- Open Access
The long non-coding RNA Kcnq1ot1 controls maternal p57 expression in muscle cells by promoting H3K27me3 accumulation to an intragenic MyoD-binding region
- Oriella Andresini†1,
- Marianna Nicoletta Rossi†2,
- Francesca Matteini1,
- Stefano Petrai1,
- Tiziana Santini3 and
- Rossella Maione1Email author
© The Author(s) 2019
- Received: 1 September 2018
- Accepted: 7 January 2019
- Published: 16 January 2019
The cell-cycle inhibitor p57kip2 plays a critical role in mammalian development by coordinating cell proliferation and differentiation in many cell types. p57kip2 expression is finely regulated by several epigenetic mechanisms, including paternal imprinting. Kcnq1ot1, a long non-coding RNA (LncRNA), whose gene maps to the p57Kip2 imprinting domain, is expressed exclusively from the paternal allele and participates in the cis-silencing of the neighboring imprinted genes through chromatin-level regulation. In light of our previous evidence of a functional interaction between myogenic factors and imprinting control elements in the regulation of the maternal p57Kip2 allele during muscle differentiation, we examined the possibility that also Kcnq1ot1 could play an imprinting-independent role in the control of p57Kip2 expression in muscle cells.
We found that Kcnq1ot1 depletion by siRNA causes the upregulation of the maternal and functional p57Kip2 allele during differentiation, suggesting a previously undisclosed role for this LncRNA. Consistently, Chromatin Oligo-affinity Precipitation assays showed that Kcnq1ot1 physically interacts not only with the paternal imprinting control region of the locus, as already known, but also with both maternal and paternal alleles of a novel p57Kip2 regulatory region, located intragenically and containing two binding sites for the muscle-specific factor MyoD. Moreover, chromatin immunoprecipitation assays after Kcnq1ot1 depletion demonstrated that the LncRNA is required for the accumulation of H3K27me3, a chromatin modification catalyzed by the histone-methyl-transferase EZH2, at the maternal p57kip2 intragenic region. Finally, upon differentiation, the binding of MyoD to this region and its physical interaction with Kcnq1ot1, analyzed by ChIP and RNA immunoprecipitation assays, correlate with the loss of EZH2 and H3K27me3 from chromatin and with p57Kip2 de-repression.
These findings highlight the existence of an imprinting-independent role of Kcnq1ot1, adding new insights into the biology of a still mysterious LncRNA. Moreover, they expand our knowledge about the molecular mechanisms underlying the tight and fine regulation of p57Kip2 during differentiation and, possibly, its aberrant silencing observed in several pathologic conditions.
- Muscle differentiation
The p57Kip2 gene (also known as Cdkn1c and hereafter termed p57) encodes a member of the Cip/Kip family of the cyclin-dependent-kinase (CDK) inhibitors. p57 is a critical regulator of cell proliferation and differentiation during mammalian development and plays unique functions respect to the other family members . In addition to cell cycle, p57 also influences other cellular activities, such as cell migration, apoptosis and senescence [2, 3]. Consistent with its multiple roles in cellular and developmental processes, the abnormal function of p57 causes several types of growth-related diseases and cancer [4–7].
The regulation of p57 expression is the object of extensive investigation. In fact, most of the human growth disorders related to p57 malfunction result from altered gene expression rather than from gene mutations. Moreover, since p57 is an imprinted gene, its transcriptional regulation represents a paradigmatic example of epigenetic control of gene expression.
p57 maps to the growth-related Cdkn1c/Kcnq1 imprinted domain, which spans about 1 Mb along the distal arm of chromosome 7 in mouse and the p15.5 region of chromosome 11 in human . This domain includes 10 protein-coding genes, including p57, which are expressed from the respective maternally derived alleles, and the non-protein-coding gene Kcnq1ot1 (Kcnq1 opposite transcript 1), which is transcribed antisense to the protein-coding gene Kcnq1 into a regulatory long non-coding RNA (LncRNA) from the paternally derived allele . A number of strategies based on epigenetic mechanisms cooperate to establish and maintain the silencing of the non-expressed p57 allele. An imprinting control region, KvDMR1 (Kv-differentially methylated region 1), located about 150 kb downstream of p57, bears differential epigenetic marks on the two parental alleles and harbors multiple and partially overlapping regulatory elements [10–12]. Among these elements, a CTCF-dependent chromatin insulator and the promoter of Kcnq1ot1, which are both hypomethylated and consequently active on the paternal KvDMR1, have been clearly involved in establishing the cis-silencing of p57 and of the other protein-coding genes of the imprinted domain [10, 13–15].
Consistent with the critical importance of the proper p57 expression dosage, not only the paternal allele is ubiquitously and permanently silenced, but also the maternal allele is tightly and finely regulated during development and differentiation . Our work in muscle cells revealed that KvDMR1, in addition to control the silencing of the imprinted p57 paternal allele, is also involved in preventing the expression of the functional p57 maternal allele until differentiation occurs [17, 18]. In particular, in undifferentiated myoblasts, KvDMR1 participates in a repressive long-range chromatin interaction with p57 promoter, mediated by CTCF. Upon differentiation, the myogenic factor MyoD binds to specific target sequences adjacent to CTCF binding sites within KvDMR1. This interaction, which is prevented by the presence of repressive chromatin marks in myogenic cell types unable to express p57 , causes the disruption of the CTCF-mediated loop and the induction of maternal p57 expression.
Kcnq1ot1 is a macro LncRNA of about 90 kb, unspliced and exclusively localized in the nucleus . Loss of paternal Kcnq1ot1, as a result of either promoter deletion  or premature transcript termination [15, 21], is associated with loss of imprinting. However, the molecular mechanisms by which Kcnq1ot1 contributes to gene silencing are far from being clarified, in large part due to its high complexity, resulting from the enormous size and to the consequent difficulties in every experimental approach to its study. Kcnq1ot1 has been shown to coat specific chromatin regions along the Cdkn1c/Kcnq1 domain [22–24]. The pattern and the extent of Kcnq1ot1-chromatin interactions correlate with the accumulation of repressive histone modifications on the regulatory regions of imprinted genes and with their silencing [25, 26]. This is at least in part explained by the property of Kcnq1ot1 to interact with histone methyltransferases, such as G9a and the Polycomb Repressive Complex 2 (PRC2) components, recruiting them to its target genes to establish their imprinted status [23, 27]. Kcnq1ot1 also interacts with the DNA Methyl Transferase 1 (DNMT1), and this interaction is required for the accumulation of DNA methylation at the promoters of some imprinted genes and for the maintenance of their silencing [28, 29].
The molecular mechanisms by which Kcnq1ot1 associates with non-overlapping target genes, spread over almost 1 Mb, are not clear. It is believed that LncRNAs can localize to specific DNA regions through affinity interactions with local factors, such as chromatin proteins and transcription factors and/or through the establishment of physical contacts between distant genomic regions resulting from chromatin looping [30, 31]. Regarding Kcnq1ot1, it has been shown that the LncRNA itself participates in the establishment of higher order intra-chromosomal interactions . Moreover, it is becoming increasingly apparent that LncRNAs, including Kcnq1ot1, can target specific DNA sequences by forming RNA–DNA triplexes .
Another unresolved question concerns the molecular mechanisms by which Kcnq1ot1, as well as other LncRNAs, associates with and organize the regulatory complexes recruited on its targets. It has been reported that a conserved 890 bp sequence, mapping at the 5’ of Kcnq1ot1 and termed silencing domain, is required for the interaction of the LncRNA with DNMT1 and for its association with chromatin . However, it is still unclear if this sequence mediates a direct or an indirect interaction of Kcnq1ot1 with chromatin and/or with DNMT1 or if it is involved in the formation of a crucial structure of the LncRNA.
Even less is known about the regulation of Kcnq1ot1 activity. Kcnq1ot1 is expressed at relatively high levels in all tissues analyzed , but its pattern of chromatin binding and its ability to interact with histone modifying complexes are different between tissues . This suggests that the target specificity of Kcnq1ot1-mediated silencing can be modulated by additional, and likely complex, regulatory interactions.
The little information available to date on the function of Kcnq1ot1 in p57 regulation concerns, almost exclusively, the imprinting control. In light of our previous evidence that some of the factors involved in the regulation of the paternal allele during imprinting, such as CTCF and KvDMR1, can be also involved in the regulation of the maternal allele during differentiation, we wanted to examine the possibility that Kcnq1ot1 could play an imprinting-independent role in the MyoD-dependent regulation of p57 during differentiation.
In the present work, we show that an additional level of transcriptional regulation of maternal p57 in muscle cells involves the functional interaction of Kcnq1ot1 with a novel and intragenic regulatory region of the p57 gene. This level of regulation implies the Kcnq1ot1-dependent accumulation of the repressive histone modification H3K27me3 in undifferentiated cells and its loss upon differentiation, correlated with the interaction of MyoD with Kcnq1ot1 at the same region.
Kcnq1ot1 depletion causes the upregulation of the p57 maternal allele
Kcnq1ot1 interacts with a p57 intragenic region at both maternal and paternal alleles
The expression of Kcnq1ot1, unlike that of p57 and of the co-imprinted gene Kcnq1, does not decrease but, rather, slightly increases in differentiating C2.7 muscle cells  (Additional file 3). This finding rules out a simple model where the upregulation of p57 would be linked with a differentiation-dependent decline of Kcnq1ot1 expression. Considering that the activities of LncRNAs are not necessarily regulated by their expression levels, but often depend on their differential interaction with chromatin or with protein complexes, we first explored whether Kcnq1ot1 was able to interact with the chromatin at the p57 locus.
These and the above results, taken together, suggested that the Kcnq1ot1-associated intragenic region is a novel regulatory element affecting the functional p57 allele in muscle cells through a mechanism involving a trans-effect of Kcnq1ot1 (see Discussion).
Kcnq1ot1 mediates the accumulation of EZH2 and H3K27me3 at the p57 intragenic region in undifferentiated cells
Since the interaction of Kcnq1ot1 with the p57i occurs both in undifferentiated and differentiated cells (Fig. 3b), we supposed that the LncRNA could function as a molecular scaffold modulating the targeting of repressive histone modifications to the maternal allele during differentiation. As mentioned above, Kcnq1ot1 interacts with several histone and DNA methyltransferases to establish the silencing of the p57 domain during imprinting. In light of several studies showing that p57 is a target of EZH2, the PRC2 catalytic subunit, in different cancer cell types [41–43] and in differentiating Schwann cells , we focused our attention on the tri-methylation of lysine 27 in histone H3 (H3K27me3), the modification catalyzed by this complex.
Of note, the association of both EZH2 and H3K27me3 with the maternal intragenic region but not with p57 promoter, decreases during differentiation (Fig. 5), further reinforcing the idea that it is the p57i, more than p57 promoter, that plays a role in the H3K27me3-mediated regulation of p57 during muscle differentiation. The same pattern, characterized by the association of H3K27me3 with the p57i and its decline in parallel with the induction of p57, occurs in differentiating C2.7 cells (Additional file 7).
These results, taken together, suggest that Kcnq1ot1 participates in the repression of maternal p57 expression in undifferentiated muscle cells by influencing H3K27me3 accumulation on the p57i and that the induction of p57 during differentiation correlates with the loss of this mark at this newly identified regulatory region.
MyoD binds to the maternal p57 intragenic region and interacts with Kcnq1ot1 in differentiated cells
Kcnq1ot1 is a well-recognized player of the machinery that participates in the silencing of paternal p57 during imprinting. The present work suggests that Kcnq1ot1, similarly to CTCF and KvDMR1, exerts a repressive function also on maternal p57, highlighting an additional and unexpected level of p57 regulation in muscle cells. It is important to notice that in this experimental setting Kcnq1ot1 depletion leads to the upregulation of the maternal active allele but not to the re-expression of the paternal imprinted allele. A possible explanation for the maintenance of imprinting after siRNA treatment could be that the transcriptional silencing and the stable repression of the paternal Cdkn1c/Kcnq1 locus is reinforced by the cooperation of more than one silencing mechanism. In fact, the establishment and maintenance of the imprinting involve not only the Kcnq1ot1-mediated recruitment of repressive chromatin modifiers, but also the CTCF-mediated enhancer-blocking activity and the chromatin looping. Moreover, despite most evidence suggests that Kcnq1ot1 exerts the silencing activity through its RNA product [23, 36, 59], some results support a model in which it is the act of Kcnq1ot1 transcription, preserved in knockdown assays, and not the RNA product per se, that plays a role in the imprinting process . Consistent with our finding, it was reported that the depletion of Kcnq1ot1, through short hairpin RNAs, did not cause loss of imprinting in mouse stem cells .
Another interesting question raised by our results is how Kcnq1ot1, which is assumed to be paternally expressed in every tissue and to act in cis, can regulate maternal p57. A maternal Kcnq1ot1 isoform, initiated from an alternative promoter located downstream of the hypermethylated CpG island, and thus escaping silencing, was described in heart tissue . However, this isoform did not affect maternal p57 expression, probably because it is non-functional due to the lack of the silencing domain, located at the 5′ of the transcript. Although it is possible that some maternally expressed isoform exists also in muscle cells, the location of the primers we used for allele-specific analysis, allows us to exclude the presence of maternal Kcnq1ot1 transcripts including the silencing domain, both in undifferentiated and differentiated cells. An additional and attractive hypothesis is that paternal Kcnq1ot1 could interact with and regulate maternal p57 through a mechanism involving allele proximity. In this regard, homologous pairing in somatic cells has emerged as a phenomenon more widespread than previously believed [62, 63]. Remarkably, one of the chromosomal regions that were reported to undergo frequent pairing in embryonic stem cells is just the Cdkn1c/Kcnq1 domain . The significance of allelic interactions in gene regulation, as well as how the homologous regions come together, has not been established yet. However, it is reasonable to expect that the allele proximity creates the opportunity for several types of trans-regulatory interactions, including those involving cis-acting LncRNAs.
Regardless of the in cis or in trans activity, the results obtained by ChOP assays prove that Kcnq1ot1 interacts with chromatin at an intragenic region of p57, not only on the paternal but also on the maternal allele. Importantly, an evident accumulation of EZH2 and H3K27me3 is present at the same region, in particular on the maternal allele. The observation that the levels of EZH2 and H3K27me3 at this region decrease after Kcnq1ot1 depletion supports the conclusion that the LncRNA plays an important role in directing the chromatin modification. These results suggest that a functional interaction between Kcnq1ot1 and PRC2 at the maternal p57 gene, and in particular at the intragenic region, participates in the repression of p57 expression in muscle cells. Histone and DNA modifications are well characterized for their regulatory effects on promoter and enhancer regions. However, also gene bodies seem to be the target of epigenetic modifications, even though their function remains unclear. It is commonly believed that repressive modifications, in particular DNA methylation, at intragenic regulatory elements may serve to prevent the occurrence of transcription initiation from non-canonical promoters . More recently, some evidence is emerging that epigenetic modifications at intragenic elements can affect the arrest or release of transcriptional elongation, in this way regulating total mRNA levels and/or alternative splicing through a co-transcriptional mechanism [65, 66]. Interestingly, it has been reported that the decrease in H3K27me3 at some intragenic regions of the muscle-specific genes Myogenin and Muscle creatine kinase  and of a number transforming growth factor β-responsive genes  are functionally correlated with the progression of RNA polymerase II through their gene bodies and with their increased expression. Previous results from our laboratory, based on Norther blot, RT-PCR and Western blot analysis, would suggest that the upregulation and downregulation of p57 in muscle cells concern a single and canonical isoform of p57 mRNA, thus rendering unlikely that the accumulation of H3K27me3 at the newly identified regulatory region may act by causing the arrest of transcriptional elongation or by promoting an alternative splicing event. More work is required not only to definitively clarify this point but also to determine whether the p57i may nucleate additional epigenetic modifications and/or promote changes of the three-dimensional architecture of the locus, resulting in transcriptional repression.
It is worth mentioning that Kcnq1ot1 is over-expressed in different cancer types, such as colorectal carcinoma , glioma , lung adenocarcinoma  and hepatoma . Moreover, the knockdown of Kcnq1ot1 exerts a tumor-suppressive effect in some of these cancers [37, 38]. How increased Kcnq1ot1 levels contribute to carcinogenesis is still unknown but it is plausible that the oncogenic function of the LncRNA is mediated, at least in part, by the repression of the maternal p57 allele, frequently silenced in cancer cells. It is important to point up that, in colorectal cancer cell lines, Kcnq1ot1 is monoallelically over-expressed , thus indicating that the observed effects do not result from loss of imprinting, but instead, may involve a functional interaction between Kcnq1ot1 and p57 similar to the one that we have highlighted in muscle cells.
In summary, this work not only highlights an additional mechanism involved in fine tuning the expression of p57 during muscle differentiation and, possibly in other physiological and pathological processes, but also discloses an imprinting-independent function of Kcnq1ot1, aimed at regulating the maternal, non-imprinted p57 allele. Moreover, it reveals that Kcnq1ot1 functionally interacts with a tissue-specific member of the bHLH family of transcription factors, adding new insight into the regulatory potential of such a mysterious LncRNA.
A more detailed knowledge of the complex roles of Kcnq1ot1 and of chromatin modifications at the multiple p57 regulatory regions not only will further clarify the molecular mechanisms underlying the tight and fine regulation of p57 expression in developing tissues and its silencing in over-growth diseases and cancer, but also will provide a tool for devising strategies aimed at restoring the expression of the CDK inhibitor.
Mouse polymorphic fibroblasts (C57BL/6 × SD7) and C2.7 muscle cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco). To induce MyoD activity and differentiation, cells were shifted to differentiation medium (DMEM supplemented with 0.5% FBS) and collected 24 or 48 h later, as indicated. Production of MyoD-expressing retrovirus and retroviral infections were performed as previously described.
- p57 prom:
- Maternal p57i:
- Paternal p57i:
- β-globin prom:
- β-Actin prom:
- Amylase prom:
- Albumin prom:
- Timm prom:
- p57i :
Gene expression analysis
- Maternal p57:
- Paternal p57:
- Maternal Kcnq1ot1:
- Paternal Kcnq1ot1:
8 × 105 C2.7 muscle cells were transfected using a mixture of four chemically synthesized siRNAs duplexes (Kcnq1ot1 MOUSE SMARTpool Dharmacon) and with a non-targeting pool (Lincode Non-targeting Control siRNAs Dharmacon) as negative control, at a final concentration of 100 nM. Kcnq1ot1 expression levels were analyzed 24 h after transfection in proliferation conditions, while 24 h after the shift to differentiation conditions (DMEM containing 0.5% FCS) samples were collected to analyze p57 and p21 expression levels.
Polymorphic fibroblasts (C57BL/6 × SD7) expressing MyoD were transfected 48 h after infection, with 200 nM siRNAs. Samples were collected 24 h after transfection to check the reduction of Kcnq1ot1 expression and 24 h after the shift to differentiation medium to determine p57 and p21 expression levels.
- Maternal KvDMR1:
- Paternal KvDMR1:
- p57 promoter:
- Maternal p57i:
- Paternal p57i:
- p57i :
- Dppa2 prom:
- Nap1l4 prom:
For statistical analysis, comparisons were performed using parametric paired Student’s t test. Statistical significance is shown as p < 0.05 (*) or p < 0.01 (**) or p < 0.001 (***).
OA and MNR contributed equally to this work, designing and performing most of the experiments with the help of SP and TS; FM was responsible for cell cultures and performed ChIP assays; RM conceived the project, supervised the work and wrote the manuscript with help of OA and MNR. All authors read and approved the final manuscript.
We thank Prof. Paolo Amati for critical reading of the manuscript. We are also grateful to Prof. Marco Tripodi and Dr. Cecilia Battistelli for helpful discussions and sharing reagents.
The authors declare that they have no competing interests.
Availability of data and materials
Data sharing is not applicable to this article as no datasets were generated or analyzed during the study.
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This work was supported by grants from Sapienza University of Rome (RP116154C9BD387B and RM11715C642DFF3B).
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- Besson A, Dowdy SF, Roberts JM. CDK inhibitors: cell cycle regulators and beyond. Dev Cell. 2008;14(2):159–69.View ArticleGoogle Scholar
- Kavanagh E, Vlachos P, Emourgeon V, Rodhe J, Joseph B. p57(KIP2) control of actin cytoskeleton dynamics is responsible for its mitochondrial pro-apoptotic effect. Cell Death Dis. 2012;3:e311.View ArticleGoogle Scholar
- Rossi MN, Antonangeli F. Cellular response upon stress: p57 contribution to the final outcome. Mediat Inflamm. 2015;2015:259325.Google Scholar
- Borriello A, Caldarelli I, Bencivenga D, Criscuolo M, Cucciolla V, Tramontano A, et al. p57(Kip2) and cancer: time for a critical appraisal. Mol Cancer Res MCR. 2011;9(10):1269–84.View ArticleGoogle Scholar
- Kalish JM, Jiang C, Bartolomei MS. Epigenetics and imprinting in human disease. Int J Dev Biol. 2014;58(2–4):291–8.View ArticleGoogle Scholar
- Kavanagh E, Joseph B. The hallmarks of CDKN1C (p57, KIP2) in cancer. Biochem Biophys Acta. 2011;1816(1):50–6.PubMedGoogle Scholar
- Pateras IS, Apostolopoulou K, Niforou K, Kotsinas A, Gorgoulis VG. p57KIP2: “Kip”ing the cell under control. Mol Cancer Res MCR. 2009;7(12):1902–19.View ArticleGoogle Scholar
- Paulsen M, Davies KR, Bowden LM, Villar AJ, Franck O, Fuermann M, et al. Syntenic organization of the mouse distal chromosome 7 imprinting cluster and the Beckwith–Wiedemann syndrome region in chromosome 11p15.5. Hum Mol Genet. 1998;7(7):1149–59.View ArticleGoogle Scholar
- Smilinich NJ, Day CD, Fitzpatrick GV, Caldwell GM, Lossie AC, Cooper PR, et al. A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith–Wiedemann syndrome. Proc Natl Acad Sci USA. 1999;96(14):8064–9.View ArticleGoogle Scholar
- Fitzpatrick GV, Pugacheva EM, Shin JY, Abdullaev Z, Yang Y, Khatod K, et al. Allele-specific binding of CTCF to the multipartite imprinting control region KvDMR1. Mol Cell Biol. 2007;27(7):2636–47.View ArticleGoogle Scholar
- Fitzpatrick GV, Soloway PD, Higgins MJ. Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet. 2002;32(3):426–31.View ArticleGoogle Scholar
- Horike S, Mitsuya K, Meguro M, Kotobuki N, Kashiwagi A, Notsu T, et al. Targeted disruption of the human LIT1 locus defines a putative imprinting control element playing an essential role in Beckwith–Wiedemann syndrome. Hum Mol Genet. 2000;9(14):2075–83.View ArticleGoogle Scholar
- Du M, Beatty LG, Zhou W, Lew J, Schoenherr C, Weksberg R, et al. Insulator and silencer sequences in the imprinted region of human chromosome 11p15.5. Hum Mol Genet. 2003;12(15):1927–39.View ArticleGoogle Scholar
- Du M, Zhou W, Beatty LG, Weksberg R, Sadowski PD. The KCNQ1OT1 promoter, a key regulator of genomic imprinting in human chromosome 11p15.5. Genomics. 2004;84(2):288–300.View ArticleGoogle Scholar
- Shin JY, Fitzpatrick GV, Higgins MJ. Two distinct mechanisms of silencing by the KvDMR1 imprinting control region. EMBO J. 2008;27(1):168–78.View ArticleGoogle Scholar
- Rossi MN, Andresini O, Matteini F, Maione R. Transcriptional regulation of p57kip2 expression during development, differentiation and disease. Front Biosci. 2018;23:83–108.View ArticleGoogle Scholar
- Battistelli C, Busanello A, Maione R. Functional interplay between MyoD and CTCF in regulating long-range chromatin interactions during differentiation. J Cell Sci. 2014;127(Pt 17):3757–67.View ArticleGoogle Scholar
- Busanello A, Battistelli C, Carbone M, Mostocotto C, Maione R. MyoD regulates p57kip2 expression by interacting with a distant cis-element and modifying a higher order chromatin structure. Nucl Acids Res. 2012;40(17):8266–75.View ArticleGoogle Scholar
- Andresini O, Ciotti A, Rossi MN, Battistelli C, Carbone M, Maione R. A cross-talk between DNA methylation and H3 lysine 9 dimethylation at the KvDMR1 region controls the induction of Cdkn1c in muscle cells. Epigenetics. 2016;11(11):791–803.View ArticleGoogle Scholar
- Kanduri C. Kcnq1ot1: a chromatin regulatory RNA. Semin Cell Dev Biol. 2011;22(4):343–50.View ArticleGoogle Scholar
- Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS, Tilghman SM. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 2006;20(10):1268–82.View ArticleGoogle Scholar
- Murakami K, Oshimura M, Kugoh H. Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet. 2007;52(11):926–33.View ArticleGoogle Scholar
- Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell. 2008;32(2):232–46.View ArticleGoogle Scholar
- Redrup L, Branco MR, Perdeaux ER, Krueger C, Lewis A, Santos F, et al. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development. 2009;136(4):525–30.View ArticleGoogle Scholar
- Lewis A, Mitsuya K, Umlauf D, Smith P, Dean W, Walter J, et al. Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet. 2004;36(12):1291–5.View ArticleGoogle Scholar
- Umlauf D, Goto Y, Cao R, Cerqueira F, Wagschal A, Zhang Y, et al. Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet. 2004;36(12):1296–300.View ArticleGoogle Scholar
- Terranova R, Yokobayashi S, Stadler MB, Otte AP, van Lohuizen M, Orkin SH, et al. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell. 2008;15(5):668–79.View ArticleGoogle Scholar
- Mohammad F, Mondal T, Guseva N, Pandey GK, Kanduri C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development. 2010;137(15):2493–9.View ArticleGoogle Scholar
- Mohammad F, Pandey GK, Mondal T, Enroth S, Redrup L, Gyllensten U, et al. Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development. 2012;139(15):2792–803.View ArticleGoogle Scholar
- Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol. 2016;17(12):756–70.View ArticleGoogle Scholar
- Kung JT, Colognori D, Lee JT. Long noncoding RNAs: past, present, and future. Genetics. 2013;193(3):651–69.View ArticleGoogle Scholar
- Zhang H, Zeitz MJ, Wang H, Niu B, Ge S, Li W, et al. Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus. J Cell Biol. 2014;204(1):61–75.View ArticleGoogle Scholar
- He S, Zhang H, Liu H, Zhu H. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. Bioinformatics. 2015;31(2):178–86.View ArticleGoogle Scholar
- Figliola R, Busanello A, Vaccarello G, Maione R. Regulation of p57(KIP2) during muscle differentiation: role of Egr1, Sp1 and DNA hypomethylation. J Mol Biol. 2008;380(2):265–77.View ArticleGoogle Scholar
- Robb GB, Brown KM, Khurana J, Rana TM. Specific and potent RNAi in the nucleus of human cells. Nat Struct Mol Biol. 2005;12(2):133–7.View ArticleGoogle Scholar
- Golding MC, Magri LS, Zhang L, Lalone SA, Higgins MJ, Mann MR. Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells. Development. 2011;138(17):3667–78.View ArticleGoogle Scholar
- Gong W, Zheng J, Liu X, Liu Y, Guo J, Gao Y, et al. Knockdown of long non-coding RNA KCNQ1OT1 restrained glioma cells’ malignancy by activating miR-370/CCNE2 axis. Front Cell Neurosci. 2017;11:84.View ArticleGoogle Scholar
- Ren K, Xu R, Huang J, Zhao J, Shi W. Knockdown of long non-coding RNA KCNQ1OT1 depressed chemoresistance to paclitaxel in lung adenocarcinoma. Cancer Chemother Pharmacol. 2017;80(2):243–50.View ArticleGoogle Scholar
- Figliola R, Maione R. MyoD induces the expression of p57Kip2 in cells lacking p21Cip1/Waf1: overlapping and distinct functions of the two cdk inhibitors. J Cell Physiol. 2004;200(3):468–75.View ArticleGoogle Scholar
- Lee MP, Hu RJ, Johnson LA, Feinberg AP. Human KVLQT1 gene shows tissue-specific imprinting and encompasses Beckwith–Wiedemann syndrome chromosomal rearrangements. Nat Genet. 1997;15(2):181–5.View ArticleGoogle Scholar
- Guo J, Cai J, Yu L, Tang H, Chen C, Wang Z. EZH2 regulates expression of p57 and contributes to progression of ovarian cancer in vitro and in vivo. Cancer Sci. 2011;102(3):530–9.View ArticleGoogle Scholar
- Sun CC, Li SJ, Li G, Hua RX, Zhou XH, Li DJ. Long intergenic noncoding RNA 00511 acts as an oncogene in non-small-cell lung cancer by binding to EZH2 and suppressing p57. Mol Ther Nucl Acids. 2016;5(11):e385.View ArticleGoogle Scholar
- Yang X, Karuturi RK, Sun F, Aau M, Yu K, Shao R, et al. CDKN1C (p57) is a direct target of EZH2 and suppressed by multiple epigenetic mechanisms in breast cancer cells. PLoS ONE. 2009;4(4):e5011.View ArticleGoogle Scholar
- Heinen A, Tzekova N, Graffmann N, Torres KJ, Uhrberg M, Hartung HP, et al. Histone methyltransferase enhancer of zeste homolog 2 regulates Schwann cell differentiation. Glia. 2012;60(11):1696–708.View ArticleGoogle Scholar
- Bhogal B, Arnaudo A, Dymkowski A, Best A, Davis TL. Methylation at mouse Cdkn1c is acquired during postimplantation development and functions to maintain imprinted expression. Genomics. 2004;84(6):961–70.View ArticleGoogle Scholar
- Fan T, Hagan JP, Kozlov SV, Stewart CL, Muegge K. Lsh controls silencing of the imprinted Cdkn1c gene. Development. 2005;132(4):635–44.View ArticleGoogle Scholar
- Wood MD, Hiura H, Tunster SJ, Arima T, Shin JY, Higgins MJ, et al. Autonomous silencing of the imprinted Cdkn1c gene in stem cells. Epigenetics. 2010;5(3):214–21.View ArticleGoogle Scholar
- Lee SM, Lee J, Noh KM, Choi WY, Jeon S, Oh GT, et al. Intragenic CpG islands play important roles in bivalent chromatin assembly of developmental genes. Proc Natl Acad Sci USA. 2017;114(10):E1885–94.View ArticleGoogle Scholar
- Caretti G, Di Padova M, Micales B, Lyons GE, Sartorelli V. The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation. Genes Dev. 2004;18(21):2627–38.View ArticleGoogle Scholar
- Puri PL, Sartorelli V. Regulation of muscle regulatory factors by DNA-binding, interacting proteins, and post-transcriptional modifications. J Cell Physiol. 2000;185(2):155–73.View ArticleGoogle Scholar
- Vaccarello G, Figliola R, Cramerotti S, Novelli F, Maione R. p57Kip2 is induced by MyoD through a p73-dependent pathway. J Mol Biol. 2006;356(3):578–88.View ArticleGoogle Scholar
- Wei Q, Paterson BM. Regulation of MyoD function in the dividing myoblast. FEBS Lett. 2001;490(3):171–8.View ArticleGoogle Scholar
- Faralli H, Dilworth FJ. Turning on myogenin in muscle: a paradigm for understanding mechanisms of tissue-specific gene expression. Comp Funct Genom. 2012;2012:836374.View ArticleGoogle Scholar
- Juan AH, Kumar RM, Marx JG, Young RA, Sartorelli V. Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells. Mol Cell. 2009;36(1):61–74.View ArticleGoogle Scholar
- Caretti G, Schiltz RL, Dilworth FJ, Di Padova M, Zhao P, Ogryzko V, et al. The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell. 2006;11(4):547–60.View ArticleGoogle Scholar
- Yu X, Zhang Y, Li T, Ma Z, Jia H, Chen Q, et al. Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD. Nat Commun. 2017;8:14016.View ArticleGoogle Scholar
- Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010;329(5992):689–93.View ArticleGoogle Scholar
- Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012;81:145–66.View ArticleGoogle Scholar
- Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, et al. Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol. 2008;28(11):3713–28.View ArticleGoogle Scholar
- Kornienko AE, Guenzl PM, Barlow DP, Pauler FM. Gene regulation by the act of long non-coding RNA transcription. BMC Biol. 2013;11:59.View ArticleGoogle Scholar
- Korostowski L, Sedlak N, Engel N. The Kcnq1ot1 long non-coding RNA affects chromatin conformation and expression of Kcnq1, but does not regulate its imprinting in the developing heart. PLoS Genet. 2012;8(9):e1002956.View ArticleGoogle Scholar
- Joyce EF, Erceg J, Wu CT. Pairing and anti-pairing: a balancing act in the diploid genome. Curr Opin Genet Dev. 2016;37:119–28.View ArticleGoogle Scholar
- Krueger C, King MR, Krueger F, Branco MR, Osborne CS, Niakan KK, et al. Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status. PLoS ONE. 2012;7(7):e38983.View ArticleGoogle Scholar
- Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature. 2017;543(7643):72–7.View ArticleGoogle Scholar
- Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol. 2004;11(11):1068–75.View ArticleGoogle Scholar
- Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem. 2015;84:165–98.View ArticleGoogle Scholar
- Seenundun S, Rampalli S, Liu QC, Aziz A, Palii C, Hong S, et al. UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis. EMBO J. 2010;29(8):1401–11.View ArticleGoogle Scholar
- Estaras C, Fueyo R, Akizu N, Beltran S, Martinez-Balbas MA. RNA polymerase II progression through H3K27me3-enriched gene bodies requires JMJD3 histone demethylase. Mol Biol Cell. 2013;24(3):351–60.View ArticleGoogle Scholar
- Sartorelli V, Puri PL. Shaping gene expression by landscaping chromatin architecture: lessons from a master. Mol Cell. 2018;71:375–88.View ArticleGoogle Scholar
- Ballarino M, Morlando M, Fatica A, Bozzoni I. Non-coding RNAs in muscle differentiation and musculoskeletal disease. J Clin Investig. 2016;126(6):2021–30.View ArticleGoogle Scholar
- Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014;15(1):7–21.View ArticleGoogle Scholar
- Neguembor MV, Jothi M, Gabellini D. Long noncoding RNAs, emerging players in muscle differentiation and disease. Skelet Muscle. 2014;4(1):8.View ArticleGoogle Scholar
- Sunamura N, Ohira T, Kataoka M, Inaoka D, Tanabe H, Nakayama Y, et al. Regulation of functional KCNQ1OT1 lncRNA by beta-catenin. Sci Rep. 2016;6:20690.View ArticleGoogle Scholar
- Wan J, Huang M, Zhao H, Wang C, Zhao X, Jiang X, et al. A novel tetranucleotide repeat polymorphism within KCNQ1OT1 confers risk for hepatocellular carcinoma. DNA Cell Biol. 2013;32(11):628–34.View ArticleGoogle Scholar
- Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell. 2008;29(4):499–509.View ArticleGoogle Scholar