LncRNA Information
ID EL0628 Name KCNQ1OT1 Aliases KCNQ1-AS2; KCNQ10T1; Kncq1; KvDMR1; KvLQT1-AS; LIT1; NCRNA00012
Species Homo sapiens Chromosome 11 Start site 2608328
End site 2699994 Chain minus Exon NO. 1
Assembly Ensembl Release 89 Class antisense NCBI accession NR_002728
Ensembl ENSG00000269821 Sequence


Disease
Disease Method Sample Expression pattern Dysfunction type Description PMID Source
prostate cancer microarray, RNA-seq, qPCR, Northern bolt, knockdown etc. prostate cancer tissue, cell lines (LNCaP, CWR22Rv1, PC3 etc.) up-regulated N/A Interestingly, nine out of these thirteen known cancer-related lncRNA showed significantly differential expression between tumor and normal prostate samples. Several lncRNA such as NEAT1, DANCR, HOTTIP, PRINS, and EGOT that have established functions in forming nuclear speckles, in development or in autoimmune disease, but were not previously known to be related to cancer, showed differential expression between tumor and normal prostate samples, suggesting their potential function in prostate cancer. 23728290 Lnc2Cancer
Beckwith-Wiedemann syndrome N/A N/A N/A locus KvDMR1 and/or its associated antisense RNA (KvLQT1-AS) represents an additional imprinting control element or center in the human 11p15.5 and mouse distal 7 imprinted domains. 10393948 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A locus The LIT1 CpG island can act as a negative regulator in cis for coordinate imprinting at the centromeric domain, thereby suggesting a role for the LIT1 locus in a BWS pathway leading to functional inactivation of p57(KIP2). 10958646 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A epigenetics The 5'end of the KCNQ1OT1 gene is hypomethylated in the Beckwith-Wiedemann syndrome. 12136243 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A N/A In vitro fertilization may increase the risk of Beckwith-Wiedemann syndrome related to the abnormal imprinting of the KCN1OT gene. 12746837 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A locus In the human and mouse BWS imprinting regions, two major elements for regulation of imprinted gene expression have been identified athe imprinting centers IC1 and IC2.IC2 appears to be the promoter of the paternally expressed probably noncoding transcript. 15590939 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A N/A LIT1 (KCNQ1OT1) may play a role in Beckwith-Wiedemann syndrome. 15888726 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A epigenetics In Beckwith-Wiedemann syndrome (BWS), approximately 50% of patients show loss of DNA methylation accompanied by loss of histone H3 Lys9 dimethylation on maternal KCNQ1OT-DMR, namely an imprinting disruption, leading to diminished expression of CDKN1C. 16575194 LncRNADisease
colorectal cancer N/A N/A N/A expression Recent studies have linked their mis-expression to diverse cancers (ANRIL: prostate cancer, XIST: female cancers, HOTAIR: breast cancer, KCNQ1OT4: colorectal cancer). 23660942 LncRNADisease
Beckwith-Wiedemann syndrome N/A N/A N/A regulation Epigenetic deregulation of lncRNAs genes is associated with disease 23791884 LncRNADisease
kidney cancer N/A N/A N/A regulation Oncogene 24373479 LncRNADisease
acute myocardial infarction N/A N/A N/A N/A Level of KCNQ1OT1 was higher in patients with MI than in healthy volunteers (P<0.01);Patients with ST-segment-elevation MI had lower levels of KCNQ1OT1 (P<0.001)when compared with patients with non-ST-segment-elevation 25035150 LncRNADisease
colorectal cancer overexpression colorectal cancer cells up-regulated N/A β-catenin can promote KCNQ1OT1 transcription through direct binding to the KCNQ1OT1 promoter 26868975
hepatocelluar carcinoma qPCR etc. HCC tissue differential expression mutation A novel tetranucleotide repeat polymorphism within KCNQ1OT1 confers risk for hepatocellular carcinoma. 23984860 LncRNADisease Lnc2Cancer
colorectal cancer qPCR, FISH etc. CRC tissue, cell lines (FBS, DLD-1, HCT-15 etc.) differential expression epigenetics epigenetic disruption 16965397 LncRNADisease Lnc2Cancer
breast cancer RNA CISH etc. breast cancer tissue up-regulated expression HOTAIR, H19 and KCNQ1OT1 had significantly higher expression levels in IBC than NA, and HOTAIR and H19 were both expressed more strongly in IBC than in DCIS tissues. 26323944 Lnc2Cancer
 


Function (not disease relevant)
Methods Sample/condition Expression pattern Dysfunction type Description PMID Source
CHIP, PCR, knockdown, RNA-guided chromatin conformation capture method N/A N/A interaction The 5' region of Kcnq1ot1 RNA orchestrates a long-range intrachromosomal loop between KvDMR1 and the Kcnq1 promoter that is required for maintenance of imprinting.PRC2 (polycomb repressive complex 2), which participates in the allelic repression of Kcnq1, is also recruited by Kcnq1ot1 RNA via EZH2. 24395636
ChIP,PCR,FISH,immuno-FISH human placenta N/A interaction The bidirectional silencing property of Kcnq1ot1 maps to a highly conserved repeat motif within the silencing domain, which directs transcriptional silencing by interaction with chromatin, resulting in histone H3 lysine 9 trimethylation. 18299392
Chromatin RNA Immunoprecipitation and RNA Immunoprecipitation,ImmunoDNA FISH,Chromatin Oligo-Affinity Precipitation placenta and liver N/A interaction our data describe a mechanism whereby Kcnq1ot1 establishes lineage-specific transcriptional silencing patterns through recruitment of chromatin remodeling complexes and maintenance of these patterns through subsequent cell divisions occurs via targeting the associated regions to the perinucleolar compartment. 18951091
 


Interaction
Interaction target Level of interaction Type of interaction Description PMID Source
chromatin RNA-DNA binding The bidirectional silencing property of Kcnq1ot1 maps to a highly conserved repeat motif within the silencing domain, which directs transcriptional silencing by interaction with chromatin, resulting in histone H3 lysine 9 trimethylation 18299392
H3K9- and H3K27-specific histone methyltransferases G9a and the PRC2 complex RNA-Protein binding Kcnq1ot1 interacts with chromatin and with the H3K9- and H3K27-specific histone methyltransferases G9a and the PRC2 complex in a lineage-specific manner. This interaction correlates with the presence of extended regions of chromatin enriched with H3K9me3 and H3K27me3 in the Kcnq1 domain in placenta, whereas fetal liver lacks both chromatin interactions and heterochromatin structures 18951091
KvDMR1 and the Kcnq1 RNA-DNA binding The 5' region of Kcnq1ot1 RNA orchestrates a long-range intrachromosomal loop between KvDMR1 and the Kcnq1 promoter that is required for maintenance of imprinting.PRC2 (polycomb repressive complex 2), which participates in the allelic repression of Kcnq1, is also recruited by Kcnq1ot1 RNA via EZH2. 24395636
SLC22A18, PHLDA2 RNA-DNA regulation Knockdown of β-catenin resulted in significant decrease of KCNQ1OT1 lncRNA-coated territory and an increase in the mRNA expression of the SLC22A18 and PHLDA2 genes that are regulated by KCNQ1OT1. 26868975
β-catenin DNA-Protein binding β-catenin can promote KCNQ1OT1 transcription through direct binding to the KCNQ1OT1 promoter. 26868975