| HGNC Family | Non-coding RNAs |
| Name | KCNQ1 opposite strand/antisense transcript 1 (non-protein coding) |
| Description | Human chromosomal region 11p15.5 contains two clusters of epigenetically-regulated genes that are expressed from only one chromosome in a parent-of-origin manner. Each cluster, or imprinted domain, is regulated by a functionally independent imprinting control region (ICR). The human CDKN1C/KCNQ1OT1 domain is regulated by an ICR located in an intron of KCNQ1, and contains at least eight genes that are expressed exclusively or preferentially from the maternally-inherited allele. The DNA of the ICR is specifically methylated on the maternally-inherited chromosome, and unmethylated on the paternally-inherited chromosome. The ICR contains the promoter of the KCNQ1OT1 gene that is exclusively expressed from the paternal allele. The KCNQ1OT1 transcript is the antisense to the KCNQ1 gene and is a unspliced long non-coding RNA. It interacts with chromatin and regulates transcription of multiple target genes through epigenetic modifications. The transcript is abnormally expressed from both chromosomes in most patients with Beckwith-Wiedemann syndrome, and the transcript also plays an important role in colorectal carcinogenesis. [provided by RefSeq, Apr 2012] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n KCNQ1OT1 (also known as LIT1) is an antisense long noncoding RNA transcribed from the imprinting control region (KvDMR1) within the 11p15.5 imprinted domain. It plays a pivotal role in establishing and maintaining allele‐specific gene silencing across this domain. Functional studies have shown that KCNQ1OT1 is essential for the bidirectional repressive activity of the KvDMR1; disruption of its promoter elements or premature termination of its transcription results in loss of silencing of nearby genes, such as KCNQ1 and CDKN1C."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " Furthermore, a highly conserved 5′ domain within KCNQ1OT1 directs transcriptional repression by associating with chromatin and promoting repressive histone modifications (e.g., H3K9 trimethylation) as well as targeting chromatin to distinct nuclear compartments during mid‐S phase, thereby reinforcing its gene‐silencing function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " In addition, KCNQ1OT1 has been shown to mediate long‐range intrachromosomal looping between regulatory elements (such as between KvDMR1 and the KCNQ1 promoter) through recruitment of epigenetic repressors like Polycomb repressive complex 2 via EZH2, a process that is critical for the maintenance of normal imprinting patterns."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Aberrant epigenetic states of KCNQ1OT1—such as loss of imprinting and disrupted methylation at KvDMR1 observed in certain cancers including colorectal cancer—further underscore its role in controlling gene expression profiles that are essential for normal development and tumor suppression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Noopur Thakur, Vijay Kumar Tiwari, Helene Thomassin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.24.18.7855-7862.2004"}], "href": "https://doi.org/10.1128/MCB.24.18.7855-7862.2004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15340049"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15340049"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Faizaan Mohammad, Radha Raman Pandey, Takashi Nagano, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.02263-07"}], "href": "https://doi.org/10.1128/MCB.02263-07"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18299392"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18299392"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "He Zhang, Michael J Zeitz, Hong Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.201304152"}], "href": "https://doi.org/10.1083/jcb.201304152"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24395636"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24395636"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Seiji Nakano, Kazuhiro Murakami, Makiko Meguro, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Sci (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1349-7006.2006.00305.x"}], "href": "https://doi.org/10.1111/j.1349-7006.2006.00305.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16965397"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16965397"}]}]}]}
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| Synonyms | LIT1, NCRNA00012, KCNQ10T1, KVLQT1-AS, KNCQ1, KVDMR1, KCNQ1-AS2 |
| NCBI Gene ID | 10984 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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KCNQ1OT1 has 2,738 functional associations with biological entities spanning 7 categories (molecular profile, organism, disease, phenotype or trait, functional term, phrase or reference, chemical, cell line, cell type or tissue, gene, protein or microRNA) extracted from 39 datasets.
Click the + buttons to view associations for KCNQ1OT1 from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles | tissues with high or low expression of KCNQ1OT1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset. | |
| Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles | tissues with high or low expression of KCNQ1OT1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset. | |
| BioGPS Mouse Cell Type and Tissue Gene Expression Profiles | cell types and tissues with high or low expression of KCNQ1OT1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset. | |
| CCLE Cell Line Gene CNV Profiles | cell lines with high or low copy number of KCNQ1OT1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset. | |
| CCLE Cell Line Gene Expression Profiles | cell lines with high or low expression of KCNQ1OT1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset. | |
| CellMarker Gene-Cell Type Associations | cell types associated with KCNQ1OT1 gene from the CellMarker Gene-Cell Type Associations dataset. | |
| ChEA Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of KCNQ1OT1 gene from the CHEA Transcription Factor Binding Site Profiles dataset. | |
| ChEA Transcription Factor Targets | transcription factors binding the promoter of KCNQ1OT1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset. | |
| CTD Gene-Disease Associations | diseases associated with KCNQ1OT1 gene/protein from the curated CTD Gene-Disease Associations dataset. | |
| ENCODE Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at KCNQ1OT1 gene from the ENCODE Histone Modification Site Profiles dataset. | |
| ENCODE Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of KCNQ1OT1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset. | |
| ENCODE Transcription Factor Targets | transcription factors binding the promoter of KCNQ1OT1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset. | |
| ESCAPE Omics Signatures of Genes and Proteins for Stem Cells | PubMedIDs of publications reporting gene signatures containing KCNQ1OT1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset. | |
| GAD Gene-Disease Associations | diseases associated with KCNQ1OT1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset. | |
| GAD High Level Gene-Disease Associations | diseases associated with KCNQ1OT1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset. | |
| GeneRIF Biological Term Annotations | biological terms co-occuring with KCNQ1OT1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset. | |
| GeneSigDB Published Gene Signatures | PubMedIDs of publications reporting gene signatures containing KCNQ1OT1 from the GeneSigDB Published Gene Signatures dataset. | |
| GEO Signatures of Differentially Expressed Genes for Diseases | disease perturbations changing expression of KCNQ1OT1 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset. | |
| GEO Signatures of Differentially Expressed Genes for Gene Perturbations | gene perturbations changing expression of KCNQ1OT1 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Kinase Perturbations | kinase perturbations changing expression of KCNQ1OT1 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Small Molecules | small molecule perturbations changing expression of KCNQ1OT1 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset. | |
| GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations | transcription factor perturbations changing expression of KCNQ1OT1 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Viral Infections | virus perturbations changing expression of KCNQ1OT1 gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset. | |
| GTEx Tissue Gene Expression Profiles | tissues with high or low expression of KCNQ1OT1 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset. | |
| GTEx Tissue Sample Gene Expression Profiles | tissue samples with high or low expression of KCNQ1OT1 gene relative to other tissue samples from the GTEx Tissue Sample Gene Expression Profiles dataset. | |
| GTEx Tissue-Specific Aging Signatures | tissue samples with high or low expression of KCNQ1OT1 gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset. | |
| HPO Gene-Disease Associations | phenotypes associated with KCNQ1OT1 gene by mapping known disease genes to disease phenotypes from the HPO Gene-Disease Associations dataset. | |
| HuGE Navigator Gene-Phenotype Associations | phenotypes associated with KCNQ1OT1 gene by text-mining GWAS publications from the HuGE Navigator Gene-Phenotype Associations dataset. | |
| JASPAR Predicted Transcription Factor Targets | transcription factors regulating expression of KCNQ1OT1 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset. | |
| Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles | cell lines with high or low copy number of KCNQ1OT1 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset. | |
| Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles | cell lines with high or low expression of KCNQ1OT1 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles dataset. | |
| KnockTF Gene Expression Profiles with Transcription Factor Perturbations | transcription factor perturbations changing expression of KCNQ1OT1 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset. | |
| MGI Mouse Phenotype Associations 2023 | phenotypes of transgenic mice caused by KCNQ1OT1 gene mutations from the MGI Mouse Phenotype Associations 2023 dataset. | |
| MPO Gene-Phenotype Associations | phenotypes of transgenic mice caused by KCNQ1OT1 gene mutations from the MPO Gene-Phenotype Associations dataset. | |
| MSigDB Signatures of Differentially Expressed Genes for Cancer Gene Perturbations | gene perturbations changing expression of KCNQ1OT1 gene from the MSigDB Signatures of Differentially Expressed Genes for Cancer Gene Perturbations dataset. | |
| OMIM Gene-Disease Associations | phenotypes associated with KCNQ1OT1 gene from the curated OMIM Gene-Disease Associations dataset. | |
| Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles | cell types and tissues with high or low DNA methylation of KCNQ1OT1 gene relative to other cell types and tissues from the Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles dataset. | |
| Roadmap Epigenomics Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at KCNQ1OT1 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset. | |
| TCGA Signatures of Differentially Expressed Genes for Tumors | tissue samples with high or low expression of KCNQ1OT1 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset. | |
