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For: Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, Yu H, Wei Y, Wu Q, Zhang Y. Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS One 2020;15:e0234696. [PMID: 32544193 PMCID: PMC7297374 DOI: 10.1371/journal.pone.0234696] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/02/2020] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Xu L, Yu Z, Xu Y, Wang Q, Wang G, Li B, Weng Q, Yi Y, Li J. An mRNA vaccine candidate encoding cholera toxin subunit B and conserved antigens of influenza viruses confers cross-protection against influenza a viruses in adult and aged mice. Hum Vaccin Immunother 2025;21:2453304. [PMID: 39957235 PMCID: PMC11834421 DOI: 10.1080/21645515.2025.2453304] [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: 11/15/2024] [Revised: 01/03/2025] [Accepted: 01/10/2025] [Indexed: 02/18/2025]  Open
2
Yao H, Zhang D, Jin H, Guo Y, Liu Y, Wang S, Li T, Yuan S, Lu G, Sun Y. RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation. BMC Biol 2025;23:147. [PMID: 40437520 PMCID: PMC12121112 DOI: 10.1186/s12915-025-02250-7] [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: 10/06/2024] [Accepted: 05/16/2025] [Indexed: 06/01/2025]  Open
3
Camperi J, Chatla K, Freund E, Galan C, Lippold S, Guilbaud A. Current Analytical Strategies for mRNA-Based Therapeutics. Molecules 2025;30:1629. [PMID: 40286229 PMCID: PMC11990077 DOI: 10.3390/molecules30071629] [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: 03/14/2025] [Revised: 04/02/2025] [Accepted: 04/03/2025] [Indexed: 04/29/2025]  Open
4
Gao Y, Takenaka K, Xu SM, Cheng Y, Janitz M. Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis. Brief Funct Genomics 2025;24:elaf005. [PMID: 40251826 PMCID: PMC12008121 DOI: 10.1093/bfgp/elaf005] [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: 12/07/2024] [Revised: 03/10/2025] [Accepted: 03/18/2025] [Indexed: 04/21/2025]  Open
5
Zhu X, Han X, Li Z, Zhou X, Yoo SH, Chen Z, Ji Z. CircaKB: a comprehensive knowledgebase of circadian genes across multiple species. Nucleic Acids Res 2025;53:D67-D78. [PMID: 39329269 PMCID: PMC11701547 DOI: 10.1093/nar/gkae817] [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: 07/27/2024] [Revised: 08/30/2024] [Accepted: 09/14/2024] [Indexed: 09/28/2024]  Open
6
Al Turihi N, Allouche D, Quéré M, Scuiller M, Legastelois I. Characterization of poly(A) and poly(T) tail lengths in plasmid DNA by liquid chromatography high-resolution mass spectrometry. Anal Bioanal Chem 2025;417:59-68. [PMID: 39547978 PMCID: PMC11695563 DOI: 10.1007/s00216-024-05654-6] [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: 07/23/2024] [Revised: 11/04/2024] [Accepted: 11/07/2024] [Indexed: 11/17/2024]
7
Mishra SK, Liu T, Wang H. Thousands of oscillating LncRNAs in the mouse testis. Comput Struct Biotechnol J 2024;23:330-346. [PMID: 38205156 PMCID: PMC10776378 DOI: 10.1016/j.csbj.2023.11.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024]  Open
8
Liu Y, Lu F, Wang J. Sequencing of Transcriptome-Wide Poly(A) Tails by PAIso-seq. Methods Mol Biol 2024;2723:215-232. [PMID: 37824073 DOI: 10.1007/978-1-0716-3481-3_13] [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: 10/13/2023]
9
Kelly D, Schratt G. Screening and Characterization of Functional circRNAs in Neuronal Cultures. Methods Mol Biol 2024;2765:311-324. [PMID: 38381347 DOI: 10.1007/978-1-0716-3678-7_17] [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: 02/22/2024]
10
Iben JR, Li T, Mattijssen S, Maraia RJ. Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform. Methods Mol Biol 2024;2723:285-301. [PMID: 37824077 DOI: 10.1007/978-1-0716-3481-3_17] [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: 10/13/2023]
11
Vignon M, Bastide A, Attina A, David A, Bousquet P, Orti V, Vialaret J, Lehmann S, Periere DD, Hirtz C. Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis. J Periodontal Res 2023;58:959-967. [PMID: 37349891 DOI: 10.1111/jre.13155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
12
Debelli A, Kienzle L, Khorami HH, Angers A, Breton S. Validation of the male-specific ORF of the paternally-transmitted mtDNA in Mytilus edulis as a protein-coding gene. Gene 2023;879:147586. [PMID: 37356740 DOI: 10.1016/j.gene.2023.147586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
13
Vlasenok M, Margasyuk S, Pervouchine DD. Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation. NAR Genom Bioinform 2023;5:lqad051. [PMID: 37260513 PMCID: PMC10227441 DOI: 10.1093/nargab/lqad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]  Open
14
Ramming A, Kappel C, Kanaoka MM, Higashiyama T, Lenhard M. Poly(A) polymerase 1 contributes to competence acquisition of pollen tubes growing through the style in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;114:651-667. [PMID: 36811355 DOI: 10.1111/tpj.16162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
15
Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023;14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
16
Ramarao KDR, Somasundram C, Razali Z, Kunasekaran W, Jin TL, Musa S, Achari VM. Antiproliferative effects of dried Moringa oleifera leaf extract on human Wharton's Jelly mesenchymal stem cells. PLoS One 2022;17:e0274814. [PMID: 36197921 PMCID: PMC9534417 DOI: 10.1371/journal.pone.0274814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/02/2022] [Indexed: 11/18/2022]  Open
17
Liu Y, Zhang Y, Wang J, Lu F. Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq. Nat Protoc 2022;17:1980-2007. [PMID: 35831615 DOI: 10.1038/s41596-022-00704-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
18
Liu M, Hao L, Yang S, Wu X. PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data. Brief Bioinform 2022;23:6620877. [PMID: 35769001 DOI: 10.1093/bib/bbac271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022]  Open
19
Bilodeau DY, Sheridan RM, Balan B, Jex AR, Rissland OS. Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia. RNA (NEW YORK, N.Y.) 2022;28:668-682. [PMID: 35110372 PMCID: PMC9014877 DOI: 10.1261/rna.078793.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
20
Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae. Cells 2021;10:cells10113173. [PMID: 34831396 PMCID: PMC8620895 DOI: 10.3390/cells10113173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/06/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022]  Open
21
Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021;9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022]  Open
22
Mishra SK, Liu T, Wang H. Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis. Int J Mol Sci 2021;22:7810. [PMID: 34360576 PMCID: PMC8346003 DOI: 10.3390/ijms22157810] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/14/2022]  Open
23
Coon SL, Li T, Iben JR, Mattijssen S, Maraia RJ. Single-molecule polyadenylated tail sequencing (SM-PAT-Seq) to measure polyA tail lengths transcriptome-wide. Methods Enzymol 2021;655:119-137. [PMID: 34183118 DOI: 10.1016/bs.mie.2021.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
24
Kandhari N, Kraupner-Taylor CA, Harrison PF, Powell DR, Beilharz TH. The Detection and Bioinformatic Analysis of Alternative 3' UTR Isoforms as Potential Cancer Biomarkers. Int J Mol Sci 2021;22:5322. [PMID: 34070203 PMCID: PMC8158509 DOI: 10.3390/ijms22105322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022]  Open
25
Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020;21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022]  Open
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