ArticleCell2012
CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors.
Article in Cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
154 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.Molecular cell · 2017Pooled it
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Reproductive phasiRNAs are the piRNAs of plants.Trends in genetics : TIG · 2026Review
- Decoding Argonaute specificity: insights fromRNA (New York, N.Y.) · 2026Review
- MUTACLASH: identifying functional small RNA target sites using crosslinking-induced mutations.RNA (New York, N.Y.) · 2026Article
- An intrinsically disordered region of Drosha selectively promotes miRNA biogenesis independent of tissue-specific Microprocessor condensates.Genes & development · 2026Article
- The H3K27me3 reader UAD-2 recruits a TAF-12-containing transcription machinery to initiate piRNA expression within heterochromatic clusters.Nature communications · 2025Article
- RG motifs promote piRNA-mediated gene silencing in C. elegans.Nucleic acids research · 2025Article
- Programmable initiation of mRNA translation by trans-RNA.Nature biotechnology · 2025Article
- The ribonuclease DISL-2 mediates piRNA degradation in C. elegans.Cell reports · 2025Article
- H3K27me3 expands the epigenetic control of piRNA transcription.Nature structural & molecular biology · 2025Article
- piRNA gene density and SUMOylation organize piRNA transcriptional condensate formation.Nature structural & molecular biology · 2025Article
- A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2025Article
- Parameters that influence bipartite reporter system expression in Caenorhabditis elegans.Genetics · 2025Article
- piRNA processing within non-membrane structures is governed by constituent proteins and their functional motifs.The FEBS journal · 2025Review
- A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals.Nature reviews. Molecular cell biology · 2025Review
- Analysis of crosslinking sites suggestsbioRxiv : the preprint server for biology · 2025Article
- An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters.Nucleic acids research · 2025Article
- Functions and applications of RNA interference and small regulatory RNAs.Acta biochimica et biophysica Sinica · 2024Review
- Advances in PIWI-piRNA function in female reproduction in mammals.Acta biochimica et biophysica Sinica · 2024Review
94 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Piwi-interacting (pi) RNAs are germline-expressed small RNAs linked to epigenetic programming. C. elegans piRNAs are thought to be transcribed as independent gene-like loci. To test this idea and to identify potential transcription start (TS) sites for piRNA precursors, we developed CapSeq, an efficient enzymatic method for 5' anchored RNA profiling. Using CapSeq, we identify candidate TS sites, defined by 70-90 nt sequence tags, for >50% of annotated Pol II loci. Surprisingly, however, these CapSeq tags failed to identify the overwhelming majority of piRNA loci. Instead, we show that the likely piRNA precursors are ∼26 nt capped small (cs) RNAs that initiate precisely 2 nt upstream of mature piRNAs and that piRNA processing or stability requires a U at the csRNA +3 position. Finally, we identify a heretofore unrecognized class of piRNAs processed from csRNAs that are expressed at promoters genome wide, nearly doubling the number of piRNAs available for genome surveillance.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.