The Long Non-Coding RNA Affects Chromatin Conformation and Expression of , but Does Not Regulate Its Imprinting in the Developing Heart

English version České info

Although many of the questions raised by the discovery of imprinting have been answered, we have not yet accounted for tissue -⁠ or stage-specific imprinting. The Kcnq1 imprinted domain exhibits complex tissue-specific expression patterns co-existing with a domain-wide cis-acting control element. Transcription of the paternally expressed antisense non-coding RNA Kcnq1ot1 silences some neighboring genes in the embryo, while others are unaffected. Kcnq1 is imprinted in early cardiac development but becomes biallelic after midgestation. To explore this phenomenon and the role of Kcnq1ot1, we used allele-specific assays and chromosome conformational studies in wild-type mice and mice with a premature termination mutation for Kcnq1ot1. We show that Kcnq1 imprinting in early heart is established and maintained independently of Kcnq1ot1 expression, thus excluding a role for Kcnq1ot1 in repressing Kcnq1, even while silencing other genes in the domain. The exact timing of the mono -⁠ to biallelic transition is strain-dependent, with the CAST/EiJ allele becoming activated earlier and acquiring higher levels than the C57BL/6J allele. Unexpectedly, Kcnq1ot1 itself also switches to biallelic expression specifically in the heart, suggesting that tissue-specific loss of imprinting may be common during embryogenesis. The maternal Kcnq1ot1 transcript is shorter than the paternal ncRNA, and its activation depends on an alternative transcriptional start site that bypasses the maternally methylated promoter. Production of Kcnq1ot1 on the maternal chromosome does not silence Cdkn1c. We find that in later developmental stages, however, Kcnq1ot1 has a role in modulating Kcnq1 levels, since its absence leads to overexpression of Kcnq1, an event accompanied by an aberrant three-dimensional structure of the chromatin. Thus, our studies reveal regulatory mechanisms within the Kcnq1 imprinted domain that operate exclusively in the heart on Kcnq1, a gene crucial for heart development and function. We also uncover a novel mechanism by which an antisense non-coding RNA affects transcription through regulating chromatin flexibility and access to enhancers.

Vyšlo v časopise: The Long Non-Coding RNA Affects Chromatin Conformation and Expression of , but Does Not Regulate Its Imprinting in the Developing Heart. PLoS Genet 8(9): e32767. doi:10.1371/journal.pgen.1002956
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002956

Souhrn

Zdroje

1. LeeJT (2009) Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev 23 : 1831–1842.

2. SleutelsF, ZwartR, BarlowDP (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415 : 810–813.

3. SmilinichNJ, DayCD, FitzpatrickGV, CaldwellGM, LossieAC, et al. (1999) 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 U S A 96 : 8064–8069.

4. BorsoniG, TonlorenziR, SimmlerMC, DandoloL, ArnaudD, et al. (1991) Characterization of a murine gene expressed from the inactive X chromosome. Nature 351 : 325–328.

5. LeeJT, LuN (1999) Targeted mutagenesis of Tsix leads to nonrandom X inactivation. Cell 99 : 47–57.

6. LeeMP, HuR, JohnsonLA, FeinbergAP (1997) Human KVLQT1 gene shows tissue-specific imprinting and encompasses Beckwith-Wiedemann syndrome chromosomal rearrangements. Nature Genet 15 : 181–185.

7. FitzpatrickGV, SolowayPD, HigginsMJ (2002) Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet 32 : 426–431.

8. Mancini-DinardoD, SteeleSJ, LevorseJM, IngramRS, TilghmanSM (2006) Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev 20 : 1268–1282.

9. LewisA, MitsuyaK, UmlaufD, SmithP, DeanW, et al. (2004) Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet 36 : 1291–1295.

10. UmlaufD, GotoY, CaoR, CerqueiraF, WagschalA, et al. (2004) Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 36 : 1296–1300.

11. PandeyRR, MondalT, MohammadF, EnrothS, RedrupL, et al. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32 : 232–246.

12. TerranovaR, YokobayashiS, StadlerMB, OtteAP, van LohuizenM, et al. (2008) Polycomb Group Proteins Ezh2 and Rnf2 Direct Genomic Contraction and Imprinted Repression in Early Mouse Embryos. Dev Cell 15 : 668–679.

13. GoldingMC, MagriLS, ZhangL, LaloneSA, HigginsMJ, et al. Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells. Development 138 : 3667–3678.

14. ShinJY, FitzpatrickGV, HigginsMJ (2008) Two distinct mechanisms of silencing by the KvDMR1 imprinting control region. Embo J 27 : 168–178.

15. GouldTD, PfeiferK (1998) Imprinting of mouse Kvlqt1 is developmentally regulated. Hum Mol Genet 7 : 483–487.

16. LatosPA, BarlowDP (2009) Regulation of imprinted expression by macro non-coding RNAs. RNA Biol 6 : 100–106.

17. PaulsenM, DaviesKR, BowdenLM, VillarAJ, FranckO, et al. (1998) Syntenic organization of the mouse distal chromosome 7 imprinting cluster and the Beckwith-Wiedemann syndrome region in chromosome 11p15.5. Hum Mol Genet 7 : 1149–1159.

18. KorostowskiL, RavalA, BreuerG, EngelN (2011) Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA. Epigenetics Chromatin 4 : 21–32.

19. BokilNJ, BaisdenJM, RadfordDJ, SummersKM (2010) Molecular genetics of long QT syndrome. Mol Genet Metab 101 : 1–8.

20. MannMR, ChungYG, NolenLD, VeronaRI, LathamKE, et al. (2003) Disruption of imprinted gene methylation and expression in cloned preimplantation stage mouse embryos. Biol Reprod 69 : 902–914.

21. FitzpatrickGV, PugachevaEM, ShinJY, AbdullaevZ, YangY, et al. (2007) Allele-specific binding of CTCF to the multipartite imprinting control region KvDMR1. Mol Cell Biol 27 : 2636–2647.

22. YatsukiH, JohK, HigashimotoK, SoejimaH, AraiY, et al. (2002) Domain regulation of imprinting cluster in Kip2/Lit1 subdomain on mouse chromosome 7F4/F5: large-scale DNA methylation analysis reveals that DMR-Lit1 is a putative imprinting control region. Genome Res 12 : 1860–1870.

23. MohammadF, MondalT, GusevaN, PandeyGK, KanduriC (2010) Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 137 : 2493–2499.

24. WoodfineK, HuddlestonJE, MurrellA (2011) Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue. Epigenetics Chromatin 4 : 1–13.

25. ChotaliaM, SmallwoodSA, RufN, DawsonC, LuciferoD, et al. (2009) Transcription is required for establishment of germline methylation marks at imprinted genes. Genes Dev 23 : 105–117.

26. MondalT, KanduriC (2012) Noncoding RNA scaffolds in pluripotency. Circ Res 110 : 1162–1165.

27. LaurentGS, SavvaYA, KapranovP (2012) Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape. Front Genet 3 : 1–11.

28. WangKC, ChangHY (2011) Molecular mechanisms of long noncoding RNAs. Mol Cell 43 : 904–914.

29. RedrupL, BrancoMR, PerdeauxER, KruegerC, LewisA, et al. (2009) The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 136 : 525–530.

30. PaulerFM, KoernerMV, BarlowDP (2007) Silencing by imprinted noncoding RNAs: is transcription the answer? Trends Genet 23 : 284–292.

31. BoniferC (2000) Developmental regulation of eukaryotic gene loci: which cis-regulatory information is required? Trends Genet 16 : 310–315.

32. EngelN, BartolomeiMS (2003) Mechanisms of insulator function in gene regulation and genomic imprinting. Int Rev Cytol 232 : 89–127.

33. RiveraRM, SteinP, WeaverJR, MagerJ, SchultzRM, et al. (2008) Manipulations of mouse embryos prior to implantation result in aberrant expression of imprinted genes on day 9.5 of development. Hum Mol Genet 17 : 1–14.

34. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2011) Geneious v5.4. http://www.geneious.com