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MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.

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Τίτλος: MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.
Συγγραφείς: Jarva T; Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA., Baugh C; The ATM Solution, Hattiesburg, Mississippi 30403, USA., Zhang J; Department of Mathematics and Statistics, Mississippi State University, Starkville, Mississippi 39762, USA., Lai EC; Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA., Flynt A; Department of Biomedical Engineering, University of Mississippi, Oxford, Mississippi 38655, USA asflynt@olemiss.edu.
Πηγή: RNA (New York, N.Y.) [RNA] 2026 Apr 16; Vol. 32 (5), pp. 584-595. Date of Electronic Publication: 2026 Apr 16.
Τύπος έκδοσης: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9509184 Publication Model: Electronic Cited Medium: Internet ISSN: 1469-9001 (Electronic) Linking ISSN: 13558382 NLM ISO Abbreviation: RNA Subsets: MEDLINE
Imprint Name(s): Publication: <2003->: Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press
Original Publication: New York, NY : Cambridge University Press, c1995-
Ιατρικοί όροι (MeSH): MicroRNAs*/genetics , MicroRNAs*/metabolism , Piwi-Interacting RNA*/genetics , Piwi-Interacting RNA*/metabolism , RNA, Small Interfering*/genetics , RNA, Small Interfering*/metabolism , Software* , RNA Processing, Post-Transcriptional*, Argonaute Proteins/metabolism ; Argonaute Proteins/genetics ; Animals
Περίληψη: Argonaute proteins mediate gene silencing via small regulatory RNAs that are generated by distinctive biogenesis pathways. In animals, three main classes are recognized: ∼21-24 nucleotide (nt) microRNAs (miRNAs), ∼21-24 nt small-interfering RNAs (siRNAs), and ∼24-32 nt Piwi-interacting RNAs (piRNAs). Mechanistic understanding of these pathways was gained from genetic, biochemical, and genomic studies in a handful of model systems, where key ribonucleolytic events were identified that specify stereotyped positioning of small RNAs relative to their precursor transcripts. With burgeoning availability of assembled genomes and small RNA data, there are abundant opportunities to characterize the diversity of small RNAs across nonmodel organisms. While several tools are well-suited to analyze specific small RNA pathways, an integrated package that can help classify and interpret all three major classes of small RNAs is wanting. To address this need, we developed a simple and efficient R package (MiSiPi.Rna) that can generate a variety of plots and statistics for preselected loci, which enable the characterization of diverse biogenesis features of miRNAs, siRNAs, and piRNAs. MiSiPi.Rna requires minimal computational expertise to run and will facilitate efforts to annotate and analyze the major classes of Argonaute-based small regulatory RNAs in arbitrary species of choice.
(© 2026 Jarva et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
Σχόλια: Update of: bioRxiv. 2023 May 09:2023.05.07.539760. doi: 10.1101/2023.05.07.539760.. (PMID: 37214880)
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Grant Information: P20 GM103476 United States GM NIGMS NIH HHS; P30 CA008748 United States CA NCI NIH HHS; R01 GM083300 United States GM NIGMS NIH HHS; R01 HD108914 United States HD NICHD NIH HHS
Contributed Indexing: Keywords: R package; machine learning; miRNA; piRNA; siRNA; small RNA annotation
Substance Nomenclature: 0 (MicroRNAs)
0 (Piwi-Interacting RNA)
0 (RNA, Small Interfering)
0 (Argonaute Proteins)
Entry Date(s): Date Created: 20260126 Date Completed: 20260701 Latest Revision: 20260824
Update Code: 20260824
PubMed Central ID: PMC13418560
DOI: 10.1261/rna.080864.125
PMID: 41587813
Βάση Δεδομένων: MEDLINE
FullText Text:
  Availability: 0
Header DbId: cmedm
DbLabel: MEDLINE
An: 41587813
AccessLevel: 3
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
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  Data: MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.
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  Data: Argonaute proteins mediate gene silencing via small regulatory RNAs that are generated by distinctive biogenesis pathways. In animals, three main classes are recognized: ∼21-24 nucleotide (nt) microRNAs (miRNAs), ∼21-24 nt small-interfering RNAs (siRNAs), and ∼24-32 nt Piwi-interacting RNAs (piRNAs). Mechanistic understanding of these pathways was gained from genetic, biochemical, and genomic studies in a handful of model systems, where key ribonucleolytic events were identified that specify stereotyped positioning of small RNAs relative to their precursor transcripts. With burgeoning availability of assembled genomes and small RNA data, there are abundant opportunities to characterize the diversity of small RNAs across nonmodel organisms. While several tools are well-suited to analyze specific small RNA pathways, an integrated package that can help classify and interpret all three major classes of small RNAs is wanting. To address this need, we developed a simple and efficient R package (MiSiPi.Rna) that can generate a variety of plots and statistics for preselected loci, which enable the characterization of diverse biogenesis features of miRNAs, siRNAs, and piRNAs. MiSiPi.Rna requires minimal computational expertise to run and will facilitate efforts to annotate and analyze the major classes of Argonaute-based small regulatory RNAs in arbitrary species of choice.&lt;br /&gt; (&#169; 2026 Jarva et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
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  Data: Update of: bioRxiv. 2023 May 09:2023.05.07.539760. doi: 10.1101/2023.05.07.539760.. (PMID: &lt;searchLink fieldCode=&quot;PM&quot; term=&quot;%2237214880%22&quot;&gt;37214880)&lt;/searchLink&gt;
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– Name: GrantInfo
  Label: Grant Information
  Group: Grant
  Data: P20 GM103476 United States GM NIGMS NIH HHS; P30 CA008748 United States CA NCI NIH HHS; R01 GM083300 United States GM NIGMS NIH HHS; R01 HD108914 United States HD NICHD NIH HHS
– Name: SubjectMinor
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  Group:
  Data: &lt;i&gt;Keywords: &lt;/i&gt;R package; machine learning; miRNA; piRNA; siRNA; small RNA annotation
– Name: NumberCAS
  Label: Substance Nomenclature
  Group: ID
  Data: 0 (MicroRNAs)&lt;br /&gt;0 (Piwi-Interacting RNA)&lt;br /&gt;0 (RNA, Small Interfering)&lt;br /&gt;0 (Argonaute Proteins)
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  Data: &lt;i&gt;Date Created: &lt;/i&gt;20260126 &lt;i&gt;Date Completed: &lt;/i&gt;20260701 &lt;i&gt;Latest Revision: &lt;/i&gt;20260824
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  Data: 20260824
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  Data: PMC13418560
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.1261/rna.080864.125
– Name: AN
  Label: PMID
  Group: ID
  Data: 41587813
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=cmedm&AN=41587813
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      – Type: doi
        Value: 10.1261/rna.080864.125
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        StartPage: 584
    Subjects:
      – SubjectFull: Argonaute Proteins metabolism
        Type: general
      – SubjectFull: Argonaute Proteins genetics
        Type: general
      – SubjectFull: Animals
        Type: general
      – SubjectFull: MicroRNAs genetics
        Type: general
      – SubjectFull: MicroRNAs metabolism
        Type: general
      – SubjectFull: Piwi-Interacting RNA genetics
        Type: general
      – SubjectFull: Piwi-Interacting RNA metabolism
        Type: general
      – SubjectFull: RNA, Small Interfering genetics
        Type: general
      – SubjectFull: RNA, Small Interfering metabolism
        Type: general
      – SubjectFull: Software
        Type: general
      – SubjectFull: RNA Processing, Post-Transcriptional
        Type: general
    Titles:
      – TitleFull: MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.
        Type: main
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            NameFull: Jarva T
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            NameFull: Zhang J
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            – D: 16
              M: 04
              Text: 2026 Apr 16
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1469-9001
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              Value: 32
            – Type: issue
              Value: 5
          Titles:
            – TitleFull: RNA (New York, N.Y.)
              Type: main
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