poly(A)-specific Ribonuclease Research Articles

Hoyeraal-Hreidarsson syndrome: a case report of dyskeratosis congenita with a novel PARN gene mutation

Introduction and importance: Dyskeratosis congenita (DC) is a rare multisystem disorder primarily characterized by bone marrow failure due to telomere shortening. Typical clinical features include oral leukoplakia, skin hyperpigmentation, and nail dystrophy, along with an increased risk of malignancies. Hoyeraal-Hreidarsson Syndrome (HH), a severe variant of DC, is associated with profound neurological and immunological complications, emphasizing the importance of early diagnosis and genetic evaluation to guide appropriate management. Case Presentation: We present a case of a 2-year-old girl diagnosed with Hoyeraal-Hreidarsson Syndrome, linked to a newly discovered mutation in the poly (A)-specific ribonuclease (PARN) gene. The patient exhibited intrauterine growth retardation (IUGR), congenital cytomegalovirus (CMV) infection, immunodeficiency, microcephaly, and cerebellar hypoplasia. Whole exome sequencing (WES) identified a novel mutation in the PARN gene. Clinical Discussion: Hoyeraal-Hreidarsson Syndrome, a severe form of DC, manifests with multisystem involvement and is genetically heterogeneous. Early genetic testing through techniques such as WES can aid in diagnosing rare syndromes like HH and guide treatment strategies, including bone marrow transplantation. Conclusion: This case underscores the importance of genetic evaluation in complex, rare syndromes like HH. Whole exome sequencing plays a crucial role in identifying pathogenic mutations and tailoring management. The patient’s prognosis is being closely monitored following bone marrow transplantation.

Poly(A)-Specific Ribonuclease Deficiency Leads to Deregulated Expression of Genes Involved in Sex Determination and Gonadal Maturation in Zebrafish

Abstract Background Deadenylation, the process of removal of poly (A) tail of messenger ribonucleic acids (mRNAs), is a rate-limiting step in mRNA stability, and poly(A)-specific ribonuclease (PARN) is the most important exonuclease involved in this process. Besides mRNA stability, PARN is also involved in several other processes including telomere maintenance, noncoding RNA maturation, ribosome biogenesis, and TP53 function. Previously, we have shown that zebrafish PARN null mutants are viable and fertile but turn out to only develop into males, indicating a role in oogenesis. The present study was focused on analyzing the expression of genes involved in sex determination and gonadal development in PARN mutant zebrafish. Materials and Methods Total RNA was extracted and quantitative real-time polymerase chain reaction was performed to determine the expression level of genes involved in gonad development in PARN mutant embryos (4 days postfertilization [dpf]) and adults (120 dpf) in comparison to their wild-type siblings. The expression levels were estimated by the ΔΔCT relative quantification method. Results At 4 dpf, the expression of germ cell-specific genes did not show any significant difference in the null mutants compared to the heterozygous and their wild-type siblings, suggesting no effect on germ cell differentiation due to the loss of PARN. However, the majority of the ovary-associated genes analyzed showed an increased expression in PARN null and heterozygous mutants compared to the wild-type siblings. Intriguingly, the expression of testis-associated genes showed decreased expression in the mutants compared to their wild-type siblings at 4 dpf. In adult stages, as expected, the expression of genes that jointly regulate the proper formation and function of ovaries and testes showed decreased expression in PARN null mutants. Interestingly, the expression of genes involved in the differentiation of testes, despite showing a decreased expression in the mutants, was comparable between the null and heterozygous mutants. Conclusion Taken together, these results suggest that the loss of PARN does not affect germ cell differentiation but affects the sexual differentiation that happens at later stages of development, particularly the process of oogenesis, in zebrafish.

PARN Maintains RNA Stability to Regulate Insulin Maturation and GSIS in Pancreatic β Cells

AbstractDiabetes, a metabolic disorder characterized by hyperglycemia, underscores the importance of normal pancreatic β‐cell development and function in maintaining glucose homeostasis. Poly(A)‐specific ribonuclease (PARN) serves as the principal regulator of messenger RNA (mRNA) stability, yet its specific role in pancreatic β cells remains unclear. This study utilizes mice with targeted PARN deficiency in β cells to elucidate this role. Notably, Parn conditional knockout mice present unaltered β‐cell development and insulin sensitivity but reduced glucose‐stimulated insulin secretion (GSIS). The observed outcomes are corroborated in NIT‐1 cells. Furthermore, transcriptomic analyses reveal aberrant mRNA expression of genes crucial for insulin secretion in PARN‐deficient β cells. Insights from linear amplification of complementary DNA ends and sequencing and coimmunoprecipitation experiments reveal an interaction between PARN and polypyrimidine tract‐binding protein 1 (PTBP1), regulating the RNA stability of solute carrier family 30, member 8 (Slc30a8) and carbohydrate sulfotransferase 3 (Chst3). Interference with either PARN or PTBP1 disrupts this stability. These data indicate that PARN deficiency hampers GSIS and insulin maturation by destabilizing Slc30a8 and Chst3 RNAs. These findings provide compelling evidence indicating that PARN is a potential therapeutic target for enhancing insulin maturation and secretion.

A Zebrafish Model of Parn-Deficiency Reveals Conserved Mechanisms Underlying Marrow Failure and Opportunities for Therapeutic Amelioration of Hematopoiesis

Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome (IBMFS) and a telomere biology disorder that is characterized by physical malformations such as nail dystrophy, oral leukoplakia, reticular hyperpigmentation, multilineage cytopenia and immunodeficiency. Definitive treatment for the hematological complications is hematopoietic stem cell transplantation (HSCT), which is associated with high risk of organ toxicity and engraftment failure in this population. Further, DC patients are prone to developing myelodysplastic syndrome (MDS) and solid tumors. Germline mutations in the poly(A)-specific ribonuclease (PARN) gene are associated with Hoyeraal-Hreidarsson syndrome, the most severe form of DC. PARN encodes a deadenylase enzyme involved in the 3'-end processing of various RNAs including the telomerase RNA component (TERC). The clinical heterogeneity of phenotypes and the paucity of primary human samples necessitate the use of animal models such as zebrafish ( Danio rerio), given their highly conserved genetic program, to elucidate underlying biology. Zebrafish have a single PARN ortholog with 64% sequence identity at the amino acid level. Using CRISPR-Cas9 mutagenesis, we generated a 1.3 kb deletion in the zebrafish parn gene, predicted to result in premature protein truncation. To measure the hematopoietic output of the parn mutants, we performed whole-mount in situ hybridization (WISH) for key hematopoietic lineage markers. At 48 hours post-fertilization (hpf), we found a reduction in lcp1 + total leukocytes, mpx + neutrophils and hbbe3 + mature erythrocytes. Impaired erythroid differentiation was accompanied by an accumulation of gata1 + erythroid progenitors. This finding was further corroborated by o-dianisidine staining, showing reduced hemoglobinized erythrocytes. Thus, erythrocyte and leukocyte differentiation are compromised in our zebrafish parn mutant, phenocopying the multilineage cytopenia observed in DC patients. Flow cytometry of the whole kidney marrow (WKM, human bone marrow equivalent) at 12 months of age revealed an increase in hematopoietic stem and progenitor cells in the parn mutants. Giemsa staining of WKM touchpreps further identified an increase in myeloid-biased progenitors. Next, we investigated the consequences of Parn loss on telomerase activity. Using the telomere repeat amplification protocol, we found reduced telomerase activity in the WKMs of parn mutant zebrafish. Using 3' rapid amplification of cDNA ends, we observed longer ends in the terc amplicons of the parn mutants, reminiscent of defective deadenylation of human TERC RNA in the setting of PARN mutations. Exogenous thymidine supplementation has been shown to support telomere elongation in human cells. Following treatment of zebrafish embryos with thymidine nucleoside, we observed an improvement in erythrocyte numbers in the parn mutants by o-dianisidine staining at 48 hpf. Collectively, our preliminary findings suggest that telomerase-dependent mechanisms may contribute to the erythropenia seen in parn-mutant zebrafish. In summary, we generated a robust zebrafish model carrying a germline parn mutation that phenocopies the molecular and hematologic features seen in DC patients. Our model holds promise as a new in vivo tool for investigating DC-related disease mechanisms and as a platform for preclinical therapeutic screening.

Cross-talk between PARN and EGFR-STAT3 Signaling Facilitates Self-Renewal and Proliferation of Glioblastoma Stem Cells.

A positive feedback loop comprising PARN and EGFR-STAT3 signaling supports self-renewal and proliferation of glioblastoma stem cells to drive tumor progression and can be targeted in glioblastoma therapeutics.

Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in Small Tail Han sheep with FecB++ genotype

The thyroid gland is an important endocrine gland in animals, which mainly secretes thyroid hormones and acts on various organs of the body. Long-chain non-coding RNA (lncRNA) plays an important role in animal reproduction. However, there is still a lack of understanding of their expression patterns and potential roles in the thyroid of Small Tail Han (STH) sheep. In this study, RNA-seq was used to examine the transcriptome expression patterns of lncRNAs and mRNAs in the follicular phase (ww_FT) and luteal phase (ww_LT) in FecB++ genotype STH Sheep. A total of 17,217 lncRNAs and 39,112 mRNAs were identified including 96 differentially expressed lncRNAs (DELs) and 1054 differentially expressed mRNAs (DEGs). Functional analysis of genes with significant differences in expression level showed that these genes could be enriched in Ras signalling pathway, hedgehog (HH) signalling pathway, ATP-binding cassette (ABC) transporters and other signalling pathways related to animal reproduction. In addition, through correlation analysis for lncRNA–mRNA co-expression and network construction, we found that LNC_009115 and LNC_005796 trans target NIK-related kinase (NRK) and poly(A)-specific ribonuclease (PARN). LNC_007189 and LNC_002045 trans target progesterone-induced blocking factor 1 (PIBF1), LNC_009013 trans targets small mothers against decapentaplegic (SMAD1) are related to animal reproduction. These genes add new resources for elucidating the regulatory mechanisms of reproduction in sheep with different reproductive cycles of the FecB++ genotype STH sheep.

Poly(A)-specific ribonuclease protein promotes the proliferation, invasion and migration of esophageal cancer cells.

Bioinformatics analysis showed that the expression of the poly(A)-specific ribonuclease (PARN) gene in gastric cancer, head and neck squamous cell carcinoma, melanoma, cervical cancer and lung squamous cell carcinoma tissues was significantly higher than that in normal tissues and was associated with high stage and poor prognosis. The expression of the PARN gene in esophageal cancer (EC) tissue is also significantly higher than that in normal tissues, but the effect of PARN on the proliferation, migration and invasion of EC cells remains unclear. To investigate the relationship between PARN and the proliferation, migration and invasion of EC cells. The EC tissues of 91 patients after EC surgery and 63 paired precancerous healthy tissues were collected. PARN mRNA levels were measured using a tissue microarray, and the PARN expression level was evaluated using immunohistochemistry to analyze the relationship between PARN expression and clinicopathologic features as well as the survival and prognosis of patients. In addition, the effects of PARN gene knockout on tumor cell proliferation, invasion and migration were studied by using shRNA during the in vitro culture of EC cell lines Eca-109 and TE-1, and the effects of the PARN gene on tumor growth in vivo were verified by a xenotransplantation nude mice model. The expression of PARN in EC tissues was higher than that in adjacent normal tissues, and the level of PARN expression was significantly positively correlated with lymphatic metastasis. Patients with high PARN levels had poor overall survival. BIM, IGFBP-5 and p21 levels were significantly increased in the PARN knockout group, while the expression levels of the antiapoptotic proteins Survivin and sTNF-R1 were significantly decreased in the apoptotic antibody array data. In addition, the expression levels of Akt, p-Akt, PIK3CA and CCND1 in the downstream signaling pathway regulating EC progression were significantly decreased. The culture of EC cell lines confirmed that the apoptosis rate of EC cells was significantly increased, the growth and proliferation of tumor cells were significantly inhibited, and the invasion and migration ability of tumor cells were significantly decreased after PARN gene knockout. In vivo experiments of BALB/c nude mice transfected with Eca-109 cells expressing control shRNA (sh-NC) and PARN shRNA (sh-PARN) showed that the tumor volume and weight of nude mice treated with sh-PARN were significantly decreased compared with those of nude mice treated with sh-NC, indicating that PARN knockdown significantly inhibited tumor growth in vivo. PARN has antiapoptotic effects on EC cells and promotes their proliferation, invasion and migration, which is associated with the development of EC and poor patient prognosis. PARN may become a potential target for the diagnosis, prognosis prediction and treatment of EC.

Poly (A)-specific ribonuclease deficiency impacts oogenesis in zebrafish

Poly (A)-specific ribonuclease (PARN) is the most important 3′–5′exonuclease involved in the process of deadenylation, the removal of poly (A) tails of mRNAs. Although PARN is primarily known for its role in mRNA stability, recent studies suggest several other functions of PARN including a role in telomere biology, non-coding RNA maturation, trimming of miRNAs, ribosome biogenesis and TP53 function. Moreover, PARN expression is de-regulated in many cancers, including solid tumours and hematopoietic malignancies. To better understand the in vivo role of PARN, we used a zebrafish model to study the physiological consequences of Parn loss-of-function. Exon 19 of the gene, which partially codes for the RNA binding domain of the protein, was targeted for CRISPR-Cas9-directed genome editing. Contrary to the expectations, no developmental defects were observed in the zebrafish with a parn nonsense mutation. Intriguingly, the parn null mutants were viable and fertile, but turned out to only develop into males. Histological analysis of the gonads in the mutants and their wild type siblings revealed a defective maturation of gonadal cells in the parn null mutants. The results of this study highlight yet another emerging function of Parn, i.e., its role in oogenesis.

A Case of Dyskeratosis Congenita: A Unifying Diagnosis for a Patient with Agammaglobulinemia

IntroductionTelomeres are the nucleotide repeat-protein complexes that cap DNA to prevent its degradation. Telomere length decreases with each cell cycle until a critical point is reached and senescence is triggered. High mitotically active cells utilize the protein telomerase to maintain a constant telomere length for continuous cellular division. Dyskeratosis congenita (DC) is a disease resulting from pathologic mutation in genes regulating this process. One such gene is poly(A)-specific ribonuclease (PARN) which stabilizes telomerase. DC can result in severe complications involving the brain, lungs, liver, intestines, skin and bone marrow (BM). BM failure results in combined immunodeficiency by age 30 and is the primary cause of mortality.Case Description: A 36-year-old male with hypogammaglobulinemia, seizure disorder, avascular necrosis of the hip, and inflammatory bowel disorder presented with hematochezia and dyspnea. His immunodeficiency was diagnosed at age 10. He had multiple prior hospitalizations for pneumonia, sinusitis, and meningitis. Exam was notable for thrush and digit clubbing. His labs showed normal WBC, low lymphocyte count, and absent immunoglobulins. His CD19+ B-cells were non-detectable, while CD4+T cells and CD16+/CD56+ NK cells were low. BM biopsy showed absent CD20+ B cells. CT head showed cerebral atrophy. He was found to be CMV/HSV positive on endoscopic biopsy. Invitae primary immunodeficiency panel showed two variants in the PARN gene, Gain (Exons 19–21) [likely pathogenic] and Gain (Exons 1–18) [uncertain significance]. Telomere length, performed by Repeat Diagnostics Inc., was at the first percentile, which in the context of multiple organ defects and immunodeficiency confirmed a diagnosis of DC. His condition eventually deteriorated, and he died of multifocal Aspergillus and Candida pneumonia. His siblings and children were referred to genetics. DiscussionThe diagnosis of DC is often a diagnosis of childhood/adolescence. This case describes a patient with poor follow up presenting to the hospital with infection, found to have agammaglobulinemia and the terminal features of DC. This case demonstrates the utility of immunology presence in the inpatient setting, the benefits of inpatient genetic testing, and the importance of noting the difference between hypogammaglobinemia and agammaglobulinemia for infectious implications as well as diagnostic purposes.

Identification of PARN nuclease activity inhibitors by computational-based docking and high-throughput screening

Poly(A)-specific ribonuclease (PARN) is a 3′-exoribonuclease that removes poly(A) tails from the 3′ end of RNAs. PARN is known to deadenylate some ncRNAs, including hTR, Y RNAs, and some miRNAs and thereby enhance their stability by limiting the access of 3′ to 5′ exonucleases recruited by oligo(A) tails. Several PARN-regulated miRNAs target p53 mRNA, and PARN knockdown leads to an increase of p53 protein levels in human cells. Thus, PARN inhibitors might be used to induce p53 levels in some human tumors and act as a therapeutic strategy to treat cancers caused by repressed p53 protein. Herein, we used computational-based molecular docking and high-throughput screening (HTS) to identify small molecule inhibitors of PARN. Validation with in vitro and cell-based assays, identified 4 compounds, including 3 novel compounds and pyrimidopyrimidin-2-one GNF-7, previously shown to be a Bcr-Abl inhibitor, as PARN inhibitors. These inhibitors can be used as tool compounds and as lead compounds for the development of improved PARN inhibitors.

Single nucleotide polymorphism in the genomic target affects the recombination efficiency of CRISPR/Cas9-mediated gene editing in zebrafish

The CRISPR/Cas9 gene editing tool is becoming increasingly popular in the scientific community as one of the most efficient gene editing tools because of its high specificity and precision in targeted mutagenesis. A typical CRISPR system includes two components: a single guide RNA (sgRNA or gRNA) and a CRISPR associated endonuclease (Cas9). In CRISPR, the specificity of the Cas9 protein in cleaving the target DNA is decided by the homology of the spacer sequence, particularly the seed sequence (8–10 bases at the 3′ end of the spacer sequence) and any mismatch in the seed sequence abolishes the target cleavage and the subsequent generation of indels. Here, using Poly (A)specific ribonuclease (PARN) as an example in zebrafish, we show that the presence of single nucleotide polymorphism (SNP) in the sgRNA target, particularly in the seed sequence, affects the Cas9 activity resulting in a reduced recombination efficiency of CRISPR. Thus, while selecting target sites, prior screening for SNPs in the chosen targets across different wild-type lines/strains could be one of the easiest and effective ways of avoiding reduced recombination efficiency of CRISPR-mediated gene editing in zebrafish.

Interstitial lung diseases associated with mutations of poly(A)-specific ribonuclease: A multicentre retrospective study.

Poly(A)-specific ribonuclease (PARN) mutations have been associated with familial pulmonary fibrosis. This study aims to describe the phenotype of patients with interstitial lung disease (ILD) and heterozygous PARN mutations. We performed a retrospective, observational, non-interventional study of patients with an ILD diagnosis and a pathogenic heterozygous PARN mutation followed up in a centre of the OrphaLung network. We included 31 patients (29 from 16 kindreds and two sporadic patients). The median age at ILD diagnosis was 59 years (range 54 to 63). In total, 23 (74%) patients had a smoking history and/or fibrogenic exposure. The pulmonary phenotypes were heterogenous, but the most frequent diagnosis was idiopathic pulmonary fibrosis (n=12, 39%). Haematological abnormalities were identified in three patients and liver disease in two. In total, 21 patients received a specific treatment for ILD: steroids (n=13), antifibrotic agents (n=11), immunosuppressants (n=5) and N-acetyl cysteine (n=2). The median forced vital capacity decline for the whole sample was 256 ml/year (range -363 to -148). After a median follow-up of 32 months (range 18 to 66), 10 patients had died and six had undergone lung transplantation. The median transplantation-free survival was 54 months (95% CI 29 to ∞). Extra-pulmonary features were less frequent with PARN mutation than telomerase reverse transcriptase (TERT) or telomerase RNA component (TERC) mutation. IPF is common among individuals with PARN mutation, but other ILD subtypes may be observed.

PARN Knockdown in Cell Lines Results in Differential and Cell-Specific Alterations in the Expression of Cancer-Associated mRNAs.

Ribonucleases (RNases) is the collective term used for the group of enzymes that are involved in mRNA degradation. The shortening of the poly (A) tail through deadenylation is the preferred mechanism of degradation of most eukaryotic mRNAs and poly (A)-specific ribonuclease (PARN) is the most important player in deadenylation. Besides its primarily role in mRNA stability, PARN is also involved in several non-conventional functions. It is conceivable that a decreased RNase activity can alter the stability of cancer-associated mRNAs and this alteration may be differential in cells of different origin. Methods:The effects of siRNA-mediated knockdown of PARN on the post-transcriptional expression of 16 oncogenes and 18 tumor suppressor genes in cells derived from different lineages (NCI-H460 and NCI-H522; lung cancer) and (HEK-293; kidney) were investigated. Further, the effects of PARN depletion on proliferation and death of the lung cancer cells were investigated. Results: Quantitative real time PCR analysis revealed an cell-specific alteration in the expression of the target onco and tumor suppressor genes upon PARN depletion, differently, for cells derived from different lineages. The tumor suppressor genes showed a consistent pattern of down regulation upon PARN depletion in all the three cell types tested. In contrast, the expression of oncogenes was not consistent; while some oncogenes showed overexpression in HEK 293 cells, the majority of them were downregulated in the lung cancer cells. Further, PARN depletion did not alter the proliferation of lung cancer cells, which was in contrast to previous reports. Conclusion:The results of this study reveal that PARN deficiency leads to an altered stability of cancer-associated mRNA, distinctly, in cells of different lineages. Despite previous reports suggesting a potential therapeutic role of PARN in cancer, our results suggest that PARN may not be an important biomarker, particularly in lung cancer.

Poly(A)-Specific Ribonuclease (PARN) Promotes the Proliferation, Migration and Metastasis of Esophageal Cancer

Background: Esophageal cancer leads to the majority of cancer deaths in the world. Surgery, radiotherapy and chemotherapy are the main treatment methods, but due to its high recurrence and metastasis rate, the overall prognosis is poor. Poly(A)-specific ribonuclease (PARN) is a multifunctional enzyme molecule, which is involved in the occurrence and development of tumors. This study explores the relationship between PARN and the proliferation, metastasis and prognosis of esophageal cancer. Methods: The esophageal cancer tissues and adjacent normal tissues were collected from 91 patients with esophageal cancer after surgery. The expression level of PARN was detected by immunohistochemistry (IHC) using tissue microarray (TMA). PARN expression and its relationships with clinicopathological characteristics and prognosis was detected. In addition, stable PARN knockdown esophageal cancer cell lines TE-1 and Eca-109 were used to study its effect on the phenotype and behavior of tumor cells. Meanwhile, the effect of PARN silencing on tumor growth in vivo was verified by xenotransplantation model in nude mice. Finally, we examined possible downstream signaling mechanisms of PARN in esophageal cancer. Findings: PARN showed high expression in esophageal carcinoma tissues and its expression was significantly correlated with lymphatic metastasis and prognosis of patients. In the culture of PARN knockdown esophageal cancer cell lines, the growth and proliferation were significantly inhibited, and the invasion and migration ability of tumor cells were also significantly decreased. In addition, inhibition of PARN suppressed tumor growth and increased survival time in xenograft murine models. In the PARN knockdown group, BIM, IGFBP-5 and p21 were significantly increased, while the expression levels of anti-apoptotic proteins Survivin and STNF-R1 were significantly down-regulated. In addition, the expression levels of Akt, p-Akt, PIK3CA and CCND1 downstream of the signaling pathway regulating esophageal cancer progression were significantly down-regulated. Interpretation: These results suggest a previously undetected role of PARN as a suppressor of tumor development and its associations of prognosis in esophageal cancer through anti-apoptotic effect. Funding Information: None. Declaration of Interests: The authors declare no conflicts of interests. Ethics Approval Statement: Ethical approval for the study was approved by the Research Ethics Committee of the Second Affiliated Hospital of Guangxi Medical University and Zhujiang Hospital Affiliated to Southern Medical University, and written patient consent was obtained from all patients. Nude mice xenograft model - This study was approved by the Guangxi Medical University Ethics Committee.

Diverse functions of deadenylases in DNA damage response and genomic integrity.

DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.

Regulation of poly(a)-specific ribonuclease activity by reversible lysine acetylation

Poly(A)-specific ribonuclease (PARN) is a 3'-exoribonuclease that plays an important role in regulating the stability and maturation of RNAs. Recently, PARN has been found to regulate the maturation of the human telomerase RNA component (hTR), a noncoding RNA required for telomere elongation. Specifically, PARN cleaves the 3'-end of immature, polyadenylated hTR to form the mature, nonpolyadenylated template. Despite PARN's critical role in mediating telomere maintenance, little is known about how PARN's function is regulated by post-translational modifications. In this study, using shRNA- and CRISPR/Cas9-mediated gene silencing and knockout approaches, along with 3'-exoribonuclease activity assays and additional biochemical methods, we examined whether PARN is post-translationally modified by acetylation and what effect acetylation has on PARN's activity. We found PARN is primarily acetylated by the acetyltransferase p300 at Lys-566 and deacetylated by sirtuin1 (SIRT1). We also revealed how acetylation of PARN can decrease its enzymatic activity both in vitro, using a synthetic RNA probe, and in vivo, by quantifying endogenous levels of adenylated hTR. Furthermore, we also found that SIRT1 can regulate levels of adenylated hTR through PARN. The findings of our study uncover a mechanism by which PARN acetylation and deacetylation regulate its enzymatic activity as well as levels of mature hTR. Thus, PARN's acetylation status may play a role in regulating telomere length.

Chemical inhibition of PAPD5/7 rescues telomerase function and hematopoiesis in dyskeratosis congenita

AbstractDyskeratosis congenita (DC) is a pediatric bone marrow failure syndrome caused by germline mutations in telomere biology genes. Mutations in DKC1 (the most commonly mutated gene in DC), the 3′ region of TERC, and poly(A)-specific ribonuclease (PARN) cause reduced levels of the telomerase RNA component (TERC) by reducing its stability and accelerating TERC degradation. We have previously shown that depleting wild-type DKC1 levels by RNA interference or expression of the disease-associated A353V mutation in the DKC1 gene leads to decay of TERC, modulated by 3′-end oligoadenylation by noncanonical poly(A) polymerase 5 (PAPD5) followed by 3′ to 5′ degradation by EXOSC10. Furthermore, the constitutive genetic silencing of PAPD5 is sufficient to rescue TERC levels, restore telomerase function, and elongate telomeres in DKC1_A353V mutant human embryonic stem cells (hESCs). Here, we tested a novel PAPD5/7 inhibitor (RG7834), which was originally discovered in screens against hepatitis B viral loads in hepatic cells. We found that treatment with RG7834 rescues TERC levels, restores correct telomerase localization in DKC1 and PARN-depleted cells, and is sufficient to elongate telomeres in DKC1_A353V hESCs. Finally, treatment with RG7834 significantly improved definitive hematopoietic potential from DKC1_A353V hESCs, indicating that the chemical inhibition of PAPD5 is a potential therapy for patients with DC and reduced TERC levels.

Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN).

Translation is spatiotemporally regulated and endoplasmic reticulum (ER)-associated mRNAs are generally in efficient translation. It is unclear whether the ER-associated mRNAs are deadenylated or degraded on the ER surface in situ or in the cytosol. Here, we showed that ER possessed active deadenylases, particularly the poly(A)-specific ribonuclease (PARN), in common cell lines and mouse tissues. Consistently, purified recombinant PARN exhibited a strong ability to insert into the Langmuir monolayer and liposome. ER-anchored PARN was found to be able to reshape the poly(A) length profile of the ER-associated RNAs by suppressing long poly(A) tails without significantly influencing the cytosolic RNAs. The shortening of long poly(A) tails did not affect global translation efficiency, which suggests that the non-specific action of PARN towards long poly(A) tails was beyond the scope of translation regulation on the ER surface. Transcriptome sequencing analysis indicated that the ER-anchored PARN trigged the degradation of a small subset of ER-enriched transcripts. The ER-anchored PARN modulated the translation of its targets by redistributing ribosomes to heavy polysomes, which suggests that PARN might play a role in dynamic ribosome reallocation. During DNA damage response, MK2 phosphorylated PARN-Ser557 to modulate PARN translocation from the ER to cytosol. The ER-anchored PARN modulated DNA damage response and thereby cell viability by promoting the decay of ER-associated MDM2 transcripts with low ribosome occupancy. These findings revealed that highly regulated communication between mRNA degradation rate and translation efficiency is present on the ER surface in situ and PARN might contribute to this communication by modulating the dynamic ribosome reallocation between transcripts with low and high ribosome occupancies.

Effects of epidermal growth factor and progesterone on oocyte meiotic resumption and the expression of maturation-related transcripts during prematuration of oocytes from small and medium-sized bovine antral follicles.

This study evaluated the effects of epidermal growth factor (EGF) and progesterone (P4) on growth, the resumption of meiosis and expression of eukaryotic translation initiation factor 4E(eIF4E), poly(A)-specific ribonuclease (PARN), oocyte-specific histone H1 (H1FOO), oocyte maturation factor Mos (cMOS), growth differentiation factor-9 (GDF9) and cyclin B1 (CCNB1) mRNA in oocytes from small and medium-sized antral follicles after prematuration and maturation invitro. Oocytes from small (<2.0mm) and medium (3.0-6.0mm) antral follicles were cultured in medium containing EGF (10ng mL-1), P4 (100 µM) or both. After culture, growth rate, resumption of meiosis and eIF4E, PARN, H1FOO, cMOS, GDF9 and CCNB1 mRNA levels were evaluated. P4 increased cMOS, H1FOO and CCNB1 mRNA levels after the culture of oocytes from small antral follicles, and EGF increased CCNB1 mRNA levels in these oocytes. In the medium-sized antral follicles, P4 alone or in combination with EGF increased oocyte diameter after prematuration invitro. In these oocytes, the presence of either EGF or P4 in the culture medium increased cMOS mRNA levels. In conclusion, P4 increases cMOS, H1FOO and CCNB1 mRNA levels after the culture of oocytes from small antral follicles. P4 and the combination of EGF and P4 promote the growth of oocytes from medium-sized antral follicles, and both EGF and P4 increase cMOS mRNA levels.

Characterizing Dyskeratosis Congenita Caused By Parn Mutations in the Zebrafish

Inherited bone marrow failure syndromes (IBMFs) are a group of rare genetic disorders characterized by deficient hematopoiesis and extra-hematologic traits. Most known entities are related to a specific gene or group of genes, but others still remain unclassified. In many cases, the involved proteins are required for critical processes involved in cell survival, such as ribosome biogenesis, maintenance of telomere length, and DNA repair. Importantly, patients with IBMFs have higher risks of developing a variety of cancers from leukemia to solid tumours of the head and neck. In 2015, we published four patients from three different families with mutations in the Poly(A)-specific ribonuclease (PARN) gene. This gene encodes a ribonuclease which is involved in degradation of the poly(A) tails, which regulate mRNA turnover, and thus gene expression. Three of the patients presented with several degrees of mental illness and/or developmental delay. The fourth patient, harbored both a monoallelic deletion and a point mutation at the catalytic domain of the protein, and presented with bone marrow failure and hypomyelination, similar to a severe form of dyskeratosis congenital (DC) known as Hoyeraal-Hreidarsson syndrome. In the last two decades, zebrafish (Danio rerio) has emerged as an excellent animal model for human disease, and is especially relevant in hematology, since many of the transcription factors and cell types are highly conserved. Zebrafish have a single PARN ortholog,with 64% sequence identity to the human gene. Using CRISPR-Cas9 genome editing and a combination of six sgRNAs, we generated a 1.2 kb deletion in the zebrafish parn ortholog extending from exon 5 to 13, causing a premature stop codon. Homozygous fish were generated by incrossing to replicate the complete loss-of-function observed in the patient with the DC-like phenotype. Using whole-mount in situ hybridization (WISH) at 48 hours post-fertilization (hpf), we observed a decrease in the number of several mature myeloid cell lineages including neutrophils (labeled with mpx; p&lt;0.0001), macrophages (lcp1; p=0.0005) and mast cells (cpa5; p=0.0005). We also observed a decrease in the amount of hemoglobin (o-dianisidine staining; p&lt;0.0001). However, the number of hematopoietic stem cells (HSCs) was unchanged in parn mutants. This data parallels similar findings using parn directed splice site and translation start site morpholinos. PARN is described as a protein involved in RNA processing, but has also been associated with telomere maintenance. This latter process is crucial for cell senescence and genome integrity, and is a known cause of several IBMFSs. The telomerase ribonucleoprotein complex is highly active in hematopoietic stem and progenitor cells (HSPCs) and plays a role in cell differentiation. This complex is composed of a reverse transcriptase (TERT), RNA template (TERC), and the dyskerin protein complex (DKC1), mutations of which represent a common cause of DC. qPCR analysis in zebrafish parn mutants revealed a 2.98-fold reduction in tert expression compared with the wild type fish. Combined, these findings suggest that PARN plays an important role in HSC differentiation into myeloid and erythroid lineages, resulting in a bone marrow failure phenotype. Our model provides a unique in vivo platform to study the role of PARN in hematopoiesis and for identifying compounds that restore normal blood cell ratios, which may have the potential to prevent future leukemic transformation. Disclosures No relevant conflicts of interest to declare.