KCNQ1OT1 is a 91kb paternally-expressed imprinted long non-coding RNA that regulates genomic imprinting at the KCNQ1 locus on chromosome 11p15.5. It silences genes in the KCNQ1 imprinted domain by recruiting Polycomb Repressive Complex 2 (PRC2) and establishing heterochromatin. Loss of imprinting leads to Beckwith-Wiedemann syndrome.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0031507 heterochromatin formation | IEA GO_REF:0000115 | ACCEPT | Summary: This is the core function of KCNQ1OT1 - it mediates heterochromatin formation at the KCNQ1 imprinted locus by recruiting Polycomb Repressive Complex 2 (PRC2) to silence genes in the imprinted domain. This is consistent with its role in genomic imprinting. Supporting Evidence: file:human/KCNQ1OT1/KCNQ1OT1-deep-research-falcon.md At the KCNQ1/KCNQ1OT1 domain, imprinting yields monoallelic expression of a cluster of genes, controlled by a differentially methylated region. |
| GO:0000512 lncRNA-mediated post-transcriptional gene silencing | IDA PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by mi... | MARK AS OVER ANNOTATED | Summary: This annotation is based on KCNQ1OT1 acting as a ceRNA/miRNA sponge in an osteogenic differentiation study using hBMSCs. While the miRNA sponging activity may be real, this represents an over-annotation of KCNQ1OT1 beyond its core genomic imprinting function. Supporting Evidence: PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by miR-320a/Smad5 axis. |
| GO:0045669 positive regulation of osteoblast differentiation | IDA PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by mi... | MARK AS OVER ANNOTATED | Summary: Based on in vitro osteogenic differentiation study. This is not the core function of KCNQ1OT1 which is genomic imprinting at the KCNQ1 locus. This represents a non-physiological over-annotation. Supporting Evidence: PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by miR-320a/Smad5 axis. |
| GO:0140869 miRNA inhibitor activity via base-pairing | IDA PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by mi... | MARK AS OVER ANNOTATED | Summary: Based on KCNQ1OT1 sponging miR-320a in osteogenic differentiation model. This is an over-annotation beyond the core genomic imprinting function. Supporting Evidence: PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by miR-320a/Smad5 axis. |
| GO:2000627 positive regulation of miRNA catabolic process | IDA PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by mi... | MARK AS OVER ANNOTATED | Summary: Based on miRNA sponging activity in osteogenic model. Over-annotation of KCNQ1OT1's core function. Supporting Evidence: PMID:32271402 KCNQ1OT1 regulates osteogenic differentiation of hBMSC by miR-320a/Smad5 axis. |
| GO:0001819 positive regulation of cytokine production | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on osteogenic differentiation study. This is an over-annotation unrelated to KCNQ1OT1's core imprinting function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0140869 miRNA inhibitor activity via base-pairing | IDA PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiot... | MARK AS OVER ANNOTATED | Summary: Based on atrial fibrillation study showing KCNQ1OT1 sponging miR-384b. This is an over-annotation beyond the core genomic imprinting function. Supporting Evidence: PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiotensin II-induced atrial fibrillation by modulating miR-384b/CACNA1C axis. |
| GO:0000512 lncRNA-mediated post-transcriptional gene silencing | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on ceRNA/miRNA sponging in osteogenic model. Over-annotation of core function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0001649 osteoblast differentiation | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on in vitro osteogenic model. Over-annotation unrelated to core genomic imprinting function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0010628 positive regulation of gene expression | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: While KCNQ1OT1 does regulate gene expression through imprinting, this annotation is from an osteogenic study focused on BMP2 regulation via miRNA sponging, not the core imprinting mechanism. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0030513 positive regulation of BMP signaling pathway | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on osteogenic differentiation study. Over-annotation unrelated to core imprinting function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0035198 miRNA binding | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on ceRNA activity in osteogenic model. Over-annotation of core function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0140869 miRNA inhibitor activity via base-pairing | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on miRNA sponging in osteogenic model. Over-annotation beyond core imprinting function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:2000627 positive regulation of miRNA catabolic process | IMP PMID:30703347 LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteoge... | MARK AS OVER ANNOTATED | Summary: Based on ceRNA activity in osteogenic model. Over-annotation of core function. Supporting Evidence: PMID:30703347 2019 Jan 28. LncRNA KCNQ1OT1 promoted BMP2 expression to regulate osteogenic differentiation by sponging miRNA-214. |
| GO:0010628 positive regulation of gene expression | IGI PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiot... | MARK AS OVER ANNOTATED | Summary: Based on atrial fibrillation model. Over-annotation unrelated to core imprinting function. Supporting Evidence: PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiotensin II-induced atrial fibrillation by modulating miR-384b/CACNA1C axis. |
| GO:0035198 miRNA binding | IDA PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiot... | MARK AS OVER ANNOTATED | Summary: Based on ceRNA activity in atrial fibrillation model. Over-annotation of core function. Supporting Evidence: PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiotensin II-induced atrial fibrillation by modulating miR-384b/CACNA1C axis. |
| GO:0005730 nucleolus | IEA GO_REF:0000115 | REMOVE | Summary: While some lncRNAs localize to the nucleolus, KCNQ1OT1's primary localization is to the KCNQ1 imprinted domain on chromosome 11p15.5 where it establishes heterochromatin. Without experimental evidence for nucleolar localization, this annotation should be questioned. |
| GO:2000627 positive regulation of miRNA catabolic process | IGI PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiot... | MARK AS OVER ANNOTATED | Summary: Based on ceRNA activity in disease model. Over-annotation of core function. Supporting Evidence: PMID:30241939 YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiotensin II-induced atrial fibrillation by modulating miR-384b/CACNA1C axis. |
| GO:0003682 chromatin binding | NAS | NEW | Summary: Added to align core_functions with existing annotations. Reason: Core function term not present in existing_annotations. Supporting Evidence: file:human/KCNQ1OT1/KCNQ1OT1-deep-research-falcon.md KCNQ1OT1 is best annotated to cis-regulatory chromatin functions at the imprinted KCNQ1/KCNQ1OT1 domain, with disease-associated miRNA-sponging studies treated cautiously as context-specific evidence. |
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