Alternative titles; symbols
HGNC Approved Gene Symbol: KCNQ1OT1
SNOMEDCT: 81780002; ICD10CM: Q87.3;
Cytogenetic location: 11p15.5 Genomic coordinates (GRCh38) : 11:2,608,328-2,699,994 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 11p15.5 | Beckwith-Wiedemann syndrome | 130650 | Autosomal dominant | 3 |
To clarify the genomic organization of the imprinted gene cluster region on chromosome 11p15, which is associated with Beckwith-Wiedemann syndrome (BWS; 130650) and a variety of human cancers, Mitsuya et al. (1999) performed an extensive screen for differentially expressed transcripts in this region, using monochromosomal hybrids with a paternal or maternal human chromosome 11. They identified KCNQ1OT1, which they called LIT1, an imprinted antisense transcript encoded by a 60-kb region spanning exon 10 of the KCNQ1 gene (607542). KCNQ1 is associated with multiple balanced chromosomal rearrangements in BWS and an additional breakpoint in embryonal rhabdoid tumors.
The KCNQ1OT1 gene maps to chromosome 11p15.5, where it overlaps the KCNQ1 gene in the antisense orientation (Mitsuya et al., 1999).
Imprinting of KCNQ1OT1
Mitsuya et al. (1999) found that LIT1 was expressed preferentially from the paternal allele and produced in most human tissues. Methylation analysis revealed that a CpG island within intron 10 of KCNQ1 was specifically methylated on the silent maternal allele.
Horike et al. (2000) generated modified human chromosomes carrying a targeted deletion of the LIT1 CpG island using recombination-proficient chicken DT40 cells. The mutation abolished LIT1 expression on the paternal chromosome, accompanied by activation of the normally silent paternal alleles of multiple imprinted loci at the centromeric domain on chromosome 11p15, including KCNQ1 and p57(KIP2) (CDKN1C; 600856). The deletion had no effect on imprinting of H19 (103280), which is located at the telomeric end of the cluster. The authors hypothesized that 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).
Higashimoto et al. (2003) studied the histone modification status at the differentially methylated CpG region of the LIT1 gene, which they called DMR-LIT1, and its mouse homolog. DMR-LIT1 is an imprinting control region and is demethylated in half of patients with BWS (see MOLECULAR GENETICS). Chromatin immunoprecipitation assays showed that, in both species, the DMR-LIT1 region with the CpG-methylated, maternally derived inactive allele showed histone H3 lys9 methylation, whereas the CpG-unmethylated, paternally active allele was acetylated on histones H3 and H4 and methylated on H3 lys4. These findings suggested that the histone modification status at DMR-LIT1 plays an important role in imprinting control within the subdomain.
Du et al. (2003) confirmed the existence of insulators in the H19 differentially methylated region (DMR) and reported 2 insulators in the IGF2 gene (147470). They also found 2 novel silencer sequences: 1 in KvDMR, a region that is thought to contain the promoter for KCNQ1OT1, and the other in the CDKN1C gene. The authors demonstrated binding of the zinc-finger protein CTCF (604167) in vitro to all the insulator and silencer sequences detected.
Mancini-DiNardo et al. (2003) showed that the imprinting control region (ICR) on mouse distal chromosome 7 contains a promoter for a paternally expressed antisense transcript, Kcnq1ot1. Three paternal-specific nuclease-hypersensitive sites, which are required for full promoter activity, lie immediately upstream from the start site. The expression of Kcnq1ot1 during pre- and postnatal development was compared to that of other imprinted genes in its vicinity, Cdkn1c and Kcnq1; a lack of coordination in their expression did not support an enhancer competition model for the action of the ICR in imprinting control. Using a stable transfection assay, the authors showed that the region contains a position-independent and orientation-independent silencer. The authors proposed that the Kcnq1 ICR may function as a silencer on the paternal chromosome to effect the repression of neighboring genes.
Mancini-DiNardo et al. (2006) found that deletion of the mouse Kcnq1ot1 promoter on the paternal allele or insertion of a premature stop downstream of the promoter region led to derepression of all silent genes tested. However, 5 highly conserved repeats in the 5-prime end of the transcript, a common feature of imprinted gene clusters, were not required for imprinting.
Khoueiry et al. (2008) examined KCNQ1OT1 methylation in the differentially methylated region KvDMR1 in human oocytes at different stages of development: germinal vesicle (GV), metaphase I (MI) or metaphase II (MII). About 60% of alleles were fully methylated in GV oocytes and full imprint was acquired in most MII oocytes. De novo methylation of DNA occurred in vitro during oocyte maturation. Following in vitro culture for 28 hours, GV and MI human oocytes were significantly more methylated when they were obtained from women with natural menstrual cycles compared to oocytes obtained from patients undergoing gonadotropin stimulation for in vitro fertilization protocols. Khoueiry et al. (2008) suggested that hyperstimulation may recruit young follicles that are unable to acquire imprint at KvDMR1 during the course of the maturation process.
Pandey et al. (2008) found that mouse Kcnq1ot1 was transcribed by RNA polymerase II (see 180660) and that it localized to the nucleus. Kcnq1ot1 was moderately stable, and its stability was important for bidirectional silencing of genes in the Kcnq1 domain. Kcnq1ot1 was transcribed in all tissues, but its association with imprinting was tissue specific. In embryonic day-14.5 placenta, Kcnq1ot1 was associated with imprinting of nearby genes, including Cdkn1c, Kcnq1, Slc22a18 (602631), and Phlda2 (602131), and also with more distant genes, including Cd81 (186845), Ascl2 (601886), Tspan32 (603853), and Tssc4 (603852). In contrast, Kcnq1ot1 was associated with imprinting of only nearby genes in day-14.5 embryonic liver. Kcnq1ot1 RNA interacted with chromatin enriched with trimethylated H3K8 and H3K27 and with H3K9- and H3K27-specific histone methyltransferases G9a (EHMT2; 604599) and polycomb repressive complex-2 (see 606245) in placenta more than in fetal liver. In addition, the Kcnq1 domain was more often found in contact with the nucleolar compartment in placenta than in liver. Pandey et al. (2008) concluded that KCNQ1OT1 mediates lineage-specific transcriptional silencing through recruitment of chromatin remodeling complexes, and that it maintains these patterns through subsequent cell divisions by targeting the KCNQ1 domain to the perinucleolar space, which is enriched with factors that maintain repressive chromatin states.
Loss of KCNQ1OT1 Imprinting and Beckwith-Wiedemann Syndrome
Mitsuya et al. (1999) showed that LIT1 is expressed preferentially from the paternal allele, and they identified a CpG island within intron 10 of KCNQ1 that is specifically methylated on the silent maternal allele. Mitsuya et al. (1999) found that 4 of 13 BWS (130650) patients showed complete loss of maternal methylation at the CpG island, suggesting that antisense regulation is involved in the development of human disease. In addition, Mitsuya et al. (1999) found that 8 of 8 Wilms tumors exhibited normal imprinting of LIT1 and 5 of 5 tumors displayed normal differential methylation at the intronic CpG island. This contrasted with 5 of 6 tumors showing loss of imprinting of IGF2 (147470). Mitsuya et al. (1999) concluded that the imprinted gene domain at the KCNQ1 locus is discordantly regulated in cancer from the imprinted domain at the IGF2 locus.
Lee et al. (1999) showed that LIT1 is normally expressed from the paternal allele, from which KCNQ1 transcription is silent, and that in most patients with BWS, LIT1 is abnormally expressed from both the paternal and maternal alleles. Eight of 16 informative BWS patients (50%) showed biallelic expression, i.e., loss of imprinting (LOI) of LIT1. Similarly, 21 of 36 (58%) BWS patients showed loss of maternal allele-specific methylation of a CpG island upstream of LIT1. The authors determined that LOI of LIT1 is the most common genetic alteration in BWS. Lee et al. (1999) proposed that 11p15 harbors 2 imprinted gene domains: a more centromeric domain including KCNQ1 and p57(KIP2) (CDKN1C; 600856), alterations in which are more common in BWS, and a more telomeric domain including IGF2, alterations in which are more common in cancer.
Bliek et al. (2001) studied the methylation status of H19 (103280) and LIT1 in a large series of BWS patients. Different patient groups were identified: group I patients (20%) with uniparental disomy and aberrant methylation of H19 and LIT1; group II patients (7%) with a BWS imprinting center-1 (BWSIC1) defect causing aberrant methylation of H19 only; group III patients (55%) with a BWS imprinting center-2 (BWSIC2) defect causing aberrant methylation of LIT1 only; and group IV patients (18%) with normal methylation patterns for both H19 and LIT1. Of 31 patients with LIT1 demethylation only (group III), none developed a tumor. However, tumors were found in 33% of patients with H19 hypermethylation (group I and II) and in 20% of patients with no detectable genetic defect (group IV). All 4 familial cases of BWS showed reduced methylation of LIT1, suggesting to the authors that in these cases the imprinting switch mechanism may be disturbed.
In a study of 125 BWS cases, Weksberg et al. (2001) confirmed the association of tumors with constitutional defects in the 11p15 telomeric domain. Six of 21 BWS cases with uniparental disomy (UPD) of 11p15 developed tumors and 1 of 3 of the rare BWS subtype with hypermethylation of the H19 gene developed tumors. Five of 32 individuals with BWS and imprinting defects in the centromeric domain developed embryonal tumors. Furthermore, the type of tumors observed in BWS cases with telomeric defects were different from those seen in BWS cases with defects limited to the centromeric domain. Whereas Wilms tumor was the most frequent tumor seen in BWS cases with UPD for 11p15 or H19 hypermethylation, none of the embryonal tumors with imprinting defects at KCNQ1OT1 was a Wilms tumor. The authors suggested that distinct tumor predisposition profiles may result from dysregulation of telomeric versus centromeric domains, and these imprinting defects may activate distinct genetic pathways for embryonal tumorigenesis.
Weksberg et al. (2002) showed that the incidence of female monozygotic twins among patients with BWS is dramatically increased over that of the general population. In skin fibroblasts from 5 monozygotic twin pairs discordant for BWS, each affected twin had an imprinting defect at the KCNQ1OT1 gene, whereas the unaffected twin did not. Five additional monozygotic twin pairs, for whom only blood was available, also displayed an imprinting defect at KCNQ1OT1. The authors hypothesized that discordance for BWS in monozygotic twins may be due to unequal splitting of the inner cell mass during twinning, thereby causing differential maintenance of imprinting at KCNQ1OT1. Alternatively, KCNQ1OT1 may be especially vulnerable to a loss of imprinting event, caused by a lack of maintenance DNA methylation at a critical stage of preimplantation development, and that this loss of imprinting may predispose to twinning as well as to discordance for BWS. The authors recommended continued surveillance of children born following assisted reproductive technologies that may impact the preimplantation embryo.
Higashimoto et al. (2003) studied the histone modification status at the differentially methylated CpG region of the LIT1 gene, which they called DMR-LIT1. In a normal individual and in patients with BWS with normal DMR-LIT1 methylation, histone H3 lys9 methylation was detected on the maternal allele; however, it disappeared completely in patients with the DMR-LIT1 imprinting defect. Higashimoto et al. (2003) suggested that loss of histone H3 lys9 methylation, together with the CpG demethylation on the maternal allele, may lead to the BWS phenotype.
Chiesa et al. (2012) described 2 maternal 11p15.5 microduplications with contrasting phenotypes. In the first case, a 1.2-Mb inverted duplication of chromosome 11p15 derived from the maternal allele resulted in Silver-Russell syndrome (SRS; 180860). The duplication encompassed the entire 11p15.5 imprinted gene cluster, and hypermethylation of CpGs throughout the ICR2 region was observed. These findings were consistent with the maintenance of genomic imprinting, with a double dosage of maternal imprinting and resulting in a lack of KCNQ1OT1 transcription. In the second case, a maternally inherited 160-kb inverted duplication that included only ICR2 and the most 5-prime 20 kb of KCNQ1OT1 resulted in a BWS phenotype in 5 individuals in 2 generations. This duplication was associated with hypomethylation of ICR2 resulting from partial loss of the imprinted methylation of the maternal allele, expression of a truncated KCNQ1OT1 transcript, and silencing of CDKN1C (600856). Chromatin RNA immunopurification studies suggested that the KCNQ1OT1 RNA interacts with chromatin through its most 5-prime 20-kb sequence, providing a mechanism for the silencing activity of this noncoding RNA. The finding of similar duplications of ICR2 resulting in different methylation imprints suggested that the ICR2 sequence is not sufficient for establishing DNA methylation on the maternal chromosome, and that some other property, possibly orientation-dependent, is needed.
Deletion of KCNQ1OT1 and Beckwith-Wiedemann Syndrome
BWS is characterized by prenatal overgrowth, midline abdominal wall defects, macroglossia, and embryonal tumors. The causes are heterogeneous, involving multiple genes on 11p15 and including infrequent instances of mutations of p57(KIP2) (CDKN1C) or loss of imprinting of either of 2 imprinted gene domains on 11p15: LIT1, which is near p57(KIP2), or H19/IGF2. Niemitz et al. (2004) reported a microdeletion involving the entire LIT1 gene, thus providing genetic confirmation of the importance of this gene region in BWS. When inherited maternally, the deletion caused BWS with silencing of p57(KIP2), indicating deletion of an element important for the regulation of p57(KIP2). When inherited paternally, there was no BWS phenotype, suggesting that LIT1 RNA itself is not necessary for normal development in humans.
Superovulation (ovarian stimulation) is an assisted reproductive technology (ART) for human subfertility/infertility treatment, which has been correlated with increased frequencies of imprinting disorders such as Angelman syndrome (105830) and BWS. Market-Velker et al. (2010) examined the effects of superovulation on genomic imprinting in individual mouse blastocyst stage embryos. Superovulation perturbed genomic imprinting of both maternally and paternally expressed genes. Loss of Snrpn (182279), Peg3 (601483), and Kcnq1ot1 and gain of H19 (103280) imprinted methylation were observed. This perturbation was dose-dependent, with aberrant imprinted methylation more frequent at higher hormone dosage. Maternal as well as paternal H19 methylation was perturbed by superovulation. Market-Velker et al. (2010) postulated that superovulation may have dual effects during oogenesis, disrupting acquisition of imprints in growing oocytes, as well as maternal-effect gene products subsequently required for imprint maintenance during preimplantation development.
In 2 related individuals with Beckwith-Wiedemann syndrome (BWS; 130650), Niemitz et al. (2004) described a microdeletion on 11p15 which included the entire LIT1 gene. In 1 case the deletion was maternally inherited; in the other, it was paternally inherited. In the case of maternal inheritance, the deletion caused BWS with silencing of p57(KIP2) (CDKN1C; 600856), indicating that an element important for the regulation of p57(KIP2) expression had been deleted. When inherited paternally, there was no BWS phenotype, suggesting that the LIT1 RNA itself is not necessary for normal development in humans.
Bliek, J., Maas, S. M., Ruijter, J. M., Hennekam, R. C. M., Alders, M., Westerveld, A., Mannens, M. M. A. M. Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS. Hum. Molec. Genet. 10: 467-476, 2001. [PubMed: 11181570] [Full Text: https://doi.org/10.1093/hmg/10.5.467]
Chiesa, N., De Crescenzo, A., Mishra, K., Perone, L., Carella, M., Palumbo, O., Mussa, A., Sparago, A., Cerrato, F., Russo, S., Lapi, E., Cubellis, M. V., Kanduri, C., Cirillo Silengo, M., Riccio, A., Ferrero, G. B. The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases. Hum. Molec. Genet. 21: 10-25, 2012. [PubMed: 21920939] [Full Text: https://doi.org/10.1093/hmg/ddr419]
Du, M., Beatty, L. G., Zhou, W., Lew, J., Schoenherr, C., Weksberg, R., Sadowski, P. D. Insulator and silencer sequences in the imprinted region of human chromosome 11p15.5. Hum. Molec. Genet. 12: 1927-1939, 2003. [PubMed: 12874112] [Full Text: https://doi.org/10.1093/hmg/ddg194]
Higashimoto, K., Urano, T., Sugiura, K., Yatsuki, H., Joh, K., Zhao, W., Iwakawa, M., Ohashi, H., Oshimura, M., Niikawa, N., Mukai, T., Soejima, H. Loss of CpG methylation is strongly correlated with loss of histone H3 lysine 9 methylation at DMR-LIT1 in patients with Beckwith-Wiedemann syndrome. Am. J. Hum. Genet. 73: 948-956, 2003. [PubMed: 12949703] [Full Text: https://doi.org/10.1086/378595]
Horike, S., Mitsuya, K., Meguro, M., Kotobuki, N., Kashiwagi, A., Notsu, T., Schulz, T. C., Shirayoshi, Y., Oshimura, M. Targeted disruption of the human LIT1 locus defines a putative imprinting control element playing an essential role in Beckwith-Wiedemann syndrome. Hum. Molec. Genet. 9: 2075-2083, 2000. [PubMed: 10958646] [Full Text: https://doi.org/10.1093/hmg/9.14.2075]
Khoueiry, R., Ibala-Rhomdane, S., Mery, L., Blachere, T., Guerin, J.-F., Lornage, J., Lefevre, A. Dynamic CpG methylation of the KCNQ1OT1 gene during maturation of human oocytes. J. Med. Genet. 45: 583-588, 2008. Note: Erratum: J. Med. Genet. 45: 832 only, 2008. [PubMed: 18762571] [Full Text: https://doi.org/10.1136/jmg.2008.057943]
Lee, M. P., DeBaun, M. R., Mitsuya, K., Galonek, H. L., Brandenburg, S., Oshimura, M., Feinberg, A. P. Loss of imprinting of a paternally expressed transcript, with antisense orientation to KvLQT1, occurs frequently in Beckwith-Wiedemann syndrome and is independent of insulin-like growth factor II imprinting. Proc. Nat. Acad. Sci. 96: 5203-5208, 1999. [PubMed: 10220444] [Full Text: https://doi.org/10.1073/pnas.96.9.5203]
Mancini-DiNardo, D., Steele, S. J. S., Ingram, R. S., Tilghman, S. M. A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. Hum. Molec. Genet. 12: 283-294, 2003. [PubMed: 12554682] [Full Text: https://doi.org/10.1093/hmg/ddg024]
Mancini-DiNardo, D., Steele, S. J. S., Levorse, J. M., Ingram, R. S., Tilghman, S. M. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 20: 1268-1282, 2006. [PubMed: 16702402] [Full Text: https://doi.org/10.1101/gad.1416906]
Market-Velker, B. A., Zhang, L., Magri, L. S., Bonvissuto, A. C., Mann, M. R. W. Dual effects of superovulation: loss of maternal and paternal imprinted methylation in a dose-dependent manner. Hum. Molec. Genet. 19: 36-51, 2010. [PubMed: 19805400] [Full Text: https://doi.org/10.1093/hmg/ddp465]
Mitsuya, K., Meguro, M., Lee, M. P., Katoh, M., Schulz, T. C., Kugoh, H., Yoshida, M. A., Niikawa, N., Feinberg, A. P., Oshimura, M. LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids. Hum. Molec. Genet. 8: 1209-1217, 1999. Note: Erratum: Hum. Molec. Genet. 8: 1585 only, 1999. [PubMed: 10369866] [Full Text: https://doi.org/10.1093/hmg/8.7.1209]
Niemitz, E. L., DeBaun, M. R., Fallon, J., Murakami, K., Kugoh, H., Oshimura, M., Feinberg, A. P. Microdeletion of LIT1 in familial Beckwith-Wiedemann syndrome. Am. J. Hum. Genet. 75: 844-849, 2004. [PubMed: 15372379] [Full Text: https://doi.org/10.1086/425343]
Pandey, R. R., Mondal, T., Mohammad, F., Enroth, S., Redrup, L., Komorowski, J., Nagano, T., Mancini-DiNardo, D., Kanduri, C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Molec. Cell 32: 232-246, 2008. [PubMed: 18951091] [Full Text: https://doi.org/10.1016/j.molcel.2008.08.022]
Weksberg, R., Nishikawa, J., Caluseriu, O., Fei, Y.-L., Shuman, C., Wei, C., Steele, L., Cameron, J., Smith, A., Ambus, I., Li, M., Ray, P. N., Sadowski, P., Squire, J. Tumor development in the Beckwith-Wiedemann syndrome is associated with a variety of constitutional molecular 11p15 alterations including imprinting defects of KCNQ1OT1. Hum. Molec. Genet. 10: 2989-3000, 2001. [PubMed: 11751681] [Full Text: https://doi.org/10.1093/hmg/10.26.2989]
Weksberg, R., Shuman, C., Caluseriu, O., Smith, A. C., Fei, Y.-L., Nishikawa, J., Stockley, T. L., Best, L., Chitayat, D., Olney, A., Ives, E., Schneider, A., Bestor, T. H., Li, M., Sadowski, P., Squire, J. Discordant KCNQ1OT1 imprinting in sets of monozygotic twins discordant for Beckwith-Wiedemann syndrome. Hum. Molec. Genet. 11: 1317-1325, 2002. [PubMed: 12019213] [Full Text: https://doi.org/10.1093/hmg/11.11.1317]