ArticleRNA (New York, N.Y.)2015
EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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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.
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Who cites it
23 citing papers in PubMed, 30 citations in OpenAlex.
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- SUMO2 promotes histone pre-mRNA processing by stabilizing histone locus body interactions and facilitating U7 snRNP assembly.Genes & development · 2025Article
- Cell-cycle-regulated transcriptional pausing ofMolecular biology of the cell · 2025Article
- Reversible proliferative arrest induced by rapid depletion of RNase MRP.Nature communications · 2025Article
- Current Analytical Strategies for mRNA-Based Therapeutics.Molecules (Basel, Switzerland) · 2025Review
- Cell cycle-regulated transcriptional pausing ofbioRxiv : the preprint server for biology · 2024Article
- Measuring the tail: Methods for poly(A) tail profiling.Wiley interdisciplinary reviews. RNA · 2023Review
- Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3'hExo.RNA biology · 2023Article
- Knockouts of TUT7 and 3'hExo show that they cooperate in histone mRNA maintenance and degradation.RNA (New York, N.Y.) · 2022Article
- The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies' association with histone locus bodies.Nature communications · 2022Article
- Tailer: a pipeline for sequencing-based analysis of nonpolyadenylated RNA 3' end processing.RNA (New York, N.Y.) · 2022Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Resolution of polycistronic RNA by SL2RNA (New York, N.Y.) · 2020Article
- A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing.Nature reviews. Molecular cell biology · 2020Review
- Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C.Nature communications · 2020Article
- Determining degradation intermediates and the pathway of 3' to 5' degradation of histone mRNA using high-throughput sequencing.Methods (San Diego, Calif.) · 2019Review
- The role of 3' end uridylation in RNA metabolism and cellular physiology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Role of oligouridylation in normal metabolism and regulated degradation of mammalian histone mRNAs.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- NMD-degradome sequencing reveals ribosome-bound intermediates with 3'-end non-templated nucleotides.Nature structural & molecular biology · 2018Article
- Birth and Death of Histone mRNAs.Trends in genetics : TIG · 2017Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3' ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3' ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3' end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3' ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1-2 nt at the 3' end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotide compositions. We increase the sensitivity of EnD-Seq by using cDNA priming to specifically enrich low-abundance tails of known sequence composition allowing identification of degradation intermediates. In addition, we show the broad applicability of our computational approach by using AppEnD to gain insight into 3' additions from diverse types of sequencing data, including data from small capped RNA sequencing and some alternative polyadenylation protocols.
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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.