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 | MARK AS OVER ANNOTATED | Summary: Nucleolus from an automated non-coding RNA mapping; the Kcnq1ot1 RNA targets its silenced domain to the perinucleolar region (PMID:18299392), which is not localization within the nucleolus. Reason: The mapping has an experimental background: the silencing domain of the Kcnq1ot1 RNA targets its locus to the perinucleolar region during S phase, where the RNA mediates transcriptional silencing (PMID:18299392). Positioning of the silenced domain beside the nucleolus is not the same as the RNA being a component of the nucleolus, and no direct evidence places KCNQ1OT1 within it; its established site of action is the imprinted chromatin domain that it coats. The term over-states a real perinucleolar association and is marked as an over-annotation rather than removed. |
| 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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