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For: Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 2012;336:233-7. [PMID: 22422859 DOI: 10.1126/science.1215704] [Citation(s) in RCA: 576] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Zhang Y, Wang C, Wu J, Liu T, Wu H, Peng Z, Liu C, Wang S, Wang Y, Luo K, Wang J, Liu S. Exploring the role of miR-430 in hybrid fish during embryonic development. Comp Biochem Physiol B Biochem Mol Biol 2025;279:111110. [PMID: 40349752 DOI: 10.1016/j.cbpb.2025.111110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2025] [Revised: 05/08/2025] [Accepted: 05/08/2025] [Indexed: 05/14/2025]
2
Li Z, Xu Q, Zhang Y, Zhong J, Zhang T, Xue J, Liu S, Gao H, Zhang ZZZ, Wu J, Shen EZ. Mechanistic insights into RNA cleavage by human Argonaute2-siRNA complex. Cell Res 2025:10.1038/s41422-025-01114-7. [PMID: 40240484 DOI: 10.1038/s41422-025-01114-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Accepted: 03/14/2025] [Indexed: 04/18/2025]  Open
3
Kim M, Pyo Y, Hyun SI, Jeong M, Choi Y, Kim VN. Exogenous RNA surveillance by proton-sensing TRIM25. Science 2025;388:eads4539. [PMID: 40179174 DOI: 10.1126/science.ads4539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 01/14/2025] [Indexed: 04/05/2025]
4
Kojima ML, Hoppe C, Giraldez AJ. The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus. Nat Rev Genet 2025;26:245-267. [PMID: 39587307 PMCID: PMC11928286 DOI: 10.1038/s41576-024-00792-0] [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] [Accepted: 10/08/2024] [Indexed: 11/27/2024]
5
Cieplak-Rotowska MK, Dadlez M, Niedzwiecka A. Exploring the CNOT1(800-999) HEAT Domain and Its Interactions with Tristetraprolin (TTP) as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry. Biomolecules 2025;15:403. [PMID: 40149939 PMCID: PMC11939966 DOI: 10.3390/biom15030403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/05/2025] [Accepted: 03/07/2025] [Indexed: 03/29/2025]  Open
6
Baena-Angulo C, Platero AI, Couso JP. Cis to trans: small ORF functions emerging through evolution. Trends Genet 2025;41:119-131. [PMID: 39603921 DOI: 10.1016/j.tig.2024.10.012] [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: 06/18/2024] [Revised: 10/14/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024]
7
Phelps WA, Ayers TN, Lee MT. Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation. Methods Mol Biol 2025;2923:163-180. [PMID: 40418449 DOI: 10.1007/978-1-0716-4522-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
8
Strayer EC, Krishna S, Lee H, Vejnar C, Neuenkirchen N, Gupta A, Beaudoin JD, Giraldez AJ. NaP-TRAP reveals the regulatory grammar in 5'UTR-mediated translation regulation during zebrafish development. Nat Commun 2024;15:10898. [PMID: 39738051 PMCID: PMC11685710 DOI: 10.1038/s41467-024-55274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/06/2024] [Indexed: 01/01/2025]  Open
9
Yin R, Zhao H, Li L, Yang Q, Zeng M, Yang C, Bian J, Xie M. Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer. Comput Struct Biotechnol J 2024;23:3020-3029. [PMID: 39171252 PMCID: PMC11338065 DOI: 10.1016/j.csbj.2024.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/13/2024] [Accepted: 07/13/2024] [Indexed: 08/23/2024]  Open
10
Sumaira S, Vijayarathna S, Hemagirri M, Adnan M, Hassan MI, Patel M, Gupta R, Shanmugapriya, Chen Y, Gopinath SC, Kanwar JR, Sasidharan S. Plant bioactive compounds driven microRNAs (miRNAs): A potential source and novel strategy targeting gene and cancer therapeutics. Noncoding RNA Res 2024;9:1140-1158. [PMID: 39022680 PMCID: PMC11250886 DOI: 10.1016/j.ncrna.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024]  Open
11
Vega-Badillo J, Zamore PD, Jouravleva K. Biochemical principles of miRNA targeting in flies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.16.623948. [PMID: 39605671 PMCID: PMC11601291 DOI: 10.1101/2024.11.16.623948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
12
Chen LL, Kim VN. Small and long non-coding RNAs: Past, present, and future. Cell 2024;187:6451-6485. [PMID: 39547208 DOI: 10.1016/j.cell.2024.10.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 10/13/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
13
Kushawah G, Amaral DB, Hassan H, Gogol M, Nowotarski SH, Bazzini AA. Critical role of Spatio-Temporally Regulated Maternal RNAs in Zebrafish Embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.07.622483. [PMID: 39574587 PMCID: PMC11580991 DOI: 10.1101/2024.11.07.622483] [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: 12/01/2024]
14
DeVore ML, Bazzini AA. Codon optimality influences homeostatic gene expression in zebrafish. G3 (BETHESDA, MD.) 2024;14:jkae247. [PMID: 39446991 PMCID: PMC11631405 DOI: 10.1093/g3journal/jkae247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 10/11/2024] [Accepted: 10/22/2024] [Indexed: 10/26/2024]
15
Vidya E, Jami-Alahmadi Y, Mayank AK, Rizwan J, Xu JMS, Cheng T, Leventis R, Sonenberg N, Wohlschlegel JA, Vera M, Duchaine TF. EDC-3 and EDC-4 regulate embryonic mRNA clearance and biomolecular condensate specialization. Cell Rep 2024;43:114781. [PMID: 39331503 DOI: 10.1016/j.celrep.2024.114781] [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: 03/20/2024] [Revised: 08/09/2024] [Accepted: 09/05/2024] [Indexed: 09/29/2024]  Open
16
Pallarés H, González López Ledesma M, Oviedo-Rouco S, Castellano L, Costa Navarro G, Fernández-Alvarez A, D’Andreiz M, Aldas-Bulos V, Alvarez D, Bazzini A, Gamarnik A. Zika virus non-coding RNAs antagonize antiviral responses by PKR-mediated translational arrest. Nucleic Acids Res 2024;52:11128-11147. [PMID: 38917323 PMCID: PMC11472168 DOI: 10.1093/nar/gkae507] [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: 01/18/2024] [Revised: 05/08/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024]  Open
17
Zhou Y, Jian N, Jiang C, Wang J. m6A modification in non-coding RNAs: Mechanisms and potential therapeutic implications in fibrosis. Biomed Pharmacother 2024;179:117331. [PMID: 39191030 DOI: 10.1016/j.biopha.2024.117331] [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: 06/11/2024] [Revised: 08/07/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024]  Open
18
Sharma A, Dsilva GJ, Deshpande G, Galande S. Exploring the versatility of zygotic genome regulators: A comparative and functional analysis. Cell Rep 2024;43:114680. [PMID: 39182225 DOI: 10.1016/j.celrep.2024.114680] [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: 04/05/2024] [Revised: 06/30/2024] [Accepted: 08/08/2024] [Indexed: 08/27/2024]  Open
19
Remsburg CM, Konrad KD, Testa MD, Stepicheva N, Lee K, Choe LH, Polson S, Bhavsar J, Huang H, Song JL. miR-31-mediated local translation at the mitotic spindle is important for early development. Development 2024;151:dev202619. [PMID: 39250531 PMCID: PMC11423917 DOI: 10.1242/dev.202619] [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: 12/15/2023] [Accepted: 07/17/2024] [Indexed: 09/11/2024]
20
Yang H, Thompson B. Widespread changes to the translational landscape in a maize microRNA biogenesis mutant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;119:1986-2000. [PMID: 38963711 DOI: 10.1111/tpj.16902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
21
Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024;27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024]  Open
22
Traber GM, Yu AM. The Growing Class of Novel RNAi Therapeutics. Mol Pharmacol 2024;106:13-20. [PMID: 38719476 PMCID: PMC11187687 DOI: 10.1124/molpharm.124.000895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/15/2024] [Indexed: 06/20/2024]  Open
23
Hernandez-Huertas L, Moreno-Sanchez I, Crespo-Cuadrado J, Vargas-Baco A, da Silva Pescador G, Santos-Pereira JM, Bazzini AA, Moreno-Mateos MA. CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595167. [PMID: 38826327 PMCID: PMC11142190 DOI: 10.1101/2024.05.22.595167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
24
Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. G3 (BETHESDA, MD.) 2024;14:jkae050. [PMID: 38466753 PMCID: PMC11075544 DOI: 10.1093/g3journal/jkae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
25
Lorenzo-Orts L, Pauli A. The molecular mechanisms underpinning maternal mRNA dormancy. Biochem Soc Trans 2024;52:861-871. [PMID: 38477334 PMCID: PMC11088918 DOI: 10.1042/bst20231122] [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: 12/14/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
26
Yin R, Zhao H, Li L, Yang Q, Zeng M, Yang C, Bian J, Xie M. Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589599. [PMID: 38659732 PMCID: PMC11042274 DOI: 10.1101/2024.04.15.589599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
27
Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024;25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [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: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024]  Open
28
Duan Y, Li L, Panzade GP, Piton A, Zinovyeva A, Ambros V. Modeling neurodevelopmental disorder-associated human AGO1 mutations in Caenorhabditis elegans Argonaute alg-1. Proc Natl Acad Sci U S A 2024;121:e2308255121. [PMID: 38412125 PMCID: PMC10927592 DOI: 10.1073/pnas.2308255121] [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: 07/10/2023] [Accepted: 11/30/2023] [Indexed: 02/29/2024]  Open
29
Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024;20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [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: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024]  Open
30
Singh M, Kim JH. Measurement of Poly A Tail Length from Drosophila Larva Brain and Cell Line. J Vis Exp 2024:10.3791/66116. [PMID: 38284531 PMCID: PMC10954090 DOI: 10.3791/66116] [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] [Indexed: 01/30/2024]  Open
31
Freen-van Heeren JJ. Posttranscriptional Events Orchestrate Immune Homeostasis of CD8+ T Cells. Methods Mol Biol 2024;2782:65-80. [PMID: 38622392 DOI: 10.1007/978-1-0716-3754-8_4] [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] [Indexed: 04/17/2024]
32
Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570431. [PMID: 38106184 PMCID: PMC10723407 DOI: 10.1101/2023.12.06.570431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
33
Di Grandi D, Dayeh DM, Kaur K, Chen Y, Henderson S, Moon Y, Bhowmick A, Ihnat PM, Fu Y, Muthusamy K, Palackal N, Pyles EA. A single-nucleotide resolution capillary gel electrophoresis workflow for poly(A) tail characterization in the development of mRNA therapeutics and vaccines. J Pharm Biomed Anal 2023;236:115692. [PMID: 37696189 DOI: 10.1016/j.jpba.2023.115692] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023]
34
Wang S, Huang T, Xie Z, Wan L, Ren H, Wu T, Xie L, Luo S, Li M, Xie Z, Fan Q, Huang J, Zeng T, Zhang Y, Zhang M, Wei Y. Transcriptomic and Translatomic Analyses Reveal Insights into the Signaling Pathways of the Innate Immune Response in the Spleens of SPF Chickens Infected with Avian Reovirus. Viruses 2023;15:2346. [PMID: 38140587 PMCID: PMC10747248 DOI: 10.3390/v15122346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]  Open
35
Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540322. [PMID: 37214951 PMCID: PMC10197686 DOI: 10.1101/2023.05.11.540322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
36
Shah VN, Neumeier J, Huberdeau MQ, Zeitler DM, Bruckmann A, Meister G, Simard MJ. Casein kinase 1 and 2 phosphorylate Argonaute proteins to regulate miRNA-mediated gene silencing. EMBO Rep 2023;24:e57250. [PMID: 37712432 PMCID: PMC10626430 DOI: 10.15252/embr.202357250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]  Open
37
Nikumbh S, Lenhard B. Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation. PLoS Comput Biol 2023;19:e1011491. [PMID: 37983292 PMCID: PMC10695386 DOI: 10.1371/journal.pcbi.1011491] [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: 04/13/2023] [Revised: 12/04/2023] [Accepted: 09/05/2023] [Indexed: 11/22/2023]  Open
38
Fang G, Xu D, Zhang T, Qiu L, Gao X, Wang G, Miao Y. Effects of hsa_circ_0074854 on colorectal cancer progression, construction of a circRNA-miRNA-mRNA network, and analysis of immune infiltration. J Cancer Res Clin Oncol 2023;149:15439-15456. [PMID: 37644235 PMCID: PMC10620273 DOI: 10.1007/s00432-023-05315-8] [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: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023]
39
Phelps WA, Hurton MD, Ayers TN, Carlson AE, Rosenbaum JC, Lee MT. Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis. eLife 2023;12:e83952. [PMID: 37787392 PMCID: PMC10569791 DOI: 10.7554/elife.83952] [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: 10/04/2022] [Accepted: 10/02/2023] [Indexed: 10/04/2023]  Open
40
Al Qaryoute A, Fallatah W, Dhinoja S, Raman R, Jagadeeswaran P. Role of microRNAs and their downstream target transcription factors in zebrafish thrombopoiesis. Sci Rep 2023;13:16066. [PMID: 37752184 PMCID: PMC10522587 DOI: 10.1038/s41598-023-42868-7] [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: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023]  Open
41
Umu SU, Paynter VM, Trondsen H, Buschmann T, Rounge TB, Peterson KJ, Fromm B. Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. CELL GENOMICS 2023;3:100348. [PMID: 37601971 PMCID: PMC10435380 DOI: 10.1016/j.xgen.2023.100348] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 08/22/2023]
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLoS Genet 2023;19:e1010845. [PMID: 37440598 PMCID: PMC10368294 DOI: 10.1371/journal.pgen.1010845] [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: 05/11/2023] [Revised: 07/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]  Open
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Seo JJ, Jung SJ, Yang J, Choi DE, Kim VN. Functional viromic screens uncover regulatory RNA elements. Cell 2023:S0092-8674(23)00675-X. [PMID: 37413987 DOI: 10.1016/j.cell.2023.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/21/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023]
44
Wu Q, Bazzini AA. Translation and mRNA Stability Control. Annu Rev Biochem 2023;92:227-245. [PMID: 37001134 DOI: 10.1146/annurev-biochem-052621-091808] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540083. [PMID: 37214839 PMCID: PMC10197650 DOI: 10.1101/2023.05.09.540083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
46
Qaryoute AA, Fallatah W, Dhinoja S, Raman R, Jagadeeswaran P. Role of MicroRNAs and their Downstream Target Transcription Factors in Zebrafish Thrombopoiesis. RESEARCH SQUARE 2023:rs.3.rs-2807790. [PMID: 37162944 PMCID: PMC10168436 DOI: 10.21203/rs.3.rs-2807790/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
47
Quesnelle DC, Bendena WG, Chin-Sang ID. A Compilation of the Diverse miRNA Functions in Caenorhabditis elegans and Drosophila melanogaster Development. Int J Mol Sci 2023;24:ijms24086963. [PMID: 37108126 PMCID: PMC10139094 DOI: 10.3390/ijms24086963] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023]  Open
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Duan Y, Li L, Panzade GP, Piton A, Zinovyeva A, Ambros V. Modeling neurodevelopmental disorder-associated hAGO1 mutations in C. elegans Argonaute ALG-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535748. [PMID: 37066388 PMCID: PMC10104039 DOI: 10.1101/2023.04.06.535748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
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Park J, Kim M, Yi H, Baeg K, Choi Y, Lee YS, Lim J, Kim VN. Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex. Nat Struct Mol Biol 2023;30:330-338. [PMID: 36849640 DOI: 10.1038/s41594-023-00930-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
50
Baig MS, Deepanshu, Prakash P, Alam P, Krishnan A. In silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA. J Biomol Struct Dyn 2023;41:12305-12327. [PMID: 36752331 DOI: 10.1080/07391102.2023.2175255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/01/2023] [Indexed: 02/09/2023]
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