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Firdous Z, Kalra S, Chattopadhyay R, Bari VK. Current insight into the role of mRNA decay pathways in fungal pathogenesis. Microbiol Res 2024; 283:127671. [PMID: 38479232 DOI: 10.1016/j.micres.2024.127671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Pathogenic fungal species can cause superficial and mucosal infections, to potentially fatal systemic or invasive infections in humans. These infections are more common in immunocompromised or critically ill patients and have a significant morbidity and fatality rate. Fungal pathogens utilize several strategies to adapt the host environment resulting in efficient and comprehensive alterations in their cellular metabolism. Fungal virulence is regulated by several factors and post-transcriptional regulation mechanisms involving mRNA molecules are one of them. Post-transcriptional controls have emerged as critical regulatory mechanisms involved in the pathogenesis of fungal species. The untranslated upstream and downstream regions of the mRNA, as well as RNA-binding proteins, regulate morphogenesis and virulence by controlling mRNA degradation and stability. The limited number of available therapeutic drugs, the emergence of multidrug resistance, and high death rates associated with systemic fungal illnesses pose a serious risk to human health. Therefore, new antifungal treatments that specifically target mRNA pathway components can decrease fungal pathogenicity and when combined increase the effectiveness of currently available antifungal drugs. This review summarizes the mRNA degradation pathways and their role in fungal pathogenesis.
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Affiliation(s)
- Zulikha Firdous
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Sapna Kalra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Rituja Chattopadhyay
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India.
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2
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Kumari P, Sarovar Bhavesh N. Birth and death view of DNA, RNA, and proteins. Gene 2023; 883:147672. [PMID: 37506987 DOI: 10.1016/j.gene.2023.147672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The potential of cells to guide their genome and configure genes to express at a given time and in response to specific stimuli is pivotal to regulate cellular processes such as tissue differentiation, organogenesis, organismal development, homeostasis, and disease. In this review, we focus on the diverse mechanisms involved in DNA replication and its degradation, mRNA synthesis, and associated regulation such as RNA capping, splicing, tailing, and export. mRNA turnover including Decapping, deadenylation, RNA interference, and Nonsense mediated mRNA decay followed by protein translation, post-translational modification, and protein turnover. We highlight recent advances in understanding the complex series of molecular mechanisms responsible for the remarkable cellular regulatory mechanisms.
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Affiliation(s)
- Pooja Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
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3
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Zhang FW, Xie XW, Chen MH, Tong J, Chen QQ, Feng J, Chen FT, Liu WQ. Poly(A)-specific ribonuclease protein promotes the proliferation, invasion and migration of esophageal cancer cells. World J Gastroenterol 2023; 29:4783-4796. [PMID: 37664151 PMCID: PMC10473923 DOI: 10.3748/wjg.v29.i31.4783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND 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. AIM To investigate the relationship between PARN and the proliferation, migration and invasion of EC cells. METHODS 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. RESULTS 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. CONCLUSION 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.
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Affiliation(s)
- Fu-Wei Zhang
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Xiao-Wei Xie
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
| | - Meng-Hua Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
| | - Jian Tong
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Qun-Qing Chen
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Jing Feng
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, Guangdong Province, China
| | - Feng-Ti Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
| | - Wen-Qi Liu
- Department of Radiation Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530000, Guangxi Zhuang Autonomous Region, China
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Zhang G, Luo H, Li X, Hu Z, Wang Q. The Dynamic Poly(A) Tail Acts as a Signal Hub in mRNA Metabolism. Cells 2023; 12:cells12040572. [PMID: 36831239 PMCID: PMC9954528 DOI: 10.3390/cells12040572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
In eukaryotes, mRNA metabolism requires a sophisticated signaling system. Recent studies have suggested that polyadenylate tail may play a vital role in such a system. The poly(A) tail used to be regarded as a common modification at the 3' end of mRNA, but it is now known to be more than just that. It appears to act as a platform or hub that can be understood in two ways. On the one hand, polyadenylation and deadenylation machinery constantly regulates its dynamic activity; on the other hand, it exhibits the ability to recruit RNA-binding proteins and then interact with diverse factors to send various signals to regulate mRNA metabolism. In this paper, we outline the main complexes that regulate the dynamic activities of poly(A) tails, explain how these complexes participate polyadenylation/deadenylation process and summarize the diverse signals this hub emit. We are trying to make a point that the poly(A) tail can metaphorically act as a "flagman" who is supervised by polyadenylation and deadenylation and sends out signals to regulate the orderly functioning of mRNA metabolism.
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Affiliation(s)
- Guiying Zhang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Haolin Luo
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Xinyi Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Correspondence: (Z.H.); (Q.W.)
| | - Quan Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
- Correspondence: (Z.H.); (Q.W.)
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Alles J, Legnini I, Pacelli M, Rajewsky N. Rapid nuclear deadenylation of mammalian messenger RNA. iScience 2022; 26:105878. [PMID: 36691625 PMCID: PMC9860345 DOI: 10.1016/j.isci.2022.105878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails in vitro and in vivo. We present evidence for genome-wide, nuclear synthesis of tails longer than 200 nt, which are rapidly shortened after transcription. Our data suggests that rapid deadenylation is a nuclear process, and that different classes of transcripts and even transcript isoforms have distinct nuclear tail lengths. For example, many long-noncoding RNAs retain long poly(A) tails. Modeling deadenylation dynamics predicts nuclear deadenylation about 10 times faster than cytoplasmic deadenylation. In summary, our data suggests that nuclear deadenylation might be a key mechanism for regulating mRNA stability, abundance, and subcellular localization.
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Affiliation(s)
- Jonathan Alles
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany
| | - Ivano Legnini
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Maddalena Pacelli
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany,Corresponding author
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Yang R, Zhan Y, Li Y, Dai SY, He SW, Ye CJ, Meng LD, Chen DQ, Dong CB, Chen L, Chen G, Dong KR, Li K, Zheng S, Li J, Yao W, Dong R. The Cellular and Molecular Landscape of Synchronous Pediatric Sialoblastoma and Hepatoblastoma. Front Oncol 2022; 12:893206. [PMID: 35860547 PMCID: PMC9289541 DOI: 10.3389/fonc.2022.893206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/31/2022] [Indexed: 01/05/2023] Open
Abstract
Sialoblastoma (SBL) is an infrequent embryonal malignant tumor originating from the salivary gland, resembling primitive salivary gland anlage, whereas hepatoblastoma (HB) is the most common pediatric liver malignancy. The simultaneous occurrence of both tumors is extremely rare. Here we reported a case of a 6-month-old infant diagnosed with synchronous SBL and HB. The patient received neoadjuvant chemotherapy followed by surgical resection. Fresh tissues of both tumors were collected before and after chemotherapy, which were further profiled by whole exome sequencing (WES) and single-cell RNA sequencing (scRNA-seq). WES analysis revealed potential somatic driver mutation PIK3CA p.Glu454Lys for SBL and canonical mutation CTNNB1 p.Ser45Pro for HB. No shared somatic variants or common copy number alterations were found between SBL and HB primary tumor samples. Though scRNA-seq, single-cell atlases were constructed for both tumors. SBL may recapitulate a pre-acinar stage in the development of salivary gland, including basaloid, duct-like, myoepithelial-like, and cycling phenotypes. In the meantime, HB was composed of tumor cells resembling different stages of the liver, including hepatocyte-like, hepatic progenitor-like, and hepatoblast-like cells. After chemotherapy, both tumors were induced into a more mature phenotype. In terms of transcriptional signatures, SBL and HB showed enhanced expression of epithelial markers KRT8, KRT18, and essential embryo development genes SDC1, MDK, indicating the disruption of normal embryo epithelium development. Finally, heterozygous deleterious germline mutation BLM and FANCI were identified which could predispose the patient to higher cancer risk. It partially explained the reason for the co-occurrence of SBL and HB. Taken together, we provided valuable resources for deciphering cellular heterogeneity and adaptive change of tumor cells after chemotherapy for synchronous SBL and HB, providing insights into the mechanisms leading to synchronous pediatric tumors.
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Affiliation(s)
- Ran Yang
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Yong Zhan
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Yi Li
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Shu-Yang Dai
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Shi-Wei He
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Chun-Jing Ye
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Ling-Du Meng
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - De-Qian Chen
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Chen-Bin Dong
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Lian Chen
- Department of Pathology, Children’s Hospital of Fudan University, Shanghai, China
| | - Gong Chen
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Kui-Ran Dong
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Kai Li
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Shan Zheng
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
| | - Jun Li
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
- *Correspondence: Rui Dong, ; Wei Yao, ; Jun Li,
| | - Wei Yao
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
- *Correspondence: Rui Dong, ; Wei Yao, ; Jun Li,
| | - Rui Dong
- Department of Pediatric Surgery, Children’s Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai, China
- *Correspondence: Rui Dong, ; Wei Yao, ; Jun Li,
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7
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Liu L, He J, Sun G, Huang N, Bian Z, Xu C, Zhang Y, Cui Z, Xu W, Sun F, Zhuang C, Man Q, Gu S. The N6-methyladenosine modification enhances ferroptosis resistance through inhibiting SLC7A11 mRNA deadenylation in hepatoblastoma. Clin Transl Med 2022; 12:e778. [PMID: 35522946 PMCID: PMC9076012 DOI: 10.1002/ctm2.778] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 03/01/2022] [Accepted: 03/07/2022] [Indexed: 01/17/2023] Open
Abstract
Background Solute carrier family 7 member 11 (SLC7A11) is overexpressed in multiple human tumours and functions as a transporter importing cystine for glutathione biosynthesis. It promotes tumour development in part by suppressing ferroptosis, a newly identified form of cell death that plays a pivotal role in the suppression of tumorigenesis. However, the role and underlying mechanisms of SLC7A11‐mediated ferroptosis in hepatoblastoma (HB) remain largely unknown. Methods Reverse transcription quantitative real‐time PCR (RT‐qPCR) and western blotting were used to measure SLC7A11 levels. Cell proliferation, colony formation, lipid reactive oxygen species (ROS), MDA concentration, 4‐HNE, GSH/GSSG ratio and cell death assays as well as subcutaneous xenograft experiments were used to elucidate the effects of SLC7A11 in HB cell proliferation and ferroptosis. Furthermore, MeRIP‐qPCR, dual luciferase reporter, RNA pulldown, RNA immunoprecipitation (RIP) and RACE‐PAT assays were performed to elucidate the underlying mechanism through which SLC7A11 was regulated by the m6A modification in HB. Results SLC7A11 expression was highly upregulated in HB. SLC7A11 upregulation promoted HB cell proliferation in vitro and in vivo, inhibiting HB cell ferroptosis. Mechanistically, SLC7A11 mRNA exhibited abnormal METTL3‐mediated m6A modification, which enhanced its stability and expression. IGF2 mRNA‐binding protein 1 (IGF2BP1) was identified as the m6A reader of SLC7A11, enhancing SLC7A11 mRNA stability and expression by inhibiting SLC7A11 mRNA deadenylation in an m6A‐dependent manner. Moreover, IGF2BP1 was found to block BTG2/CCR4‐NOT complex recruitment via competitively binding to PABPC1, thereby suppressing SLC7A11 mRNA deadenylation. Conclusions Our findings demonstrated that the METTL3‐mediated SLC7A11 m6A modification enhances HB ferroptosis resistance. The METTL3/IGF2BP1/m6A modification promotes SLC7A11 mRNA stability and upregulates its expression by inhibiting the deadenylation process. Our study highlights a critical role of the m6A modification in SLC7A11‐mediated ferroptosis, providing a potential strategy for HB therapy through blockade of the m6A‐SLC7A11 axis.
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Affiliation(s)
- Li Liu
- Department of Clinical LaboratoryShanghai Fourth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Jiangtu He
- Department of Clinical LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Guifeng Sun
- Department of Clinical LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Nan Huang
- Department of Clinical LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Zhixuan Bian
- Department of Laboratory MedicineShanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Chang Xu
- Department of Clinical LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Yue Zhang
- Department of Central LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Zhongqi Cui
- Department of Clinical LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Wenqiang Xu
- Department of Clinical LaboratoryShanghai Fourth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Fenyong Sun
- Department of Clinical LaboratoryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Chengle Zhuang
- Colorectal Cancer CenterShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
- Department of Gastrointestinal SurgeryShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Qiuhong Man
- Department of Clinical LaboratoryShanghai Fourth People's HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Song Gu
- Department of SurgeryShanghai Children's Medical CenterSchool of medicineShanghai Jiaotong UniversityShanghaiChina
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Jagoda E, Xue JR, Reilly SK, Dannemann M, Racimo F, Huerta-Sanchez E, Sankararaman S, Kelso J, Pagani L, Sabeti PC, Capellini TD. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Mol Biol Evol 2022; 39:msab304. [PMID: 34662402 PMCID: PMC8760939 DOI: 10.1093/molbev/msab304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.
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Affiliation(s)
- Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - James R Xue
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven K Reilly
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, UCLA, Los Angeles, CA, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Zhao LW, Zhu YZ, Wu YW, Pi SB, Shen L, Fan HY. Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development. Nucleic Acids Res 2021; 50:458-472. [PMID: 34904664 PMCID: PMC8855302 DOI: 10.1093/nar/gkab1213] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the maternally encoded mRNA decay pathway (M-decay) and the zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. In this study, we identified the zygotically encoded nuclear poly(A) binding protein 1 (PABPN1) as a factor required for maternal mRNA turnover, with a previously undescribed cytoplasmic function. Cytoplasmic PABPN1 docks on 3'-uridylated transcripts, downstream of terminal uridylyl transferases TUT4 and TUT7, and recruits 3'-5' exoribonuclease DIS3L2 to its targets, facilitating maternal mRNA decay. Pabpn1-knockout in mice resulted in preimplantation stage mortality due to early developmental arrest at the morula stage. Maternal mRNAs to be eliminated via the Z-decay pathway failed to be removed from Pabpn1-depleted embryos. Furthermore, PABPN1-mediated Z-decay is essential for major ZGA and regulates the expression of cell fate-determining factors in mouse preimplantation embryos. This study revealed an unforeseen cytoplasmic function of PABPN1 coupled with early embryonic development, characterized the presence of a zygotic destabilizer of maternal mRNA, and elucidated the Z-decay process mechanisms, which potentially contribute to human fertility.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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10
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Poetz F, Corbo J, Levdansky Y, Spiegelhalter A, Lindner D, Magg V, Lebedeva S, Schweiggert J, Schott J, Valkov E, Stoecklin G. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation. Nat Commun 2021; 12:7175. [PMID: 34887419 PMCID: PMC8660800 DOI: 10.1038/s41467-021-27471-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
The CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified RNF219 as an acetylation-regulated cofactor. We demonstrate that RNF219 is an active RING-type E3 ligase which stably associates with CCR4-NOT via NOT9 through a short linear motif (SLiM) embedded within the C-terminal low-complexity region of RNF219. By using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 inhibits deadenylation through the direct interaction of the α-helical SLiM with the NOT9 module. Transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, with differential requirement of its RING domain. Our results establish RNF219 as an inhibitor of CCR4-NOT-mediated deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.
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Affiliation(s)
- Fabian Poetz
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, 21702-1201, USA
| | - Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, 21702-1201, USA
| | - Alexander Spiegelhalter
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Doris Lindner
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Vera Magg
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Svetlana Lebedeva
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
| | - Jörg Schweiggert
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Johanna Schott
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, 21702-1201, USA.
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany.
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany.
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11
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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12
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Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae. Nat Commun 2021; 12:4951. [PMID: 34400637 PMCID: PMC8367983 DOI: 10.1038/s41467-021-25251-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023] Open
Abstract
The polyadenosine tail (poly[A]-tail) is a universal modification of eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). In budding yeast, Pap1-synthesized mRNA poly(A) tails enhance export and translation, whereas Trf4/5-mediated polyadenylation of ncRNAs facilitates degradation by the exosome. Using direct RNA sequencing, we decipher the extent of poly(A) tail dynamics in yeast defective in all relevant exonucleases, deadenylases, and poly(A) polymerases. Predominantly ncRNA poly(A) tails are 20-60 adenosines long. Poly(A) tails of newly transcribed mRNAs are 50 adenosine long on average, with an upper limit of 200. Exonucleolysis by Trf5-assisted nuclear exosome and cytoplasmic deadenylases trim the tails to 40 adenosines on average. Surprisingly, PAN2/3 and CCR4-NOT deadenylase complexes have a large pool of non-overlapping substrates mainly defined by expression level. Finally, we demonstrate that mRNA poly(A) tail length strongly responds to growth conditions, such as heat and nutrient deprivation.
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13
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Dai X, Jiang Y, Gu J, Jiang Z, Wu Y, Yu C, Yin H, Zhang J, Shi Q, Shen L, Sha Q, Fan H. The CNOT4 Subunit of the CCR4-NOT Complex is Involved in mRNA Degradation, Efficient DNA Damage Repair, and XY Chromosome Crossover during Male Germ Cell Meiosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003636. [PMID: 34026442 PMCID: PMC8132151 DOI: 10.1002/advs.202003636] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/23/2021] [Indexed: 05/03/2023]
Abstract
The CCR4-NOT complex is a major mRNA deadenylase in eukaryotes, comprising the catalytic subunits CNOT6/6L and CNOT7/8, as well as CNOT4, a regulatory subunit with previously undetermined functions. These subunits have been hypothesized to play synergistic biochemical functions during development. Cnot7 knockout male mice have been reported to be infertile. In this study, viable Cnot6/6l double knockout mice are constructed, and the males are fertile. These results indicate that CNOT7 has CNOT6/6L-independent functions in vivo. It is also demonstrated that CNOT4 is required for post-implantation embryo development and meiosis progression during spermatogenesis. Conditional knockout of Cnot4 in male germ cells leads to defective DNA damage repair and homologous crossover between X and Y chromosomes. CNOT4 functions as a previously unrecognized mRNA adaptor of CCR4-NOT by targeting mRNAs to CNOT7 for deadenylation of poly(A) tails, thereby mediating the degradation of a subset of transcripts from the zygotene to pachytene stage. The mRNA removal promoted by the CNOT4-regulated CCR4-NOT complex during the zygotene-to-pachytene transition is crucial for the appropriate expression of genes involved in the subsequent events of spermatogenesis, normal DNA double-strand break repair during meiosis, efficient crossover between X and Y chromosomes, and ultimately, male fertility.
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Affiliation(s)
- Xing‐Xing Dai
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Yu Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Jia‐Hui Gu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhi‐Yan Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Yun‐Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Chao Yu
- College of Life ScienceZhejiang UniversityHangzhou310058China
| | - Hao Yin
- First Affiliated Hospital of USTCHefei National Laboratory for Physical Sciences at MicroscaleSchool of Basic Medical SciencesDivision of Life Sciences and MedicineCAS Center for Excellence in Molecular Cell ScienceUniversity of Science and Technology of ChinaHefei230027China
| | - Jue Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan ProvinceReproductive and Genetic Hospital of CITIC‐XIANGYAChangsha410008China
| | - Qing‐Hua Shi
- First Affiliated Hospital of USTCHefei National Laboratory for Physical Sciences at MicroscaleSchool of Basic Medical SciencesDivision of Life Sciences and MedicineCAS Center for Excellence in Molecular Cell ScienceUniversity of Science and Technology of ChinaHefei230027China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Qian‐Qian Sha
- Fertility Preservation LaboratoryReproductive Medicine CenterGuangdong Second Provincial General HospitalGuangzhou510317China
| | - Heng‐Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
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14
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13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking. Blood 2021; 136:946-956. [PMID: 32384149 DOI: 10.1182/blood.2019004684] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in the FMS-like tyrosine kinase 3 (FLT3) gene in 13q12.2 are among the most common driver events in acute leukemia, leading to increased cell proliferation and survival through activation of the phosphatidylinositol 3-kinase/AKT-, RAS/MAPK-, and STAT5-signaling pathways. In this study, we examine the pathogenetic impact of somatic hemizygous 13q12.2 microdeletions in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) using 5 different patient cohorts (in total including 1418 cases). The 13q12.2 deletions occur immediately 5' of FLT3 and involve the PAN3 locus. By detailed analysis of the 13q12.2 segment, we show that the deletions lead to loss of a topologically associating domain border and an enhancer of FLT3. This results in increased cis interactions between the FLT3 promoter and another enhancer located distally to the deletion breakpoints, with subsequent allele-specific upregulation of FLT3 expression, expected to lead to ligand-independent activation of the receptor and downstream signaling. The 13q12.2 deletions are highly enriched in the high-hyperdiploid BCP ALL subtype (frequency 3.9% vs 0.5% in other BCP ALL) and in cases that subsequently relapsed. Taken together, our study describes a novel mechanism of FLT3 involvement in leukemogenesis by upregulation via chromatin remodeling and enhancer hijacking. These data further emphasize the role of FLT3 as a driver gene in BCP ALL.
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15
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Cabrera-Quio LE, Schleiffer A, Mechtler K, Pauli A. Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition. PLoS Genet 2021; 17:e1009390. [PMID: 33600438 PMCID: PMC7924785 DOI: 10.1371/journal.pgen.1009390] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/02/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression is crucial during the oocyte-to-embryo transition, a highly dynamic process characterized by the absence of nuclear transcription. Thus, changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which machineries contribute to remodeling the maternal transcriptome. Here, we focused on the degradation factor Ski7 in zebrafish. Homozygous ski7 mutant fish had higher proportions of both poor quality eggs and eggs that were unable to develop beyond the one-cell stage. Consistent with the idea that Ski7 participates in remodeling the maternal RNA content, transcriptome profiling identified hundreds of misregulated mRNAs in the absence of Ski7. Furthermore, upregulated genes were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. Finally, GO enrichment and proteomic analyses of misregulated factors implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Our results provide first insights into the physiological role of vertebrate Ski7 as a post-transcriptional regulator during the oocyte-to-embryo transition.
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Affiliation(s)
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Biotechnology, IMBA, Campus Vienna-Biocenter (VBC), Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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16
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Yu C, Cvetesic N, Hisler V, Gupta K, Ye T, Gazdag E, Negroni L, Hajkova P, Berger I, Lenhard B, Müller F, Vincent SD, Tora L. TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage. Nat Commun 2020; 11:6439. [PMID: 33353944 PMCID: PMC7755920 DOI: 10.1038/s41467-020-20239-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/20/2020] [Indexed: 01/28/2023] Open
Abstract
During oocyte growth, transcription is required to create RNA and protein reserves to achieve maternal competence. During this period, the general transcription factor TATA binding protein (TBP) is replaced by its paralogue, TBPL2 (TBP2 or TRF3), which is essential for RNA polymerase II transcription. We show that in oocytes TBPL2 does not assemble into a canonical TFIID complex. Our transcript analyses demonstrate that TBPL2 mediates transcription of oocyte-expressed genes, including mRNA survey genes, as well as specific endogenous retroviral elements. Transcription start site (TSS) mapping indicates that TBPL2 has a strong preference for TATA-like motif in core promoters driving sharp TSS selection, in contrast with canonical TBP/TFIID-driven TATA-less promoters that have broader TSS architecture. Thus, we show a role for the TBPL2/TFIIA complex in the establishment of the oocyte transcriptome by using a specific TSS recognition code.
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Affiliation(s)
- Changwei Yu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Nevena Cvetesic
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Vincent Hisler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Kapil Gupta
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Emese Gazdag
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Petra Hajkova
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Imre Berger
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Boris Lenhard
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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17
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Zaporozhchenko IA, Rykova EY, Laktionov PP. The Fundamentals of miRNA Biology: Structure, Biogenesis, and Regulatory Functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816202001015x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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Forrest ME, Pinkard O, Martin S, Sweet TJ, Hanson G, Coller J. Codon and amino acid content are associated with mRNA stability in mammalian cells. PLoS One 2020; 15:e0228730. [PMID: 32053646 PMCID: PMC7018022 DOI: 10.1371/journal.pone.0228730] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in the cell and is a major control point for modulating gene expression. In yeast and other model organisms, codon identity is a powerful determinant of transcript stability, contributing broadly to impact half-lives. General principles governing mRNA stability are poorly understood in mammalian systems. Importantly, however, the degradation machinery is highly conserved, thus it seems logical that mammalian transcript half-lives would also be strongly influenced by coding determinants. Herein we characterize the contribution of coding sequence towards mRNA decay in human and Chinese Hamster Ovary cells. In agreement with previous studies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. Surprisingly, however, we also observe that the amino acid content of a gene is an additional determinant correlating with transcript stability. The impact of codon and amino acid identity on mRNA decay appears to be associated with underlying tRNA and intracellular amino acid concentrations. Accordingly, genes of similar physiological function appear to coordinate their mRNA stabilities in part through codon and amino acid content. Together, these results raise the possibility that intracellular tRNA and amino acid levels interplay to mediate coupling between translational elongation and mRNA degradation rate in mammals.
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Affiliation(s)
- Megan E. Forrest
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Otis Pinkard
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sophie Martin
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas J. Sweet
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gavin Hanson
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jeff Coller
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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19
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Sohrabi-Jahromi S, Hofmann KB, Boltendahl A, Roth C, Gressel S, Baejen C, Soeding J, Cramer P. Transcriptome maps of general eukaryotic RNA degradation factors. eLife 2019; 8:47040. [PMID: 31135339 PMCID: PMC6570525 DOI: 10.7554/elife.47040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/27/2019] [Indexed: 12/27/2022] Open
Abstract
RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs. Cells contain a large group of DNA-like molecules called RNAs. While DNA stores and preserves information, RNA influences how cells use and regulate that information. As such, regulating the quantities of different RNAs is a key part of how cells survive, grow, adapt and respond to changes. For example, messenger RNAs (or mRNAs for short) carry genetic information from DNA which the cell reads to produce proteins. RNAs that are not needed can be degraded and removed from the cell by RNA degradation proteins. Most RNA degradation proteins need to be able to bind to RNA in order to work. A technique called “photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation”, often shortened to PAR-CLIP, can detect these proteins on their targets. The PAR-CLIP technique irreversibly links RNA-binding proteins to RNA and then collects those proteins and their bound RNAs for analysis. As with DNA, the RNAs can be identified using genetic sequencing. Degradation often starts at RNA ends, where specialized structures protect the RNA from accidental damage. Using PAR-CLIP, Sohrabi-Jahromi, Hofmann et al performed a detailed study of 30 RNA degradation proteins in the yeast Saccharomyces cerevisiae. The results highlight the specialization of different proteins to different groups of RNAs. One group of proteins, for example, remove the protective ‘cap’ structure at the start of RNAs. Those mRNAs that are not efficiently producing proteins attracted a lot of these cap-removing proteins. The findings also identify proteins involved in RNA degradation in the cell nucleus – the compartment that houses most of the cell’s DNA. Together these findings provide an extensive data resource for cell biologists. It offers many links between different RNAs and their degradation proteins. Understanding these key cellular processes helps to reveal more about the mechanisms underlying all of biology. It can also shed light on what happens when these processes fail and the diseases that may result.
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Affiliation(s)
- Salma Sohrabi-Jahromi
- Quantitative and Computational Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Katharina B Hofmann
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Andrea Boltendahl
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Roth
- Quantitative and Computational Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Saskia Gressel
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carlo Baejen
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Johannes Soeding
- Quantitative and Computational Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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20
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Gomez-Cambronero J. Lack of effective translational regulation of PLD expression and exosome biogenesis in triple-negative breast cancer cells. Cancer Metastasis Rev 2019; 37:491-507. [PMID: 30091053 DOI: 10.1007/s10555-018-9753-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is difficult to treat since cells lack the three receptors (ES, PR, or HER) that the most effective treatments target. We have used a well-established TNBC cell line (MDA-MB-231) from which we found evidence in support for a phospholipase D (PLD)-mediated tumor growth and metastasis: high levels of expression of PLD, as well as the absence of inhibitory miRs (such as miR-203) and 3'-mRNA PARN deadenylase activity in these cells. Such findings are not present in a luminal B cell line, MCF-7, and we propose a new miR•PARN•PLD node that is not uniform across breast cancer molecular subtypes and as such TNBC could be pharmacologically targeted differentially. We review the participation of PLD and phosphatidic acid (PA), its enzymatic product, as new "players" in breast cancer biology, with the aspects of regulation of the tumor microenvironment, macrophage polarization, regulation of PLD transcripts by specific miRs and deadenylases, and PLD-regulated exosome biogenesis. A new signaling miR•PARN•PLD node could serve as new biomarkers for TNBC abnormal signaling and metastatic disease staging, potentially before metastases are able to be visualized using conventional imaging.
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Affiliation(s)
- Julian Gomez-Cambronero
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, 3640 Colonel Glenn Highway, Dayton, OH, 45435, USA.
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21
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Saramago M, da Costa PJ, Viegas SC, Arraiano CM. The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:85-98. [PMID: 31342438 DOI: 10.1007/978-3-030-19966-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA degradation is considered a critical posttranscriptional regulatory checkpoint, maintaining the correct functioning of organisms. When a specific RNA transcript is no longer required in the cell, it is signaled for degradation through a number of highly regulated steps. Ribonucleases (or simply RNases) are key enzymes involved in the control of RNA stability. These enzymes can perform the RNA degradation alone or cooperate with other proteins in RNA degradation complexes. Important findings over the last years have shed light into eukaryotic RNA degradation by members of the RNase II/RNB family of enzymes. DIS3 enzyme belongs to this family and represents one of the catalytic subunits of the multiprotein complex exosome. This RNase has a diverse range of functions, mainly within nuclear RNA metabolism. Humans encode two other DIS3-like enzymes: DIS3L (DIS3L1) and DIS3L2. DIS3L1 also acts in association with the exosome but is strictly cytoplasmic. In contrast, DIS3L2 acts independently of the exosome and shows a distinctive preference for uridylated RNAs. These enzymes have been shown to be involved in important cellular processes, such as mitotic control, and associated with human disorders like cancer. This review shows how the impairment of function of each of these enzymes is implicated in human disease.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisboa, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisbon, Lisboa, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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22
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Mugridge JS, Coller J, Gross JD. Structural and molecular mechanisms for the control of eukaryotic 5'-3' mRNA decay. Nat Struct Mol Biol 2018; 25:1077-1085. [PMID: 30518847 DOI: 10.1038/s41594-018-0164-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022]
Abstract
5'-3' RNA decay pathways are critical for quality control and regulation of gene expression. Structural and biochemical studies have provided insights into the key nucleases that carry out deadenylation, decapping, and exonucleolysis during 5'-3' decay, but detailed understanding of how these activities are coordinated is only beginning to emerge. Here we review recent mechanistic insights into the control of 5'-3' RNA decay, including coupling between translation and decay, coordination between the complexes and activities that process 5' and 3' RNA termini, conformational control of enzymatic activity, liquid phase separation, and RNA modifications.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Jeff Coller
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
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23
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Komori H, Golden KL, Kobayashi T, Kageyama R, Lee CY. Multilayered gene control drives timely exit from the stem cell state in uncommitted progenitors during Drosophila asymmetric neural stem cell division. Genes Dev 2018; 32:1550-1561. [PMID: 30463902 PMCID: PMC6295162 DOI: 10.1101/gad.320333.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/09/2018] [Indexed: 12/23/2022]
Abstract
Self-renewal genes maintain stem cells in an undifferentiated state by preventing the commitment to differentiate. Robust inactivation of self-renewal gene activity following asymmetric stem cell division allows uncommitted stem cell progeny to exit from an undifferentiated state and initiate the commitment to differentiate. Nonetheless, how self-renewal gene activity at mRNA and protein levels becomes synchronously terminated in uncommitted stem cell progeny is unclear. We demonstrate that a multilayered gene regulation system terminates self-renewal gene activity at all levels in uncommitted stem cell progeny in the fly neural stem cell lineage. We found that the RNA-binding protein Brain tumor (Brat) targets the transcripts of a self-renewal gene, deadpan (dpn), for decay by recruiting the deadenylation machinery to the 3' untranslated region (UTR). Furthermore, we identified a nuclear protein, Insensible, that complements Cullin-mediated proteolysis to robustly inactivate Dpn activity by limiting the level of active Dpn through protein sequestration. The synergy between post-transcriptional and transcriptional control of self-renewal genes drives timely exit from the stem cell state in uncommitted progenitors. Our proposed multilayered gene regulation system could be broadly applicable to the control of exit from stemness in all stem cell lineages.
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Affiliation(s)
- Hideyuki Komori
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Krista L Golden
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Taeko Kobayashi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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24
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Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA (NEW YORK, N.Y.) 2018; 24:1195-1213. [PMID: 29914874 PMCID: PMC6097657 DOI: 10.1261/rna.065524.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/14/2018] [Indexed: 05/31/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
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Affiliation(s)
- Sophie R Atkinson
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Samuel Marguerat
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Danny A Bitton
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Maria Rodríguez-López
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pawel Smialowski
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Philipp Korber
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - François Bachand
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
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25
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Towler BP, Newbury SF. Regulation of cytoplasmic RNA stability: Lessons from Drosophila. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1499. [PMID: 30109918 DOI: 10.1002/wrna.1499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/06/2018] [Accepted: 07/01/2018] [Indexed: 12/19/2022]
Abstract
The process of RNA degradation is a critical level of regulation contributing to the control of gene expression. In the last two decades a number of studies have shown the specific and targeted nature of RNA decay and its importance in maintaining homeostasis. The key players within the pathways of RNA decay are well conserved with their mutation or disruption resulting in distinct phenotypes as well as human disease. Model organisms including Drosophila melanogaster have played a substantial role in elucidating the mechanisms conferring control over RNA stability. A particular advantage of this model organism is that the functions of ribonucleases can be assessed in the context of natural cells within tissues in addition to individual immortalized cells in culture. Drosophila RNA stability research has demonstrated how the cytoplasmic decay machines, such as the exosome, Dis3L2 and Xrn1, are responsible for regulating specific processes including apoptosis, proliferation, wound healing and fertility. The work discussed here has begun to identify specific mRNA transcripts that appear sensitive to specific decay pathways representing mechanisms through which the ribonucleases control mRNA stability. Drosophila research has also contributed to our knowledge of how specific RNAs are targeted to the ribonucleases including AU rich elements, miRNA targeting and 3' tailing. Increased understanding of these mechanisms is critical to elucidating the control elicited by the cytoplasmic ribonucleases which is relevant to human disease. This article is categorized under: RNA in Disease and Development > RNA in Development RNA Turnover and Surveillance > Regulation of RNA Stability RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Benjamin P Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
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26
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Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:a032839. [PMID: 29311343 PMCID: PMC5932591 DOI: 10.1101/cshperspect.a032839] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.
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Affiliation(s)
- Adam M Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
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27
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Panagopoulos I, Gorunova L, Andersen HK, Bergrem A, Dahm A, Andersen K, Micci F, Heim S. PAN3- PSMA2 fusion resulting from a novel t(7;13)(p14;q12) chromosome translocation in a myelodysplastic syndrome that evolved into acute myeloid leukemia. Exp Hematol Oncol 2018; 7:7. [PMID: 29560286 PMCID: PMC5859504 DOI: 10.1186/s40164-018-0099-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/14/2018] [Indexed: 11/30/2022] Open
Abstract
Background Acquired primary chromosomal changes in cancer are sometimes found as sole karyotypic abnormalities. They are specifically associated with particular types of neoplasia, essential in establishing the neoplasm, and they often lead to the generation of chimeric genes of pathogenetic, diagnostic, and prognostic importance. Thus, the report of new primary cancer-specific chromosomal aberrations is not only of scientific but also potentially of clinical interest, as is the detection of their gene-level consequences. Case presentation RNA-sequencing was performed on a bone marrow sample from a patient with myelodysplastic syndrome (MDS). The karyotype was 46,XX,t(7;13)(p14;q12)[2]/46,XX[23]. The MDS later evolved into acute myeloid leukemia (AML) at which point the bone marrow cells also contained additional, secondary aberrations. The 7;13-translocation resulted in fusion of the gene PAN3 from 13q12 with PSMA2 from 7p14 to generate an out-of-frame PAN3–PSMA2 fusion transcript whose presence was verified by RT-PCR together with Sanger sequencing. Interphase fluorescence in situ hybridization analysis confirmed the existence of the chimeric gene. Conclusions The novel t(7;13)(p14;q12)/PAN3–PSMA2 in the neoplastic bone marrow cells could affect two key protein complex: (a) the PAN2/PAN3 complex (PAN3 rearrangement) which is responsible for deadenylation, the process of removing the poly(A) tail from RNA, and (b) the proteasome (PSMA2 rearrangement) which is responsible for degradation of intracellular proteins. The patient showed a favorable response to decitabine after treatment with 5-azacitidine and conventional intensive chemotherapy had failed. Whether this might represent a consistent feature of MDS/AML with this particular gene fusion, remains unknown.
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Affiliation(s)
- Ioannis Panagopoulos
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, PO Box 49534 Nydalen, 0424 Oslo, Norway
| | - Ludmila Gorunova
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, PO Box 49534 Nydalen, 0424 Oslo, Norway
| | - Hege Kilen Andersen
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, PO Box 49534 Nydalen, 0424 Oslo, Norway
| | - Astrid Bergrem
- 2Department of Haematology, Akershus University Hospital, Nordbyhagen, Norway
| | - Anders Dahm
- 2Department of Haematology, Akershus University Hospital, Nordbyhagen, Norway.,3Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kristin Andersen
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, PO Box 49534 Nydalen, 0424 Oslo, Norway
| | - Francesca Micci
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, PO Box 49534 Nydalen, 0424 Oslo, Norway
| | - Sverre Heim
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, PO Box 49534 Nydalen, 0424 Oslo, Norway.,3Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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28
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Pseudo-DUBs as allosteric activators and molecular scaffolds of protein complexes. Biochem Soc Trans 2018; 46:453-466. [PMID: 29472364 DOI: 10.1042/bst20160268] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 12/17/2022]
Abstract
The ubiquitin (Ub) proteasome system and Ub signalling networks are crucial to cell biology and disease development. Deubiquitylases (DUBs) control cell signalling by removing mono-Ub and polyubiquitin chains from substrates. DUBs take part in almost all processes that regulate cellular life and are frequently dysregulated in disease. We have catalogued 99 currently known DUBs in the human genome and sequence conservation analyses of catalytic residues suggest that 11 lack enzyme activity and are classed as pseudo-DUBs. These pseudoenzymes play important biological roles by allosterically activating catalytically competent DUBs as well as other active enzymes. Additionally, pseudoenzymes act as assembly scaffolds of macromolecular complexes. We discuss how pseudo-DUBs have lost their catalytic activity, their diverse mechanisms of action and their potential as therapeutic targets. Many known pseudo-DUBs play crucial roles in cell biology and it is likely that unstudied and overlooked pseudo-DUB genes will have equally important functions.
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29
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Chen CYA, Zhang Y, Xiang Y, Han L, Chang JT, Shyu AB. Antagonistic actions of two human Pan3 isoforms on global mRNA turnover. RNA (NEW YORK, N.Y.) 2017; 23:1404-1418. [PMID: 28559491 PMCID: PMC5558910 DOI: 10.1261/rna.061556.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/25/2017] [Indexed: 05/03/2023]
Abstract
Deadenylation is a fundamental process that regulates eukaryotic gene expression. Mammalian deadenylation exhibits biphasic kinetics, with the Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes mediating the first and second phase, respectively; however, the significance of the biphasic nature of deadenylation in mRNA turnover remains unclear. In this study, we discovered that two distinct isoforms of human Pan3 display opposing properties necessary for coordinating the two phases of deadenylation. The shorter isoform (Pan3S) interacts more strongly with PABP than the longer isoform (Pan3L) does. Pan2 deadenylase activity is enhanced by Pan3S but suppressed by Pan3L. Knocking down individual Pan3 isoforms has opposing effects on the global poly(A) tail length profile, P-body formation, and different mRNA decay pathways. Transcriptome-wide analysis of Pan3 knockdown effects on mRNA turnover shows that depleting either Pan3 isoform causes profound and extensive changes in mRNA stability globally. These results reveal a new fundamental step governing mammalian mRNA metabolism. We propose that the first phase of deadenylation, coordinated through the interplay among the two Pan3 isoforms, Pan2, and PABP, represents a cytoplasmic mRNA maturation step important for proper mRNA turnover.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yueqiang Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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30
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Gomez-Cambronero J, Fite K, Miller TE. How miRs and mRNA deadenylases could post-transcriptionally regulate expression of tumor-promoting protein PLD. Adv Biol Regul 2017; 68:107-119. [PMID: 28964725 DOI: 10.1016/j.jbior.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
Phospholipase D (PLD) plays a key role in both cell membrane lipid reorganization and architecture, as well as a cell signaling protein via the product of its enzymatic reaction, phosphatidic acid (PA). PLD is involved in promoting breast cancer cell growth, proliferation, and metastasis and both gene and protein expression are upregulated in breast carcinoma human samples. In spite of all this, the ultimate reason as to why PLD expression is high in cancer cells vs. their normal counterparts remains largely unknown. Until we understand this and the associated signaling pathways, it will be difficult to establish PLD as a bona fide target to explore new potential cancer therapeutic approaches. Recently, our lab has identified several molecular mechanisms by which PLD expression is high in breast cancer cells and they all involve post-transcriptional control of its mRNA. First, PA, a mitogen, functions as a protein and mRNA stabilizer that counteracts natural decay and degradation. Second, there is a repertoire of microRNAs (miRs) that keep PLD mRNA translation at low levels in normal cells, but their effects change with starvation and during endothelial-to-mesenchymal transition (EMT) in cancer cells. Third, there is a novel way of post-transcriptional regulation of PLD involving 3'-exonucleases, specifically the deadenylase, Poly(A)-specific Ribonuclease (PARN), which tags mRNA for mRNA for degradation. This would enable PLD accumulation and ultimately breast cancer cell growth. We review in depth the emerging field of post-transcriptional regulation of PLD, which is only recently beginning to be understood. Since, surprisingly, so little is known about post-transcriptional regulation of PLD and related phospholipases (PLC or PLA), this new knowledge could help our understanding of how post-transcriptional deregulation of a lipid enzyme expression impacts tumor growth.
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Affiliation(s)
- Julian Gomez-Cambronero
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA.
| | - Kristen Fite
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Taylor E Miller
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
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31
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Miller TE, Gomez-Cambronero J. A feedback mechanism between PLD and deadenylase PARN for the shortening of eukaryotic poly(A) mRNA tails that is deregulated in cancer cells. Biol Open 2017; 6:176-186. [PMID: 28011629 PMCID: PMC5312095 DOI: 10.1242/bio.021261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The removal of mRNA transcript poly(A) tails by 3′→5′ exonucleases is the rate-limiting step in mRNA decay in eukaryotes. Known cellular deadenylases are the CCR4-NOT and PAN complexes, and poly(A)-specific ribonuclease (PARN). The physiological roles and regulation for PARN is beginning to be elucidated. Since phospholipase D (PLD2 isoform) gene expression is upregulated in breast cancer cells and PARN is downregulated, we examined whether a signaling connection existed between these two enzymes. Silencing PARN with siRNA led to an increase in PLD2 protein, whereas overexpression of PARN had the opposite effect. Overexpression of PLD2, however, led to an increase in PARN expression. Thus, PARN downregulates PLD2 whereas PLD2 upregulates PARN. Co-expression of both PARN and PLD2 mimicked this pattern in non-cancerous cells (COS-7 fibroblasts) but, surprisingly, not in breast cancer MCF-7 cells, where PARN switches from inhibition to activation of PLD2 gene and protein expression. Between 30 and 300 nM phosphatidic acid (PA), the product of PLD enzymatic reaction, added exogenously to culture cells had a stabilizing role of both PARN and PLD2 mRNA decay. Lastly, by immunofluorescence microscopy, we observed an intracellular co-localization of PA-loaded vesicles (0.1-1 nm) and PARN. In summary, we report for the first time the involvement of a phospholipase (PLD2) and PA in mediating PARN-induced eukaryotic mRNA decay and the crosstalk between the two enzymes that is deregulated in breast cancer cells. Summary: Cell signaling enzyme phospholipase D2 (PLD2) and its reaction product, phospholipid phosphatidic acid (PA), are involved in mediating PARN-induced eukaryotic mRNA decay.
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Affiliation(s)
- Taylor E Miller
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA
| | - Julian Gomez-Cambronero
- Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA .,Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA
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32
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Evans JM, Noorai RE, Tsai KL, Starr-Moss AN, Hill CM, Anderson KJ, Famula TR, Clark LA. Beyond the MHC: A canine model of dermatomyositis shows a complex pattern of genetic risk involving novel loci. PLoS Genet 2017; 13:e1006604. [PMID: 28158183 PMCID: PMC5315411 DOI: 10.1371/journal.pgen.1006604] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/17/2017] [Accepted: 01/24/2017] [Indexed: 01/04/2023] Open
Abstract
Juvenile dermatomyositis (JDM) is a chronic inflammatory myopathy and vasculopathy driven by genetic and environmental influences. Here, we investigated the genetic underpinnings of an analogous, spontaneous disease of dogs also termed dermatomyositis (DMS). As in JDM, we observed a significant association with a haplotype of the major histocompatibility complex (MHC) (DLA-DRB1*002:01/-DQA1*009:01/-DQB1*001:01), particularly in homozygosity (P-val = 0.0001). However, the high incidence of the haplotype among healthy dogs indicated that additional genetic risk factors are likely involved in disease progression. We conducted genome-wide association studies in two modern breeds having common ancestry and detected strong associations with novel loci on canine chromosomes 10 (P-val = 2.3X10-12) and 31 (P-val = 3.95X10-8). Through whole genome resequencing, we identified primary candidate polymorphisms in conserved regions of PAN2 (encoding p.Arg492Cys) and MAP3K7CL (c.383_392ACTCCACAAA>GACT) on chromosomes 10 and 31, respectively. Analyses of these polymorphisms and the MHC haplotypes revealed that nine of 27 genotypic combinations confer high or moderate probability of disease and explain 93% of cases studied. The pattern of disease risk across PAN2 and MAP3K7CL genotypes provided clear evidence for a significant epistatic foundation for this disease, a risk further impacted by MHC haplotypes. We also observed a genotype-phenotype correlation wherein an earlier age of onset is correlated with an increased number of risk alleles at PAN2 and MAP3K7CL. High frequencies of multiple genetic risk factors are unique to affected breeds and likely arose coincident with artificial selection for desirable phenotypes. Described herein is the first three-locus association with a complex canine disease and two novel loci that provide targets for exploration in JDM and related immunological dysfunction.
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Affiliation(s)
- Jacquelyn M. Evans
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Rooksana E. Noorai
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Genomics and Computational Laboratory, Clemson University, Clemson, South Carolina, United States of America
| | - Kate L. Tsai
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Alison N. Starr-Moss
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Cody M. Hill
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Kendall J. Anderson
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Thomas R. Famula
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Leigh Anne Clark
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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Shan L, Wu C, Chen D, Hou L, Li X, Wang L, Chu X, Hou Y, Wang Z. Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis. J Genet Genomics 2017; 44:95-106. [DOI: 10.1016/j.jgg.2016.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/14/2016] [Accepted: 12/28/2016] [Indexed: 11/25/2022]
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Alhusaini N, Coller J. The deadenylase components Not2p, Not3p, and Not5p promote mRNA decapping. RNA (NEW YORK, N.Y.) 2016; 22:709-721. [PMID: 26952104 PMCID: PMC4836645 DOI: 10.1261/rna.054742.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
Decay of mRNA is essential for the efficient regulation of gene expression. A major pathway of mRNA degradation is initiated by the shortening of the poly(A) tail via the CCR4/NOT deadenylase complex. Deadenylation is followed by removal of the 5' cap (i.e., decapping) and then 5' to 3' exonucleolytic decay of the message body. The highly conserved CCR4/NOT deadenylase complex consists of the exonucleases CCR4 and POP2/CAF1, as well as a group of four or five (depending on organism) accessory factors of unknown function, i.e., the NOT proteins. In this study, we find thatSaccharomyces cerevisiaeNot2p, Not3p, and Not5p (close paralogs of each other) are involved in promoting mRNA decapping. Furthermore, we find that Not3p and Not5p bind to the decapping activator protein Pat1p. Together, these data implicate the deadenylase complex in coordinating the downstream decapping reaction via Not2p, Not3p, and Not5p. This suggests that the coupling of deadenylation with decapping is, in part, a direct consequence of coordinated assembly of decay factors.
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Affiliation(s)
- Najwa Alhusaini
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Ma X, Chen J, Tian Y. Pregnane X receptor as the "sensor and effector" in regulating epigenome. J Cell Physiol 2015; 230:752-7. [PMID: 25294580 DOI: 10.1002/jcp.24838] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 09/22/2014] [Indexed: 12/20/2022]
Abstract
The pregnane X receptor (PXR, NR1I2) is a ligand-activated nuclear receptor which plays an essential role in organism's metabolic detoxification system by sensing the presence of xenobiotics and triggering detoxification responses. In addition to its role in xenobiotic metabolism, PXR has pleiotropic functions in regulating immune/inflammatory responses, cell proliferation, bile acid/cholesterol metabolism, glucose and lipid metabolism, steroid/endocrine homeostasis, and bone metabolism. Recent research suggests that the PXR is required for maintaining healthy commensalism between microbiota and gut. Interestingly, the metabolites such as indole derivatives from commensal microbes serve as the ligands for the PXR in intestinal epithelium forming an intricate mutualistic interaction between host and microbiota. PXR-regulated gene responses are controlled at epigenetic level by chromatin modifications, DNA methylation and noncoding RNA. Developmental alterations of the epigenome by exposure to the xenobiotics or diseases may produce persistent changes in PXR-regulated physiological responses. These new areas of research promise to vastly increase our understanding of PXR-regulated responses. In this review we highlight recent results on the epigenetic mechanisms for the PXR-regulated gene expression and discuss the physiological significance of these findings.
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Affiliation(s)
- Xi Ma
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
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Dełeńko K, Niedojadło J, Łabędzka A, Wiśniewska E, Bednarska-Kozakiewicz E. Dedifferentiation of Arabidopsis thaliana cells is accompanied by a strong decrease in RNA polymerase II transcription activity and poly(A+) RNA and 25S rRNA eradication from the cytoplasm. PROTOPLASMA 2015; 252:537-46. [PMID: 25248757 PMCID: PMC4335095 DOI: 10.1007/s00709-014-0700-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/09/2014] [Indexed: 05/09/2023]
Abstract
The mechanisms of plant cell dedifferentiation and the acquisition of totipotency are poorly understood. One of the methods to induce the dedifferentiation process in plant cells is simple and requires the removal of the cell wall. After cell wall removal in protoplasts, large-scale chromatin decondensation is observed (Tessadori et al. in J Cell Sci 120:1200-1208, 2007). Here, we show that in Arabidopsis thaliana protoplasts, despite chromatin decondensation, RNA polymerase II transcriptional activity is reduced. The subsequent investigated stages displayed a clear decrease in the quantity of 25S ribosomal RNA (rRNA) first and then poly(A+) RNA, particularly in the cytoplasm. Therefore, the reduced transcription activity and the removal of these RNA transcripts from the cytoplasm is a crucial process in obtaining totipotency in plant cells. After the cytoplasm cleaning of transcripts derived from mesophyll cells, we observed the resynthesis of these RNAs. An increase in the amount of examined molecules to a level similar to that in differentiated mesophyll cells precedes the divisions of already undifferentiated cells. In this work, we show changes in RNA polymerase II transcription dynamics and the quantity of poly(A+) RNA and 25S rRNA during dedifferentiation and re-entry into the cell cycle.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Janusz Niedojadło
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Agata Łabędzka
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Ewa Wiśniewska
- Department of Clinical Pathomorphology, Ludwik Rydygier Collegium Medium Bydgoszcz, Nicolaus Copernicus University in Toruń, Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland
| | - Elżbieta Bednarska-Kozakiewicz
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
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Roque S, Cerciat M, Gaugué I, Mora L, Floch AG, de Zamaroczy M, Heurgué-Hamard V, Kervestin S. Interaction between the poly(A)-binding protein Pab1 and the eukaryotic release factor eRF3 regulates translation termination but not mRNA decay in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2015; 21:124-134. [PMID: 25411355 PMCID: PMC4274632 DOI: 10.1261/rna.047282.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Eukaryotic release factor 3 (eRF3) is implicated in translation termination and also interacts with the poly(A)-binding protein (PABP, Pab1 in yeast), a major player in mRNA metabolism. Despite conservation of this interaction, its precise function remains elusive. First, we showed experimentally that yeast eRF3 does not contain any obvious consensus PAM2 (PABP-interacting motif 2). Thus, in yeast this association is different from the well described interaction between the metazoan factors. To gain insight into the exact function of this interaction, we then analyzed the phenotypes resulting from deleting the respective binding domains. Deletion of the Pab1 interaction domain on eRF3 did not affect general mRNA stability or nonsense-mediated mRNA decay (NMD) pathway and induced a decrease in translational readthrough. Furthermore, combined deletions of the respective interacting domains on eRF3 and on Pab1 were viable, did not affect Pab1 function in mRNA stability and harbored an antisuppression phenotype. Our results show that in Saccharomyces cerevisiae the role of the Pab1 C-terminal domain in mRNA stability is independent of eRF3 and the association of these two factors negatively regulates translation termination.
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Affiliation(s)
- Sylvain Roque
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Marie Cerciat
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Isabelle Gaugué
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Liliana Mora
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Aurélie G Floch
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Miklos de Zamaroczy
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Valérie Heurgué-Hamard
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Stephanie Kervestin
- CNRS FRE3630 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris 75005, France Metabolism and function of RNA in the nucleus, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris 75013, France
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38
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Martin S, Coller J. PAN-orama: three convergent views of a eukaryotic deadenylase. Nat Struct Mol Biol 2014; 21:577-8. [PMID: 24992224 DOI: 10.1038/nsmb.2850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sophie Martin
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland. Ohio, USA
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland. Ohio, USA
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Abstract
Translational control is central to the gene expression pathway and was the focus of the 2013 annual Translation UK meeting held at the University of Kent. The meeting brought together scientists at all career stages to present and discuss research in the mRNA translation field, with an emphasis on the presentations on the research of early career scientists. The diverse nature of this field was represented by the broad range of papers presented at the meeting. The complexity of mRNA translation and its control is emphasized by the interdisciplinary research approaches required to address this area with speakers highlighting emerging systems biology techniques and their application to understanding mRNA translation and the network of pathways controlling it.
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Wolf J, Valkov E, Allen MD, Meineke B, Gordiyenko Y, McLaughlin SH, Olsen TM, Robinson CV, Bycroft M, Stewart M, Passmore LA. Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation. EMBO J 2014; 33:1514-26. [PMID: 24872509 PMCID: PMC4158885 DOI: 10.15252/embj.201488373] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The conserved eukaryotic Pan2–Pan3 deadenylation complex shortens cytoplasmic mRNA 3′ polyA tails to regulate mRNA stability. Although the exonuclease activity resides in Pan2, efficient deadenylation requires Pan3. The mechanistic role of Pan3 is unclear. Here, we show that Pan3 binds RNA directly both through its pseudokinase/C-terminal domain and via an N-terminal zinc finger that binds polyA RNA specifically. In contrast, isolated Pan2 is unable to bind RNA. Pan3 binds to the region of Pan2 that links its N-terminal WD40 domain to the C-terminal part that contains the exonuclease, with a 2:1 stoichiometry. The crystal structure of the Pan2 linker region bound to a Pan3 homodimer shows how the unusual structural asymmetry of the Pan3 dimer is used to form an extensive high-affinity interaction. This binding allows Pan3 to supply Pan2 with substrate polyA RNA, facilitating efficient mRNA deadenylation by the intact Pan2–Pan3 complex.
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Affiliation(s)
- Jana Wolf
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Eugene Valkov
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Mark D Allen
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Birthe Meineke
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Tayla M Olsen
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | | | - Mark Bycroft
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Murray Stewart
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | - Lori A Passmore
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
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41
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Temme C, Simonelig M, Wahle E. Deadenylation of mRNA by the CCR4-NOT complex in Drosophila: molecular and developmental aspects. Front Genet 2014; 5:143. [PMID: 24904643 PMCID: PMC4033318 DOI: 10.3389/fgene.2014.00143] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/02/2014] [Indexed: 11/13/2022] Open
Abstract
Controlled shortening of the poly(A) tail of mRNAs is the first step in eukaryotic mRNA decay and can also be used for translational inactivation of mRNAs. The CCR4-NOT complex is the most important among a small number of deadenylases, enzymes catalyzing poly(A) tail shortening. Rates of poly(A) shortening differ between mRNAs as the CCR4-NOT complex is recruited to specific mRNAs by means of either sequence-specific RNA binding proteins or miRNAs. This review summarizes our current knowledge concerning the subunit composition and deadenylation activity of the Drosophila CCR4-NOT complex and the mechanisms by which the complex is recruited to particular mRNAs. We discuss genetic data implicating the complex in the regulation of specific mRNAs, in particular in the context of development.
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Affiliation(s)
- Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg Halle, Germany
| | - Martine Simonelig
- Genetics and Development, Institute of Human Genetics - CNRS UPR1142 Montpellier, France
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg Halle, Germany
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42
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Inada T, Makino S. Novel roles of the multi-functional CCR4-NOT complex in post-transcriptional regulation. Front Genet 2014; 5:135. [PMID: 24904636 PMCID: PMC4033010 DOI: 10.3389/fgene.2014.00135] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/25/2014] [Indexed: 11/30/2022] Open
Abstract
The CCR4-NOT complex is a highly conserved specific gene silencer that also serves more general post-transcriptional functions. Specific regulatory proteins including the miRNA-induced silencing complex and its associated proteins, bind to 3’-UTR elements of mRNA and recruit the CCR4-NOT complex thereby promoting poly(A) shortening and repressing translation and/or mRNA degradation. Recent studies have shown that the CCR4-NOT complex that is tethered to mRNA by such regulator(s) represses translation and facilitates mRNA decay independent of a poly(A) tail and its shortening. In addition to deadenylase activity, the CCR4-NOT complex also has an E3 ubiquitin ligase activity and is involved in a novel protein quality control system, i.e., co-translational proteasomal-degradation of aberrant proteins. In this review, we describe recent progress in elucidation of novel roles of the multi-functional complex CCR4-NOT in post-transcriptional regulation.
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Affiliation(s)
- Toshifumi Inada
- Laboratory of Gene Regulation, Graduate School of Pharmaceutical Sciences, Tohoku University Sendai, Japan
| | - Shiho Makino
- Laboratory of Gene Regulation, Graduate School of Pharmaceutical Sciences, Tohoku University Sendai, Japan
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