ArticlePloS one2014
Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 77 citations in OpenAlex.
- Single nucleotide polymorphisms in ZNRD1-AS1 increase cancer risk in an Asian population.Oncotarget · 2017Pooled it
- Rebalancing the non-coding RNA research agenda: future directions for long non-coding RNA and circular RNA research.Experimental & molecular medicine · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- Distinctive physical properties of DNA shared by RNA polymerase II gene promoters and 5'-flanking regions of tRNA genes.Journal of biochemistry · 2024Article
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- Endothelial Cell GATA2 Modulates the Cardiomyocyte Stress Response through the Regulation of Two Long Non-Coding RNAs.Biology · 2022Article
- HiMoRNA: A Comprehensive Database of Human lncRNAs Involved in Genome-Wide Epigenetic Regulation.Non-coding RNA · 2022Article
- A Quartet Network Analysis Identifying Mechanically Responsive Long Noncoding RNAs in Bone Remodeling.Frontiers in bioengineering and biotechnology · 2022Article
- Non-coding RNA crosstalk with nuclear receptors in liver disease.Biochimica et biophysica acta. Molecular basis of disease · 2021Review
- Article
- Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives.Non-coding RNA · 2020Review
- Emerging crosstalk between long non-coding RNAs and Nrf2 signaling.Cancer letters · 2020Article
- Blood-based biomarkers for early detection of esophageal squamous cell carcinoma.World journal of gastroenterology · 2020Review
- Practical Guidance in Genome-Wide RNA:DNA Triple Helix Prediction.International journal of molecular sciences · 2020Article
- Long non-coding RNAs regulating macrophage functions in homeostasis and disease.Vascular pharmacology · 2019Review
- Induction of a Long Noncoding RNA Transcript, NR_045064, Promotes Defense Gene Transcription and Facilitates Intestinal Epithelial Cell Responses againstJournal of immunology (Baltimore, Md. : 1950) · 2018Article
- Coordinate regulation of long non-coding RNAs and protein-coding genes in germ-free mice.BMC genomics · 2018Article
- Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics.BMC bioinformatics · 2018Article
- Towards a complete map of the human long non-coding RNA transcriptome.Nature reviews. Genetics · 2018Review
- HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.Nucleic acids research · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.
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.