ArticlePLoS biology2010
Most "dark matter" transcripts are associated with known genes.
Article in PLoS biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 255 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
255 citing papers in PubMed.
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- A comprehensive analysis of Atlantic salmon gonad and pituitary transcriptomes identifies novel players in sexual maturation.BMC genomics · 2025Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- A quantitative prediction method utilizing whole omics data for biosensing.Scientific reports · 2025Article
- Extracellular vesicles carry transcriptional 'dark matter' revealing tissue-specific information.Journal of extracellular vesicles · 2024Article
- Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes.Cell reports · 2024Article
- Review
- Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism AssociatedbioRxiv : the preprint server for biology · 2024Article
- Host long noncoding RNAs in bacterial infections.Frontiers in immunology · 2024Review
- Hidden regulators: the emerging roles of lncRNAs in brain development and disease.Frontiers in neuroscience · 2024Review
- A review of plant epigenetics through the lens of almond.The plant genome · 2023Review
- LncRNA-Top: Controlled deep learning approaches for lncRNA gene regulatory relationship annotations across different platforms.iScience · 2023Article
- Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin.Nucleic acids research · 2023Article
- Article
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review.Environmental science and pollution research international · 2023Review
- ChEAP: ChIP-exo analysis pipeline and the investigation ofComputational and structural biotechnology journal · 2023Article
- LncRNAs in breast cancer: a link to future approaches.Cancer gene therapy · 2022Review
- ortho2align: a sensitive approach for searching for orthologues of novel lncRNAs.BMC bioinformatics · 2022Article
- Placenta-specific lncRNA 1600012P17Rik is expressed in spongiotrophoblast and glycogen trophoblast cells of mouse placenta.Histochemistry and cell biology · 2022Article
195 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
A series of reports over the last few years have indicated that a much larger portion of the mammalian genome is transcribed than can be accounted for by currently annotated genes, but the quantity and nature of these additional transcripts remains unclear. Here, we have used data from single- and paired-end RNA-Seq and tiling arrays to assess the quantity and composition of transcripts in PolyA+ RNA from human and mouse tissues. Relative to tiling arrays, RNA-Seq identifies many fewer transcribed regions ("seqfrags") outside known exons and ncRNAs. Most nonexonic seqfrags are in introns, raising the possibility that they are fragments of pre-mRNAs. The chromosomal locations of the majority of intergenic seqfrags in RNA-Seq data are near known genes, consistent with alternative cleavage and polyadenylation site usage, promoter- and terminator-associated transcripts, or new alternative exons; indeed, reads that bridge splice sites identified 4,544 new exons, affecting 3,554 genes. Most of the remaining seqfrags correspond to either single reads that display characteristics of random sampling from a low-level background or several thousand small transcripts (median length = 111 bp) present at higher levels, which also tend to display sequence conservation and originate from regions with open chromatin. We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported.
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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.