ArticleBMC genomics2017
The coding and noncoding transcriptome of Neurospora crassa.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 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.
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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
21 citing papers in PubMed, 29 citations in OpenAlex.
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- Discovering the hidden function in fungal genomes.Nature communications · 2024Review
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- The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogenMicrobial genomics · 2023Article
- Identification of Long Intergenic Noncoding RNAs inMicrobiology spectrum · 2023Article
- Antisense Transcription of theJournal of biological rhythms · 2023Article
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- Nuclear genome organization in fungi: from gene folding to Rabl chromosomes.FEMS microbiology reviews · 2023Article
- Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705.Archives of microbiology · 2023Article
- The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology.G3 (Bethesda, Md.) · 2022Article
- lncRsp1, a long noncoding RNA, influences Fgsp1 expression and sexual reproduction in Fusarium graminearum.Molecular plant pathology · 2022Article
- Identification of Long Non-Coding RNAs and Their Target Genes from Mycelium and Primordium in Model MushroomMycobiology · 2022Article
- Article
- Transcriptome-wide expression profiling ofMicrobial genomics · 2020Article
- Extracting novel hypotheses and findings from RNA-seq data.FEMS yeast research · 2020Review
- Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci.BMC genomics · 2019Article
- Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response inFrontiers in microbiology · 2019Article
- Distribution, Characteristics, and Regulatory Potential of Long Noncoding RNAs in Brown-Rot Fungi.International journal of genomics · 2019Article
- A current view on long noncoding RNAs in yeast and filamentous fungi.Applied microbiology and biotechnology · 2018Review
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundLong non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete.
resultsWe have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 natural antisense transcripts, indicating that 20% of the RNA Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncRNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. Our analysis showed that the vast majority of lincRNAs and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincRNA genes. We show furthermore most lincRNA sequences evolve rapidly, even between phylogenetically close species.
conclusionsOur transcriptome analyses revealed distinct features of Neurospora lincRNAs and antisense transcripts in comparison to mRNAs and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncRNAs.
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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.