ArticleNature protocols2019
Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 40 citations in OpenAlex.
- Epigenetic modifications in cancer drug resistance: molecular mechanisms and therapeutic interventions.Molecular biomedicine · 2026Review
- Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression.eLife · 2026Article
- Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes.BMC biology · 2026Article
- LncRNA:DNA Binding Prediction Using LongTarget and Its Revised Version.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Gain of Alternative Allele Expression of LINC02449 at rs149707223 in Schizophrenia and Bipolar Disorder: Inducing Synaptic Transmission and Behavioral Deficits in Mice.Nature communications · 2025Article
- Human-specific protein-coding and lncRNA genes cast sex-biased genes in the brain and their relationships with brain diseases.Biology of sex differences · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Pan-glioma analyses reveal species- and tumor-specific regulation of neuron-glioma synapse genes by lncRNAs.Frontiers in genetics · 2023Article
- SALIS transcriptionally represses IGFBP3/Caspase-7-mediated apoptosis by associating with STAT5A to promote hepatocellular carcinoma.Cell death & disease · 2022Article
- The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors.Nature communications · 2022Article
- A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis.Nature communications · 2022Article
- Long Noncoding RNAs and Human Liver Disease.Annual review of pathology · 2022Review
- Article
- Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.Frontiers in genetics · 2022Article
- LncRNA-AC006129.1 reactivates a SOCS3-mediated anti-inflammatory response through DNA methylation-mediated CIC downregulation in schizophrenia.Molecular psychiatry · 2021Article
- Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives.Non-coding RNA · 2020Review
- Unraveling the structure and biological functions of RNA triple helices.Wiley interdisciplinary reviews. RNA · 2020Review
- Extended transcriptome analysis reveals genome-wide lncRNA-mediated epigenetic dysregulation in colorectal cancer.Computational and structural biotechnology journal · 2020Article
- Article
- Decrypting noncoding RNA interactions, structures, and functional networks.Genome research · 2019Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Abundant long, noncoding RNAs (lncRNAs) in mammals can bind to DNA sequences and recruit histone- and DNA-modifying enzymes to binding sites to epigenetically regulate target genes. However, most lncRNAs' binding motifs and target sites are unknown. The large numbers of lncRNAs and target sites in the whole genome make it infeasible to examine lncRNA binding to DNA purely experimentally. Here, we report a protocol for lncRNA/DNA-binding analysis that is built upon a database containing the GENCODE-annotated human and mouse lncRNAs, the orthologs of these lncRNAs in 17 mammals, and the genome sequences of the 17 mammals. Cross-species and genome-wide lncRNA/DNA-binding analysis begins with and is driven by database search. The predicted DNA-binding motifs and binding sites answer the general question of which lncRNAs may epigenetically regulate which genes, and can be used to identify potential sites for genome and epigenome editing. To use the protocol, preliminary knowledge of the base-pairing rules that guide the binding of noncoding RNAs to DNA to form triplexes, as well as the skills required to use the UCSC Genome Browser, are needed. A genome-wide prediction takes from 2 to 10 d, and the results are sent to users automatically by e-mail. The platform is updated continuously, making it possible to study more lncRNAs and larger genomic regions in less computational time.
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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.