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1. Exploring the interplay between PARP1 and circRNA biogenesis and function

   https://doi.org/10.1002/wrna.1823  

   Dhahri, Hejer ; Fondufe‐Mittendorf, Yvonne N. ( November 2023 , WIREs RNA)

   PARP1 (poly‐ADP‐ribose polymerase 1) is a multidomain protein with a flexible and self‐folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non‐covalently through its PAR moieties induced by auto‐PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1‐mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers.

   This article is categorized under:

   RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications

   Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs

   RNA Processing > Splicing Regulation/Alternative Splicing

    

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2. PARP1 Regulates Circular RNA Biogenesis though Control of Transcriptional Dynamics

   https://doi.org/10.3390/cells12081160  

   Eleazer, Rebekah ; De Silva, Kalpani ; Andreeva, Kalina ; Jenkins, Zoe ; Osmani, Nour ; Rouchka, Eric C. ; Fondufe-Mittendorf, Yvonne ( April 2023 , Cells)

   Circular RNAs (circRNAs) are a recently discovered class of RNAs derived from protein-coding genes that have important biological and pathological roles. They are formed through backsplicing during co-transcriptional alternative splicing; however, the unified mechanism that accounts for backsplicing decisions remains unclear. Factors that regulate the transcriptional timing and spatial organization of pre-mRNA, including RNAPII kinetics, the availability of splicing factors, and features of gene architecture, have been shown to influence backsplicing decisions. Poly (ADP-ribose) polymerase I (PARP1) regulates alternative splicing through both its presence on chromatin as well as its PARylation activity. However, no studies have investigated PARP1’s possible role in regulating circRNA biogenesis. Here, we hypothesized that PARP1’s role in splicing extends to circRNA biogenesis. Our results identify many unique circRNAs in PARP1 depletion and PARylation-inhibited conditions compared to the wild type. We found that while all genes producing circRNAs share gene architecture features common to circRNA host genes, genes producing circRNAs in PARP1 knockdown conditions had longer upstream introns than downstream introns, whereas flanking introns in wild type host genes were symmetrical. Interestingly, we found that the behavior of PARP1 in regulating RNAPII pausing is distinct between these two classes of host genes. We conclude that the PARP1 pausing of RNAPII works within the context of gene architecture to regulate transcriptional kinetics, and therefore circRNA biogenesis. Furthermore, this regulation of PARP1 within host genes acts to fine tune their transcriptional output with implications in gene function. 

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3. Cooperative nucleic acid binding by Poly ADP-ribose polymerase 1

   https://doi.org/10.1038/s41598-024-58076-w  

   Melikishvili, Manana ; Fried, Michael G. ; Fondufe-Mittendorf, Yvonne N. ( March 2024 , Scientific Reports)

   Poly (ADP)-ribose polymerase 1 (PARP1) is an abundant nuclear protein well-known for its role in DNA repair yet also participates in DNA replication, transcription, and co-transcriptional splicing, where DNA is undamaged. Thus, binding to undamaged regions in DNA and RNA is likely a part of PARP1’s normal repertoire. Here we describe analyses of PARP1 binding to two short single-stranded DNAs, a single-stranded RNA, and a double stranded DNA. The investigations involved comparing the wild-type (WT) full-length enzyme with mutants lacking the catalytic domain (∆CAT) or zinc fingers 1 and 2 (∆Zn1∆Zn2). All three protein types exhibited monomeric characteristics in solution and formed saturated 2:1 complexes with single-stranded T₂₀and U₂₀oligonucleotides. These complexes formed without accumulation of 1:1 intermediates, a pattern suggestive of positive binding cooperativity. The retention of binding activities by ∆CAT and ∆Zn1∆Zn2 enzymes suggests that neither the catalytic domain nor zinc fingers 1 and 2 are indispensable for cooperative binding. In contrast, when a double stranded 19mer DNA was tested, WT PARP1 formed a 4:1 complex while the ∆Zn1Zn2 mutant binding saturated at 1:1 stoichiometry. These deviations from the 2:1 pattern observed with T₂₀and U₂₀oligonucleotides show that PARP’s binding mechanism can be influenced by the secondary structure of the nucleic acid. Our studies show that PARP1:nucleic acid interactions are strongly dependent on the nucleic acid type and properties, perhaps reflecting PARP1’s ability to respond differently to different nucleic acid ligands in cells. These findings lay a platform for understanding how the functionally versatile PARP1 recognizes diverse oligonucleotides within the realms of chromatin and RNA biology.

    

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4. Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?)

   https://doi.org/10.1002/bies.202200015  

   Sanchez, Anthony ; Buck‐Koehntop, Bethany A. ; Miller, Kyle M. ( May 2022 , BioEssays)

   The lysine demethylase KDM5A collaborates with PARP1 and the histone variant macroH2A1.2 to modulate chromatin to promote DNA repair. Indeed, KDM5A engages poly(ADP‐ribose) (PAR) chains at damage sites through a previously uncharacterized coiled‐coil domain, a novel binding mode for PAR interactions. While KDM5A is a well‐known transcriptional regulator, its function in DNA repair is only now emerging. Here we review the molecular mechanisms that regulate this PARP1‐macroH2A1.2‐KDM5A axis in DNA damage and consider the potential involvement of this pathway in transcription regulation and cancer. Using KDM5A as an example, we discuss how multifunctional chromatin proteins transition between several DNA‐based processes, which must be coordinated to protect the integrity of the genome and epigenome. The dysregulation of chromatin and loss of genome integrity that is prevalent in human diseases including cancer may be related and could provide opportunities to target multitasking proteins with these pathways as therapeutic strategies.

    

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5. The Phantom Mark: Enigmatic roles of phospho‐Threonine 4 modification of the C‐terminal domain of RNA polymerase II

   https://doi.org/10.1002/wrna.1771  

   Kempen, Ryan P. ; Dabas, Preeti ; Ansari, Aseem Z. ( January 2023 , WIREs RNA)

   The largest subunit of RNA polymerase II (Pol II) has an unusual carboxyl‐terminal domain (CTD). This domain is composed of a tandemly repeating heptapeptide, Y₁S₂P₃T₄S₅P₆S₇, that has multiple roles in regulating Pol II function and processing newly synthesized RNA. Transient phosphorylation of Ser2 and Ser5 of the YS₂PTS₅PS repeat have well‐defined roles in recruiting different protein complexes and coordinating sequential steps in gene transcription. As such, these phospho‐marks encipher a molecular recognition code, colloquially termed the CTD code. In contrast, the contribution of phospho‐Threonine 4 (pThr4/pT4) to the CTD code remains opaque and contentious. Fuelling the debate on the relevance of this mark to gene expression are the findings that replacing Thr4 with a valine or alanine has varied impact on cellular function in different species and independent proteomic analyses disagree on the relative abundance of pThr4 marks. Yet, substitution with negatively charged residues is lethal and even benign mutations selectively disrupt synthesis and 3′ processing of distinct sets of coding and non‐coding transcripts. Suggestive of non‐canonical roles, pThr4 marked Pol II regulates distinct gene classes in a species‐ and signal‐responsive manner. Hinting at undiscovered roles of this elusive mark, multiple signal‐responsive kinases phosphorylate Thr4 at target genes. Here, we focus on this under‐explored residue and postulate that the pThr4 mark is superimposed on the canonical CTD code to selectively regulate expression of targeted genes without perturbing genome‐wide transcriptional processes.

   This article is categorized under:

   RNA Processing > 3′ End Processing

   RNA Processing > Processing of Small RNAs

   RNA Processing > Splicing Regulation/Alternative Splicing

    

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