ArticleGenome research2018
NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 74 citations in OpenAlex.
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- A conserved Pol II elongator SPT6L mediates Pol V transcription to regulate RNA-directed DNA methylation in Arabidopsis.Nature communications · 2024Article
- Premeiotic 24-nt phasiRNAs are present in theProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Premeiotic 24-nt phasiRNAs are present in thebioRxiv : the preprint server for biology · 2024Article
- Heat stress promotes Arabidopsis AGO1 phase separation and association with stress granule components.iScience · 2024Article
- Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts.PLoS genetics · 2023Article
- Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.The EMBO journal · 2023Article
- PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave.The Plant cell · 2022Article
- Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus.The Plant cell · 2022Article
- RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm.PLoS biology · 2022Article
- An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.Genome biology · 2022Article
- Innate, translation-dependent silencing of an invasive transposon in Arabidopsis.EMBO reports · 2022Article
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- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Diverse RNA 5' ends are generated through both transcriptional and post-transcriptional processes. These important modes of gene regulation often vary across cell types and can contribute to the diversification of transcriptomes and thus cellular differentiation. Therefore, the identification of primary and processed 5' ends of RNAs is important for their functional characterization. Methods have been developed to profile either RNA 5' ends from primary transcripts or the products of RNA degradation genome-wide. However, these approaches either require high amounts of starting RNA or are performed in the absence of paired gene-body mRNA-seq data. This limits current efforts in RNA 5' end annotation to whole tissues and can prevent accurate RNA 5' end classification due to biases in the data sets. To enable the accurate identification and precise classification of RNA 5' ends from standard and low-input RNA, we developed a next-generation sequencing-based method called nanoPARE and associated software. By integrating RNA 5' end information from nanoPARE with gene-body mRNA-seq data from the same RNA sample, our method enables the identification of transcription start sites at single-nucleotide resolution from single-cell levels of total RNA, as well as small RNA-mediated cleavage events from at least 10,000-fold less total RNA compared to conventional approaches. NanoPARE can therefore be used to accurately profile transcription start sites, noncapped RNA 5' ends, and small RNA targeting events from individual tissue types. As a proof-of-principle, we utilized nanoPARE to improve
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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.