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For: Axtell MJ. ShortStack: comprehensive annotation and quantification of small RNA genes. RNA 2013;19:740-51. [PMID: 23610128 PMCID: PMC3683909 DOI: 10.1261/rna.035279.112] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Number Cited by Other Article(s)
1
Ta H, Nonomura KI. Profiling of 24-nt phasiRNAs in Rice Anther by Massively Parallel Sequencing and Stem-Loop Reverse Transcription PCR. Methods Mol Biol 2025;2869:135-146. [PMID: 39499474 DOI: 10.1007/978-1-0716-4204-7_14] [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: 11/07/2024]
2
Hernandez NP, Rawls A, Chen J, Zhang X, Wang Y, Gao X, Parisien M, Karaky M, Meloto CB, Montagna F, Dang H, Pan Y, Zhao Y, McLean S, Linnstaedt S, Diatchenko L, Nackley AG. miR-374 family is a key regulator of chronic primary pain onset. Pain Rep 2024;9:e1199. [PMID: 39430682 PMCID: PMC11487220 DOI: 10.1097/pr9.0000000000001199] [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: 05/08/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 10/22/2024]  Open
3
Pal AK, Gandhivel VHS, Nambiar AB, Shivaprasad PV. Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler. Nat Commun 2024;15:7807. [PMID: 39242590 PMCID: PMC11379814 DOI: 10.1038/s41467-024-52239-z] [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: 09/01/2023] [Accepted: 08/29/2024] [Indexed: 09/09/2024]  Open
4
Berube B, Ernst E, Cahn J, Roche B, de Santis Alves C, Lynn J, Scheben A, Grimanelli D, Siepel A, Ross-Ibarra J, Kermicle J, Martienssen RA. Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature 2024;633:380-388. [PMID: 39112710 PMCID: PMC11390486 DOI: 10.1038/s41586-024-07788-0] [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: 06/14/2023] [Accepted: 07/04/2024] [Indexed: 08/17/2024]
5
Kumar D, Venkadesan S, Prabha R, Begam S, Dutta B, Mishra DC, Chaturvedi KK, Jha GK, Solanke AU, Sevanthi AM. RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice. Database (Oxford) 2024;2024:baae076. [PMID: 39167719 PMCID: PMC11338179 DOI: 10.1093/database/baae076] [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: 02/02/2024] [Revised: 05/27/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
6
Vega JM, Podio M, Orjuela J, Siena LA, Pessino SC, Combes MC, Mariac C, Albertini E, Pupilli F, Ortiz JPA, Leblanc O. Chromosome-scale genome assembly and annotation of Paspalum notatum Flüggé var. saurae. Sci Data 2024;11:891. [PMID: 39152143 PMCID: PMC11329641 DOI: 10.1038/s41597-024-03731-0] [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: 02/19/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]  Open
7
Díez-Sainz E, Milagro FI, Aranaz P, Riezu-Boj JI, Lorente-Cebrián S. MicroRNAs from edible plants reach the human gastrointestinal tract and may act as potential regulators of gene expression. J Physiol Biochem 2024;80:655-670. [PMID: 38662188 PMCID: PMC11502557 DOI: 10.1007/s13105-024-01023-0] [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: 06/23/2023] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
8
Sun Y, Yang X, Wu R, Lv S, Li Y, Jia H, Yang Y, Li B, Chen W, Allan AC, Jiang G, Shi YN, Chen K. DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024;66:1718-1734. [PMID: 38896078 DOI: 10.1111/jipb.13681] [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: 01/30/2024] [Accepted: 05/02/2024] [Indexed: 06/21/2024]
9
de Oliveira AC, Bovolenta LA, Figueiredo L, Ribeiro ADO, Pereira BJA, de Almeida TRA, Campos VF, Patton JG, Pinhal D. MicroRNA Transcriptomes Reveal Prevalence of Rare and Species-Specific Arm Switching Events During Zebrafish Ontogenesis. Evol Bioinform Online 2024;20:11769343241263230. [PMID: 39055772 PMCID: PMC11271096 DOI: 10.1177/11769343241263230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024]  Open
10
Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F. Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis. Sci Data 2024;11:678. [PMID: 38909042 PMCID: PMC11193728 DOI: 10.1038/s41597-024-03513-8] [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: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024]  Open
11
Wu X, Chen S, Lin F, Muhammad F, Xu H, Wu L. Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;118:1955-1971. [PMID: 38491864 DOI: 10.1111/tpj.16721] [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: 12/28/2023] [Revised: 02/01/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
12
Cherubino Ribeiro TH, Baldrich P, de Oliveira RR, Fernandes-Brum CN, Mathioni SM, de Sousa Cardoso TC, de Souza Gomes M, do Amaral LR, Pimenta de Oliveira KK, Dos Reis GL, Meyers BC, Chalfun-Junior A. The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024;118:1848-1863. [PMID: 38488203 DOI: 10.1111/tpj.16713] [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: 09/13/2023] [Revised: 12/05/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
13
Takei T, Tsukada M, Tamura K, Hara-Nishimura I, Fukao Y, Kurihara Y, Matsui M, Saze H, Tsuzuki M, Watanabe Y, Hamada T. ARGONAUTE1-binding Tudor domain proteins function in small interfering RNA production for RNA-directed DNA methylation. PLANT PHYSIOLOGY 2024;195:1333-1346. [PMID: 38446745 DOI: 10.1093/plphys/kiae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
14
Ressel S, Kumar S, Bermúdez-Barrientos JR, Gordon K, Lane J, Wu J, Abreu-Goodger C, Schwarze J, Buck A. RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity. Nucleic Acids Res 2024;52:4872-4888. [PMID: 38412296 PMCID: PMC11109944 DOI: 10.1093/nar/gkae116] [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: 07/05/2023] [Revised: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024]  Open
15
Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. Proc Natl Acad Sci U S A 2024;121:e2402285121. [PMID: 38739785 PMCID: PMC11127045 DOI: 10.1073/pnas.2402285121] [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: 02/04/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024]  Open
16
Gravot A, Liégard B, Quadrana L, Veillet F, Aigu Y, Bargain T, Bénéjam J, Lariagon C, Lemoine J, Colot V, Manzanares-Dauleux MJ, Jubault M. Two adjacent NLR genes conferring quantitative resistance to clubroot disease in Arabidopsis are regulated by a stably inherited epiallelic variation. PLANT COMMUNICATIONS 2024;5:100824. [PMID: 38268192 PMCID: PMC11121752 DOI: 10.1016/j.xplc.2024.100824] [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: 09/05/2023] [Revised: 12/21/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
17
Sun MS, Jia Y, Chen XY, Chen JS, Guo Y, Fu FF, Xue LJ. Regulatory microRNAs and phasiRNAs of paclitaxel biosynthesis in Taxus chinensis. FRONTIERS IN PLANT SCIENCE 2024;15:1403060. [PMID: 38779066 PMCID: PMC11109412 DOI: 10.3389/fpls.2024.1403060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
18
Edelbroek B, Kjellin J, Biryukova I, Liao Z, Lundberg T, Noegel A, Eichinger L, Friedländer M, Söderbom F. Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity. Nucleic Acids Res 2024;52:3121-3136. [PMID: 38375870 PMCID: PMC11014262 DOI: 10.1093/nar/gkae109] [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: 11/14/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]  Open
19
Enriquez-Felix EE, Pérez-Salazar C, Rico-Ruiz JG, Calheiros de Carvalho A, Cruz-Morales P, Villalobos-Escobedo JM, Herrera-Estrella A. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiol Spectr 2024;12:e0316523. [PMID: 38441469 PMCID: PMC10986496 DOI: 10.1128/spectrum.03165-23] [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: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 04/06/2024]  Open
20
Zhan J, Bélanger S, Lewis S, Teng C, McGregor M, Beric A, Schon MA, Nodine MD, Meyers BC. Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587306. [PMID: 38617318 PMCID: PMC11014486 DOI: 10.1101/2024.03.29.587306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
21
Li G, Chen C, Chen P, Meyers BC, Xia R. sRNAminer: A multifunctional toolkit for next-generation sequencing small RNA data mining in plants. Sci Bull (Beijing) 2024;69:784-791. [PMID: 38246798 DOI: 10.1016/j.scib.2023.12.049] [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: 10/13/2023] [Revised: 11/25/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
22
Dew-Budd KJ, Chow HT, Kendall T, David BC, Rozelle JA, Mosher RA, Beilstein MA. Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. PLANT PHYSIOLOGY 2024;194:2136-2148. [PMID: 37987565 DOI: 10.1093/plphys/kiad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
23
Čermák V, Kašpar T, Fischer L. SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway. FRONTIERS IN PLANT SCIENCE 2024;15:1372880. [PMID: 38576781 PMCID: PMC10991848 DOI: 10.3389/fpls.2024.1372880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
24
Zhang Y, Huang J, Xie F, Huang Q, Jiao H, Cheng W. Identification of plant microRNAs using convolutional neural network. FRONTIERS IN PLANT SCIENCE 2024;15:1330854. [PMID: 38567128 PMCID: PMC10985208 DOI: 10.3389/fpls.2024.1330854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024]
25
Gu C, Pei MS, Guo ZH, Wu L, Qi KJ, Wang XP, Liu H, Liu Z, Lang Z, Zhang S. Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism. Genome Biol 2024;25:70. [PMID: 38486226 PMCID: PMC10938805 DOI: 10.1186/s13059-024-03200-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024]  Open
26
Zayakin P. sRNAflow: A Tool for the Analysis of Small RNA-Seq Data. Noncoding RNA 2024;10:6. [PMID: 38250806 PMCID: PMC10801628 DOI: 10.3390/ncrna10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024]  Open
27
Kesidou D, Bennett M, Monteiro JP, McCracken IR, Klimi E, Rodor J, Condie A, Cowan S, Caporali A, Wit JBM, Mountford JC, Brittan M, Beqqali A, Baker AH. Extracellular vesicles from differentiated stem cells contain novel proangiogenic miRNAs and induce angiogenic responses at low doses. Mol Ther 2024;32:185-203. [PMID: 38096818 PMCID: PMC10787168 DOI: 10.1016/j.ymthe.2023.11.023] [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: 05/16/2023] [Revised: 10/10/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024]  Open
28
Felgines L, Rymen B, Martins LM, Xu G, Matteoli C, Himber C, Zhou M, Eis J, Coruh C, Böhrer M, Kuhn L, Chicher J, Pandey V, Hammann P, Wohlschlegel J, Waltz F, Law JA, Blevins T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573199. [PMID: 38234754 PMCID: PMC10793415 DOI: 10.1101/2023.12.26.573199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
29
Díez-Sainz E, Lorente-Cebrián S, Aranaz P, Amri EZ, Riezu-Boj JI, Milagro FI. miR482f and miR482c-5p from edible plant-derived foods inhibit the expression of pro-inflammatory genes in human THP-1 macrophages. Front Nutr 2023;10:1287312. [PMID: 38099184 PMCID: PMC10719859 DOI: 10.3389/fnut.2023.1287312] [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: 09/01/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]  Open
30
Ma X, Nie Z, Huang H, Yan C, Li S, Hu Z, Wang Y, Yin H. Small RNA profiling reveals that an ovule-specific microRNA, cja-miR5179, targets a B-class MADS-box gene in Camellia japonica. ANNALS OF BOTANY 2023;132:1007-1020. [PMID: 37831901 PMCID: PMC10808017 DOI: 10.1093/aob/mcad155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
31
Guo Y, Qi Y, Feng Y, Yang Y, Xue L, El-Kassaby YA, Wang G, Fu F. Inferring the Regulatory Network of miRNAs on Terpene Trilactone Biosynthesis Affected by Environmental Conditions. Int J Mol Sci 2023;24:17002. [PMID: 38069325 PMCID: PMC10707241 DOI: 10.3390/ijms242317002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]  Open
32
Xie Y, Ying S, Li Z, Zhang Y, Zhu J, Zhang J, Wang M, Diao H, Wang H, Zhang Y, Ye L, Zhuang Y, Zhao F, Teng W, Zhang W, Tong Y, Cho J, Dong Z, Xue Y, Zhang Y. Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat. Nat Commun 2023;14:7465. [PMID: 37978184 PMCID: PMC10656477 DOI: 10.1038/s41467-023-42771-9] [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: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]  Open
33
Berube B, Ernst E, Cahn J, Roche B, de Santis Alves C, Lynn J, Scheben A, Siepel A, Ross-Ibarra J, Kermicle J, Martienssen R. Teosinte Pollen Drive guides maize diversification and domestication by RNAi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548689. [PMID: 37503269 PMCID: PMC10370002 DOI: 10.1101/2023.07.12.548689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
34
Meijer A, Atighi MR, Demeestere K, De Meyer T, Vandepoele K, Kyndt T. Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses. PLANT PHYSIOLOGY 2023;193:2071-2085. [PMID: 37052181 DOI: 10.1093/plphys/kiad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
35
Regmi R, Newman TE, Khentry Y, Kamphuis LG, Derbyshire MC. Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets. BMC Genomics 2023;24:582. [PMID: 37784009 PMCID: PMC10544508 DOI: 10.1186/s12864-023-09686-7] [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: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]  Open
36
Noureddine Y, da Rocha M, An J, Médina C, Mejias J, Mulet K, Quentin M, Abad P, Zouine M, Favery B, Jaubert-Possamai S. AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023;74:5752-5766. [PMID: 37310189 DOI: 10.1093/jxb/erad208] [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: 11/23/2022] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
37
Zayakin P, Sadovska L, Eglītis K, Romanchikova N, Radoviča-Spalviņa I, Endzeliņš E, Liepniece-Karele I, Eglītis J, Linē A. Extracellular Vesicles-A Source of RNA Biomarkers for the Detection of Breast Cancer in Liquid Biopsies. Cancers (Basel) 2023;15:4329. [PMID: 37686605 PMCID: PMC10487078 DOI: 10.3390/cancers15174329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]  Open
38
Colicchio JM, Amstutz CL, Garcia N, Prabhu KN, Cairns TM, Akman M, Gottilla T, Gollery T, Stricklin SL, Bayer TS. A tool for rapid, automated characterization of population epigenomics in plants. Sci Rep 2023;13:12915. [PMID: 37591855 PMCID: PMC10435466 DOI: 10.1038/s41598-023-38356-7] [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: 02/16/2023] [Accepted: 07/06/2023] [Indexed: 08/19/2023]  Open
39
Mann CWG, Sawyer A, Gardiner DM, Mitter N, Carroll BJ, Eamens AL. RNA-Based Control of Fungal Pathogens in Plants. Int J Mol Sci 2023;24:12391. [PMID: 37569766 PMCID: PMC10418863 DOI: 10.3390/ijms241512391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]  Open
40
Li Y, Shi Y, Li Y, Lu J, Sun Y, Zhang Y, Chen W, Yang X, Grierson D, Lang Z, Jiang G, Chen K. DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry. HORTICULTURE RESEARCH 2023;10:uhad131. [PMID: 37560014 PMCID: PMC10407599 DOI: 10.1093/hr/uhad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/19/2023] [Indexed: 08/11/2023]
41
Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R, Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet 2023;19:e1010914. [PMID: 37643184 PMCID: PMC10495008 DOI: 10.1371/journal.pgen.1010914] [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: 03/07/2023] [Revised: 09/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]  Open
42
Bakirbas A, Castro-Rodriguez R, Walker EL. The Small RNA Component of Arabidopsis thaliana Phloem Sap and Its Response to Iron Deficiency. PLANTS (BASEL, SWITZERLAND) 2023;12:2782. [PMID: 37570935 PMCID: PMC10421156 DOI: 10.3390/plants12152782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
43
Payne D, Li Y, Govindan G, Kumar A, Thomas J, Addo-Quaye CA, Pereira A, Sunkar R. High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness. Int J Mol Sci 2023;24:11631. [PMID: 37511395 PMCID: PMC10380806 DOI: 10.3390/ijms241411631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]  Open
44
Liu ZW, Liu J, Liu F, Zhong X. Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis. Nucleic Acids Res 2023;51:6039-6054. [PMID: 37094065 PMCID: PMC10325890 DOI: 10.1093/nar/gkad306] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023]  Open
45
Rego N, Libisch MG, Rovira C, Tosar JP, Robello C. Comparative microRNA profiling of Trypanosoma cruzi infected human cells. Front Cell Infect Microbiol 2023;13:1187375. [PMID: 37424776 PMCID: PMC10322668 DOI: 10.3389/fcimb.2023.1187375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023]  Open
46
Manley BF, Lotharukpong JS, Barrera-Redondo J, Llewellyn T, Yildirir G, Sperschneider J, Corradi N, Paszkowski U, Miska EA, Dallaire A. A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis. G3 (BETHESDA, MD.) 2023;13:jkad077. [PMID: 36999556 PMCID: PMC10234402 DOI: 10.1093/g3journal/jkad077] [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: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 06/02/2023]
47
Natali L, Luna Pizarro G, Moyano S, de la Cruz-Thea B, Musso J, Rópolo AS, Eichner N, Meister G, Musri MM, Feliziani C, Touz MC. The Exosome-like Vesicles of Giardia Assemblages A, B, and E Are Involved in the Delivering of Distinct Small RNA from Parasite to Parasite. Int J Mol Sci 2023;24:ijms24119559. [PMID: 37298511 DOI: 10.3390/ijms24119559] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023]  Open
48
Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023;21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [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: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]  Open
49
Hari Sundar G V, Swetha C, Basu D, Pachamuthu K, Raju S, Chakraborty T, Mosher RA, Shivaprasad PV. Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. Genome Res 2023;33:715-728. [PMID: 37277199 PMCID: PMC10317121 DOI: 10.1101/gr.277353.122] [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: 09/22/2022] [Accepted: 04/16/2023] [Indexed: 06/07/2023]
50
Wajnberg G, Allain EP, Roy JW, Srivastava S, Saucier D, Morin P, Marrero A, O’Connell C, Ghosh A, Lewis SM, Ouellette RJ, Crapoulet N. Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy. FRONTIERS IN BIOINFORMATICS 2023;3:1127661. [PMID: 37252342 PMCID: PMC10213969 DOI: 10.3389/fbinf.2023.1127661] [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: 12/19/2022] [Accepted: 04/17/2023] [Indexed: 05/31/2023]  Open
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