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Kong S, Zhu M, Pan D, Lane B, Smith RS, Roeder AHK. Tradeoff between speed and robustness in primordium initiation mediated by auxin-CUC1 interaction. Nat Commun 2024; 15:5911. [PMID: 39003301 PMCID: PMC11246466 DOI: 10.1038/s41467-024-50172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we find that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases the intensity of auxin maxima and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we find that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validate experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.
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Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Mingyuan Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - David Pan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Brendan Lane
- Department of Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Richard S Smith
- Department of Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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Kong S, Zhu M, Pan D, Lane B, Smith RS, Roeder AHK. Tradeoff Between Speed and Robustness in Primordium Initiation Mediated by Auxin-CUC1 Interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.569401. [PMID: 38076982 PMCID: PMC10705432 DOI: 10.1101/2023.11.30.569401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we found that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases auxin maxima intensity and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we found that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validated experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.
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Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mingyuan Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Present address: Department of Biology, Duke University, Durham, NC 27708, USA
| | - David Pan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Brendan Lane
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Richard S. Smith
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adrienne H. K. Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Lead Contact
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Kong S, Zhu M, Scarpin MR, Pan D, Jia L, Martinez RE, Alamos S, Vadde BVL, Garcia HG, Qian SB, Brunkard JO, Roeder AHK. DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.07.536060. [PMID: 37066395 PMCID: PMC10104159 DOI: 10.1101/2023.04.07.536060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.
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Anjum F, Kaushik K, Salam A, Yadav A, Nandi CK. Super-Resolution Microscopy Unveils Synergistic Structural Changes of Organelles Upon Point Mutation. Adv Biol (Weinh) 2024; 8:e2300399. [PMID: 38053236 DOI: 10.1002/adbi.202300399] [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: 08/03/2023] [Revised: 11/02/2023] [Indexed: 12/07/2023]
Abstract
Ethyl methanesulphonate (EMS), is a widely used chemical mutagen that causes high-frequency germline null mutation by inserting an alkyl group into the nucleotide guanine in eukaryotic cells. The effect of EMS on the dynamics of the aneuploid genome, increased cellular instability, and carcinogenicity in relation to benign and malignant tumors are reported, but the molecular level understanding of morphological changes of higher-order chromatin structure has poorly been understood. This is due to a lack of sufficient resolution in conventional microscopic techniques to see small structures below the diffraction limit. Here, using super-resolution radial fluctuation, a largely fragmented, decompaction, and less dense heterochromatin structure upon EMS treatment to HEK 293A cells without any change in nuclear DNA domains is observed. This result suggests an early stage of carcinogenicity happened due to the point mutation. In addition, the distinct structural changes with an elongated morphology of lysosomes are also observed. On the other hand, fragmented and increased heterogeneous populations with an increased cytoplasmic occupancy of mitochondria are observed.
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Affiliation(s)
- Farhan Anjum
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Kush Kaushik
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Abdul Salam
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Aditya Yadav
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Chayan Kanti Nandi
- School of Chemical Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
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Lu GA, Zhang J, Zhao Y, Chen Q, Lin P, Tang T, Tang Z, Wen H, Liufu Z, Wu CI. Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed. Mol Biol Evol 2023; 40:6974681. [PMID: 36617265 PMCID: PMC9866258 DOI: 10.1093/molbev/msad005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Recent studies have increasingly pointed to microRNAs (miRNAs) as the agent of gene regulatory network (GRN) stabilization as well as developmental canalization against constant but small environmental perturbations. To analyze mild perturbations, we construct a Dicer-1 knockdown line (dcr-1 KD) in Drosophila that modestly reduces all miRNAs by, on average, ∼20%. The defining characteristic of stabilizers is that, when their capacity is compromised, GRNs do not change their short-term behaviors. Indeed, even with such broad reductions across all miRNAs, the changes in the transcriptome are very modest during development in stable environment. By comparison, broad knockdowns of other regulatory genes (esp. transcription factors) by the same method should lead to drastic changes in the GRNs. The consequence of destabilization may thus be in long-term development as postulated by the theory of canalization. Flies with modest miRNA reductions may gradually deviate from the developmental norm, resulting in late-stage failures such as shortened longevity. In the optimal culture condition, the survival to adulthood is indeed normal in the dcr-1 KD line but, importantly, adult longevity is reduced by ∼90%. When flies are stressed by high temperature, dcr-1 KD induces lethality earlier in late pupation and, as the perturbations are shifted earlier, the affected stages are shifted correspondingly. Hence, in late stages of development with deviations piling up, GRN would be increasingly in need of stabilization. In conclusion, miRNAs appear to be a solution to weak but constant environmental perturbations.
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Affiliation(s)
| | | | | | | | | | - Tian Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510275, China
| | - Zhixiong Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510275, China
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Jin C, Wang T, Zhang D, Yang P, Zhang C, Peng W, Jin K, Wang L, Zhou J, Peng C, Tan Y, Ji J, Chen Z, Sun Q, Yang S, Tang J, Feng Y, Sun Y. Acetyltransferase NAT10 regulates the Wnt/β-catenin signaling pathway to promote colorectal cancer progression via ac 4C acetylation of KIF23 mRNA. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:345. [PMID: 36522719 PMCID: PMC9753290 DOI: 10.1186/s13046-022-02551-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/26/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND N4-acetylcytidine (ac4C) as a significant RNA modification has been reported to maintain the stability of mRNA and to regulate the translation process. However, the roles of both ac4C and its 'writer' protein N-acetyltransferase 10 (NAT10) played in the disease especially colorectal cancer (CRC) are unclear. At this point, we discover the underlying mechanism of NAT10 modulating the progression of CRC via mRNA ac4C modification. METHODS The clinical significance of NAT10 was explored based on the TCGA and GEO data sets and the 80 CRC patients cohort of our hospital. qRT-PCR, dot blot, WB, and IHC were performed to detect the level of NAT10 and ac4C modification in CRC tissues and matched adjacent tissues. CCK-8, colony formation, transwell assay, mouse xenograft, and other in vivo and in vitro experiments were conducted to probe the biological functions of NAT10. The potential mechanisms of NAT10 in CRC were clarified by RNA-seq, RIP-seq, acRIP-seq, luciferase reporter assays, etc. RESULTS: The levels of NAT10 and ac4C modification were significantly upregulated. Also, the high expression of NAT10 had important clinical values like poor prognosis, lymph node metastasis, distant metastasis, etc. Furthermore, the in vitro experiments showed that NAT10 could inhibit apoptosis and enhance the proliferation, migration, and invasion of CRC cells and also arrest them in the G2/M phase. The in vivo experiments discovered that NAT10 could promote tumor growth and liver/lung metastasis. In terms of mechanism, NAT10 could mediate the stability of KIF23 mRNA by binding to its mRNA 3'UTR region and up-regulating its mRNA ac4c modification. And then the protein level of KIF23 was elevated to activate the Wnt/β-catenin pathway and more β-catenin was transported into the nucleus which led to the CRC progression. Besides, the inhibitor of NAT10, remodelin, was applied in vitro and vivo which showed an inhibitory effect on the CRC cells. CONCLUSIONS NAT10 promotes the CRC progression through the NAT10/KIF23/GSK-3β/β-catenin axis and its expression is mediated by GSK-3β which forms a feedback loop. Our findings provide a potential prognosis or therapeutic target for CRC and remodelin deserves more attention.
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Affiliation(s)
- Chi Jin
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Tuo Wang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Dongsheng Zhang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Peng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Chuan Zhang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Wen Peng
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Kangpeng Jin
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Lu Wang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Jiahui Zhou
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Chaofan Peng
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yuqian Tan
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Jiangzhou Ji
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Zhihao Chen
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Qingyang Sun
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Junwei Tang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yifei Feng
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
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Bortolin-Cavaillé ML, Quillien A, Thalalla Gamage S, Thomas J, Sas-Chen A, Sharma S, Plisson-Chastang C, Vandel L, Blader P, Lafontaine DLJ, Schwartz S, Meier J, Cavaillé J. Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution. Nucleic Acids Res 2022; 50:6284-6299. [PMID: 35648437 PMCID: PMC9226516 DOI: 10.1093/nar/gkac404] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/28/2022] [Accepted: 05/31/2022] [Indexed: 01/06/2023] Open
Abstract
NAT10 is an essential enzyme that catalyzes N4-acetylcytidine (ac4C) in eukaryotic transfer RNA and 18S ribosomal RNA. Recent studies suggested that rRNA acetylation is dependent on SNORD13, a box C/D small nucleolar RNA predicted to base-pair with 18S rRNA via two antisense elements. However, the selectivity of SNORD13-dependent cytidine acetylation and its relationship to NAT10's essential function remain to be defined. Here, we demonstrate that SNORD13 is required for acetylation of a single cytidine of human and zebrafish 18S rRNA. In-depth characterization revealed that SNORD13-dependent ac4C is dispensable for human cell growth, ribosome biogenesis, translation and development. This loss of function analysis inspired a cross-evolutionary survey of the eukaryotic rRNA acetylation 'machinery' that led to the characterization of many novel metazoan SNORD13 genes. This includes an atypical SNORD13-like RNA in Drosophila melanogaster which guides ac4C to 18S rRNA helix 45 despite lacking one of the two rRNA antisense elements. Finally, we discover that Caenorhabditis elegans 18S rRNA is not acetylated despite the presence of an essential NAT10 homolog. Our findings shed light on the molecular mechanisms underlying SNORD13-mediated rRNA acetylation across eukaryotic evolution and raise new questions regarding the biological and evolutionary relevance of this highly conserved rRNA modification.
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Affiliation(s)
- Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | | | | | - Justin M Thomas
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sunny Sharma
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041 Gosselies, Belgium
| | - Célia Plisson-Chastang
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Laurence Vandel
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Patrick Blader
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041 Gosselies, Belgium
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Jérôme Cavaillé
- To whom correspondence should be addressed. Tel: +33 561335927; Fax: +33 561335886;
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8
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Katsanos D, Ferrando-Marco M, Razzaq I, Aughey G, Southall TD, Barkoulas M. Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID. Development 2021; 148:dev199452. [PMID: 34397094 PMCID: PMC7613258 DOI: 10.1242/dev.199452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/05/2021] [Indexed: 12/19/2022]
Abstract
The epidermis of Caenorhabditis elegans is an essential tissue for survival because it contributes to the formation of the cuticle barrier as well as facilitating developmental progression and animal growth. Most of the epidermis consists of the hyp7 hypodermal syncytium, the nuclei of which are largely generated by the seam cells, which exhibit stem cell-like behaviour during development. How seam cell progenitors differ transcriptionally from the differentiated hypodermis is poorly understood. Here, we introduce Targeted DamID (TaDa) in C. elegans as a method for identifying genes expressed within a tissue of interest without cell isolation. We show that TaDa signal enrichment profiles can be used to identify genes transcribed in the epidermis and use this method to resolve differences in gene expression between the seam cells and the hypodermis. Finally, we predict and functionally validate new transcription and chromatin factors acting in seam cell development. These findings provide insights into cell type-specific gene expression profiles likely associated with epidermal cell fate patterning.
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Affiliation(s)
- Dimitris Katsanos
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mar Ferrando-Marco
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Iqrah Razzaq
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Tony D. Southall
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Michalis Barkoulas
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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