1
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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. Nat Commun 2024; 15:5270. [PMID: 38902233 PMCID: PMC11190236 DOI: 10.1038/s41467-024-48344-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/25/2024] [Indexed: 06/22/2024] Open
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent mRNA stability in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for mRNA stability and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA stability and protein expression.
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Affiliation(s)
- Rebeccah K Stewart
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Patrick Nguyen
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jessica K Sawyer
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Donald T Fox
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA.
- Duke Regeneration Center, Duke University, Durham, NC, USA.
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2
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Rong C, Liang C, Shen J, Zhang Y, Wang Q, Yang F, Chen Y, Luo Y, Gu M, Gao P, Xia Y, Duan S. CLLU1 as an emerging biomarker in chronic lymphoid leukemia. Hum Cell 2024; 37:625-632. [PMID: 38507118 DOI: 10.1007/s13577-024-01051-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
CLLU1, a disease-specific gene associated with chronic lymphoid leukemia (CLL), is located on chromosome 12q22. Previous studies considered CLLU1 to be a non-coding RNA; however, recent research has discovered that its coding sequence region possesses the potential to encode a short peptide similar to interleukin-4. Remarkably, abnormally elevated expression of CLLU1 has only been detected in chronic lymphoid leukemia among all hematological cancers. High CLLU1 expression often indicates more malignant pathological features and an unfavorable prognosis for patients. Importantly, the expression level of CLLU1 remains unaffected by the passage of time or therapeutic interventions, thus rendering it a novel prognostic marker. This article provides a comprehensive summary of relevant research findings on CLLU1 in the context of CLL prognosis and clinical applications, aiming to guide subsequent theoretical and clinical investigations in this field.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Neoplasm Proteins/genetics
- RNA, Long Noncoding/genetics
- Biomarkers, Tumor/genetics
- Genes, Neoplasm
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Affiliation(s)
- Chunmeng Rong
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Chenhao Liang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yuhua Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Fang Yang
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yalu Chen
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yuqing Luo
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Meier Gu
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Panpan Gao
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yongming Xia
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China.
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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3
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Zhukova M, Schedl P, Shidlovskii YV. The role of secondary structures in the functioning of 3' untranslated regions of mRNA: A review of functions of 3' UTRs' secondary structures and hypothetical involvement of secondary structures in cytoplasmic polyadenylation in Drosophila. Bioessays 2024; 46:e2300099. [PMID: 38161240 DOI: 10.1002/bies.202300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
3' untranslated regions (3' UTRs) of mRNAs have many functions, including mRNA processing and transport, translational regulation, and mRNA degradation and stability. These different functions require cis-elements in 3' UTRs that can be either sequence motifs or RNA structures. Here we review the role of secondary structures in the functioning of 3' UTRs and discuss some of the trans-acting factors that interact with these secondary structures in eukaryotic organisms. We propose potential participation of 3'-UTR secondary structures in cytoplasmic polyadenylation in the model organism Drosophila melanogaster. Because the secondary structures of 3' UTRs are essential for post-transcriptional regulation of gene expression, their disruption leads to a wide range of disorders, including cancer and cardiovascular diseases. Trans-acting factors, such as STAU1 and nucleolin, which interact with 3'-UTR secondary structures of target transcripts, influence the pathogenesis of neurodegenerative diseases and tumor metastasis, suggesting that they are possible therapeutic targets.
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Affiliation(s)
- Mariya Zhukova
- Laboratory of Gene Expression Regulation in Development, Russian Academy of Sciences, Institute of Gene Biology, Moscow, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Russian Academy of Sciences, Institute of Gene Biology, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Yulii V Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Russian Academy of Sciences, Institute of Gene Biology, Moscow, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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4
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Kikuta H, Aramaki T, Mabu S, Akada R, Hoshida H. The presence of an intron relieves gene repression caused by promoter-proximal four-bp specific sequences in yeast. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194982. [PMID: 37659722 DOI: 10.1016/j.bbagrm.2023.194982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Introns can enhance gene expression in eukaryotic cells in a process called intron-mediated enhancement (IME). The levels of enhancement are affected not only by the intron sequence but also by coding sequences (CDSs). However, the parts of CDSs responsible for mediating IME have not yet been identified. In this study, we identified an IME-mediating sequence by analyzing three pairs of IME-sensitive and -insensitive CDSs in Saccharomyces cerevisiae. Expression of the CDSs yCLuc, yRoGLU1, and KmBGA1 was enhanced by the presence of an intron (i.e., they were IME sensitive), but the expression of each corresponding codon-changed CDS, which encoded the identical amino acid sequence, was not enhanced (i.e., they were IME insensitive). Interestingly, the IME-insensitive CDSs showed higher expression levels that were like intron-enhanced expression of IME-sensitive CDSs, suggesting that expression of IME-sensitive CDSs was repressed. A four-nucleotide sequence (TCTT) located in the promoter-proximal position of either the untranslated or coding region was found to be responsible for repression in IME-sensitive CDSs, and repression caused by the TCTT sequence was relieved by the presence of an intron. Further, it was found that the expression of intron-containing yeast-native genes, UBC4 and MPT5, was repressed by TCTT in the CDS but relieved by the introns. These results indicate that TCTT sequences in promoter-proximal positions repress gene expression and that introns play a role in relieving gene repression caused by sequences such as TCTT.
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Affiliation(s)
- Hiroki Kikuta
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Takahiro Aramaki
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Shingo Mabu
- Division of Electrical, Electronic and Information Engineering, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Rinji Akada
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8315, Japan; Yamaguchi University Biomedical Engineering Center, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Hisashi Hoshida
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8315, Japan; Yamaguchi University Biomedical Engineering Center, 2-16-1 Tokiwadai, Ube 755-8611, Japan.
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Zhang Q, Weng W, Gu X, Xiang J, Yang Y, Zhu MX, Gu W, He Z, Li Y. hnRNPA1 SUMOylation promotes cold hypersensitivity in chronic inflammatory pain by stabilizing TRPA1 mRNA. Cell Rep 2023; 42:113401. [PMID: 37943660 DOI: 10.1016/j.celrep.2023.113401] [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: 03/09/2023] [Revised: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
TRPA1 is pivotal in cold hypersensitivity, but its regulatory mechanisms in inflammatory cold hyperalgesia remain poorly understood. We show here that the upregulation of SUMO1-conjugated protein levels in a complete Freund's adjuvant (CFA)-induced inflammatory pain model enhances TRPA1 mRNA stability, ultimately leading to increased expression levels. We further demonstrate that hnRNPA1 binds to TRPA1 mRNA, and its SUMOylation, upregulated in CFA-induced inflammatory pain, contributes to stabilizing TRPA1 mRNA by accumulating hnRNPA1 in the cytoplasm. Moreover, we find that wild-type hnRNPA1 viral infection in dorsal root ganglia neurons, and not infection with the SUMOylation-deficient hnRNPA1 mutant, can rescue the reduced ability of hnRNPA1-knockdown mice to develop inflammatory cold pain hypersensitivity. These results suggest that hnRNPA1 is a regulator of TRPA1 mRNA stability, the capability of which is enhanced upon SUMO1 conjugation at lysine 3 in response to peripheral inflammation, and the increased expression of TRPA1 in turn underlies the development of chronic inflammatory cold pain hypersensitivity.
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Affiliation(s)
- Qiao Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weiji Weng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokun Gu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinhua Xiang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Michael X Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weidong Gu
- Department of Anesthesiology, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China.
| | - Zhenzhou He
- Department of Anesthesiology, Minhang Hospital Affiliated to Fudan University, Shanghai 201199, China.
| | - Yong Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Niu F, Li Z, Ren Y, Li Z, Guan H, Li Y, Zhang Y, Li Y, Yang J, Qian L, Shi W, Fan X, Li J, Shi L, Yu Y, Xiong Y. Aberrant hyper-expression of the RNA binding protein GIGYF2 in endothelial cells modulates vascular aging and function. Redox Biol 2023; 65:102824. [PMID: 37517320 PMCID: PMC10400931 DOI: 10.1016/j.redox.2023.102824] [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: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023] Open
Abstract
Vascular endothelial cells (ECs) senescence plays a crucial role in vascular aging that promotes the initiation and progression of cardiovascular disease. The mutation of Grb10-interacting GYF protein 2 (GIGYF2) is strongly associated with the pathogenesis of aging-related diseases, whereas its role in regulating ECs senescence and dysfunction still remains elusive. In this study, we found aberrant hyperexpression of GIGYF2 in senescent human ECs and aortas of old mice. Silencing GIGYF2 in senescent ECs suppressed eNOS-uncoupling, senescence, and endothelial dysfunction. Conversely, in nonsenescent cells, overexpressing GIGYF2 promoted eNOS-uncoupling, cellular senescence, endothelial dysfunction, and activation of the mTORC1-SK61 pathway, which were ablated by rapamycin or antioxidant N-Acetyl-l-cysteine (NAC). Transcriptome analysis revealed that staufen double-stranded RNA binding protein 1 (STAU1) is remarkably downregulated in the GIGYF2-depleted ECs. STAU1 depletion significantly attenuated GIGYF2-induced cellular senescence, dysfunction, and inflammation in young ECs. Furthermore, we disclosed that GIGYF2 acting as an RNA binding protein (RBP) enhances STAU1 mRNA stability, and that the intron region of the late endosomal/lysosomal adaptor MAPK and mTOR activator 4 (LAMTOR4) could bind to STAU1 protein to upregulate LAMTOR4 expression. Immunofluorescence staining showed that GIGYF2 overexpression promoted the translocation of mTORC1 to lysosome. In the mice model, GIGYF2flox/flox Cdh-Cre+ mice protected aged mice from aging-associated vascular endothelium-dependent relaxation and arterial stiffness. Our work discloses that GIGYF2 serving as an RBP enhances the mRNA stability of STAU1 that upregulates LAMTOR4 expression through binding with its intron region, which activates the mTORC1-S6K1 signaling via recruitment of mTORC1 to the lysosomal membrane, ultimately leading to ECs senescence, dysfunction, and vascular aging. Disrupting the GIGYF2-STAU1-mTORC1 signaling cascade may represent a promising therapeutic approach against vascular aging and aging-related cardiovascular diseases.
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Affiliation(s)
- Fanglin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Zhuozhuo Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yuanyuan Ren
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Zi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Hua Guan
- Shaanxi Key Laboratory of Ischemic Cardiovascular Diseases & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, 710018, PR China
| | - Yang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yan Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yirong Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Junle Yang
- Department of Radiology, Xi' an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Lu Qian
- Department of Endocrinology, Xi' an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Wenzhen Shi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Xiaobin Fan
- Department of Obstetrics and Gynecology, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China
| | - Jinli Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Lele Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yi Yu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China.
| | - Yuyan Xiong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, PR China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, PR China.
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7
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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550700. [PMID: 37546801 PMCID: PMC10402044 DOI: 10.1101/2023.07.26.550700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent expression in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for expression control and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA and protein expression.
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8
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Balcerak A, Macech-Klicka E, Wakula M, Tomecki R, Goryca K, Rydzanicz M, Chmielarczyk M, Szostakowska-Rodzos M, Wisniewska M, Lyczek F, Helwak A, Tollervey D, Kudla G, Grzybowska EA. The RNA-Binding Landscape of HAX1 Protein Indicates Its Involvement in Translation and Ribosome Assembly. Cells 2022; 11:cells11192943. [PMID: 36230905 PMCID: PMC9564044 DOI: 10.3390/cells11192943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/18/2022] Open
Abstract
HAX1 is a human protein with no known homologues or structural domains. Mutations in the HAX1 gene cause severe congenital neutropenia through mechanisms that are poorly understood. Previous studies reported the RNA-binding capacity of HAX1, but the role of this binding in physiology and pathology remains unexplained. Here, we report the transcriptome-wide characterization of HAX1 RNA targets using RIP-seq and CRAC, indicating that HAX1 binds transcripts involved in translation, ribosome biogenesis, and rRNA processing. Using CRISPR knockouts, we find that HAX1 RNA targets partially overlap with transcripts downregulated in HAX1 KO, implying a role in mRNA stabilization. Gene ontology analysis demonstrated that genes differentially expressed in HAX1 KO (including genes involved in ribosome biogenesis and translation) are also enriched in a subset of genes whose expression correlates with HAX1 expression in four analyzed neoplasms. The functional connection to ribosome biogenesis was also demonstrated by gradient sedimentation ribosome profiles, which revealed differences in the small subunit:monosome ratio in HAX1 WT/KO. We speculate that changes in HAX1 expression may be important for the etiology of HAX1-linked diseases through dysregulation of translation.
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Affiliation(s)
- Anna Balcerak
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Ewelina Macech-Klicka
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Maciej Wakula
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Rafal Tomecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, 02-106 Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies University of Warsaw, 02-097 Warsaw, Poland
| | - Malgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Mateusz Chmielarczyk
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Malgorzata Szostakowska-Rodzos
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Marta Wisniewska
- Laboratory of Biological Chemistry of Metal Ions, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Filip Lyczek
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ewa A. Grzybowska
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
- Correspondence:
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