expression.

Abstract 1373: Circular RNAs generated from the BRCA1 pseudogene regulates the DNA damage response through SERBP1 RNA-binding protein

The genomic region encompassing the BRCA1 gene includes the BRCA1P1 pseudogene (BRCA1P1) within ~170kb at chromosome 17q21. The homology and proximity of BRCA1 and BRCA1P1 create a hot spot for recombination, resulting in a large genomic rearrangement found in some families with breast and ovarian cancers. While the significant role of BRCA1 in regulating the DNA damage response (DDR) is well defined, little is known about the biological properties of the BRCA1P1 pseudogene. To functionally annotate BRCA1P1, we conducted a CRISPR-Cas 9 knockout of the pseudogene, as well as knockdown of the expression using antisense oligonucleotides. Both knockout and knockdown of the pseudogene result in increases in apoptosis and sensitivity to DNA damaging drugs. Depletion of BRCA1P1 accumulates spontaneous DNA damage foci and leads to replication fork stalling. Mechanical studies reveal that the BRCA1P1 generates circular RNAs, which are retained in nuclei. Mass spectrometry followed by chromatin isolation by RNA purification (ChIRP) identifies a specific association of the circular RNAs with SERBP1 RNA-binding protein, which was confirmed by ChIRP-Western. Consequently, BRCA1P1 knockout decreased SERBP1 protein expression in the nuclei. Based on the previous report that SERBP1 binds to mRNAs of DDR proteins and controls their translation, we propose a mechanism of BRCA1P1-driven regulation of DDR protein expression through SERBP1. Our data indicate that the BRCA1P1 pseudogene plays a role in regulating replication fork progression and genomic instability in breast cancer cells through an interaction with SERBP1 RNA-binding protein.

Citation Format: Yoo J. Han, Jing Zhang, Jennifer M. Mason, Toshio F. Yoshimatsu, Xinxin Du, Ian Hurley, Danny E. Kim, Aparna Anantharaman, Laia P. Brunet, Aleix Prat, John Kwon, Kannanganattu V. Prasanth, Olufunmilayo I. Olopade. Circular RNAs generated from the BRCA1 pseudogene regulates the DNA damage response through SERBP1 RNA-binding protein [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1373.

RNA-editing enzymes ADAR1 and ADAR2 coordinately regulate the editing and expression of Ctn RNA

Adenosine deaminases acting on RNA (ADARs) are proteins that catalyse widespread A-to-I editing within RNA sequences. We recently reported that ADAR2 edits and stabilizes nuclear-retained Cat2 transcribed nuclear RNA (Ctn RNA). Here, we report that ADAR1 coordinates with ADAR2 to regulate editing and stability of Ctn RNA. We observe an RNA-dependent interaction between ADAR1 and ADAR2. Furthermore, ADAR1 negatively regulates interaction of Ctn RNA with RNA-destabilizing proteins. We also show that breast cancer (BC) cells display elevated ADAR1 but not ADAR2 levels, compared to nontumourigenic cells. Additionally, BC patients with elevated levels of ADAR1 show low survival. Our findings provide insights into overlapping substrate preferences of ADARs and potential involvement of ADAR1 in BC.

ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins

Adenosine deaminases acting on RNA (ADARs) catalyze the editing of adenosine residues to inosine (A-to-I) within RNA sequences, mostly in the introns and UTRs (un-translated regions). The significance of editing within non-coding regions of RNA is poorly understood. Here, we demonstrate that association of ADAR2 with RNA stabilizes a subset of transcripts. ADAR2 interacts with and edits the 3΄UTR of nuclear-retained Cat2 transcribed nuclear RNA (Ctn RNA). In absence of ADAR2, the abundance and half-life of Ctn RNA are significantly reduced. Furthermore, ADAR2-mediated stabilization of Ctn RNA occurred in an editing-independent manner. Unedited Ctn RNA shows enhanced interaction with the RNA-binding proteins HuR and PARN [Poly(A) specific ribonuclease deadenylase]. HuR and PARN destabilize Ctn RNA in absence of ADAR2, indicating that ADAR2 stabilizes Ctn RNA by antagonizing its degradation by PARN and HuR. Transcriptomic analysis identified other RNAs that are regulated by a similar mechanism. In summary, we identify a regulatory mechanism whereby ADAR2 enhances target RNA stability by limiting the interaction of RNA-destabilizing proteins with their cognate substrates.