Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain

Proceedings of the National Academy of Sciences of the United States of America

Volumn 114, Issue 14, 2017, Pages E2882-E2890

  Keown, Christopher L ^a   Berletch, Joel B ^b   Castanon, Rosa ^c   Nery, Joseph R ^c   Disteche, Christine M ^b   Ecker, Joseph R ^c,d   Mukamel, Eran A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Bcor; DNA methylation; Imprinting; Non CG; X chromosome inactivation

Indexed keywords

DINUCLEOTIDE; SPACER DNA; LONG UNTRANSLATED RNA; XIST NON-CODING RNA;

ALLELE; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; AUTOSOME; CHROMATIN; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; FEMALE; FRONTAL CORTEX; GENETIC REGULATION; GENOME IMPRINTING; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION INITIATION; WHOLE GENOME SEQUENCING; X CHROMOSOME INACTIVATION; ANIMAL; BRAIN; C57BL MOUSE; GENETIC EPIGENESIS; GENETICS; METABOLISM; MUTANT MOUSE STRAIN; PHYSIOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME;

ALLELES; ANIMALS; BRAIN; CHROMATIN; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENOMIC IMPRINTING; MALE; MICE, INBRED C57BL; MICE, MUTANT STRAINS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, LONG NONCODING; X CHROMOSOME; X CHROMOSOME INACTIVATION;

EID: 85016952714     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1611905114     Document Type: Article

References (42)

1. Reik W, Walter J (2001) Genomic imprinting: Parental influence on the genome. Nat Rev Genet 2(1):21-32.
2. McGrath J, Solter D (1984) Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37(1):179-183.
3. Lyon MF (1961) Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 190:372-373.
4. Rovet JF (1993) The psychoeducational characteristics of children with Turner syndrome. J Learn Disabil 26(5):333-341.
5. Buiting K, et al. (1995) Inherited microdeletions in the Angelman and Prader-Willi syndromes define an imprinting centre on human chromosome 15. Nat Genet 9(4):395-400.
6. Xie W, et al. (2012) Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148(4):816-831.
7. Augui S, Nora EP, Heard E (2011) Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 12(6):429-442.
8. Berletch JB, et al. (2015) Escape from X inactivation varies in mouse tissues. PLoS Genet 11(3):e1005079.
9. Carrel L, Willard HF (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434(7031):400-404.
10. Sharp AJ, et al. (2011) DNA methylation profiles of human active and inactive X chromosomes. Genome Res 21(10):1592-1600.
11. Lister R, et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341(6146):1237905.
12. Mo A, et al. (2015) Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron 86(6):1369-1384.
13. Chen L, et al. (2015) MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome. Proc Natl Acad Sci USA 112(17):5509-5514.
14. Gabel HW, et al. (2015) Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature 522(7554):89-93.
15. Hoki Y, et al. (2009) A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse. Development 136(1):139-146.
16. Wang L, et al. (2014) Programming and inheritance of parental DNA methylomes in mammals. Cell 157(4):979-991.
17. Schultz MD, et al. (2015) Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523(7559):212-216.
18. Lee JT, Strauss WM, Dausman JA, Jaenisch R (1996) A 450 kb transgene displays properties of the mammalian X-inactivation center. Cell 86(1):83-94.
19. Nora EP, et al. (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398):381-385.
20. Reinius B, et al. (2012) Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome. BMC Genomics 13(1): 607.
21. Horakova AH, et al. (2012) The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. Genome Biol 13(8):R70.
22. Deng X, et al. (2015) Bipartite structure of the inactive mouse X chromosome. Genome Biol 16:152.
23. Burger L, Gaidatzis D, Schübeler D, Stadler MB (2013) Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res 41(16):e155.
24. Joo JE, et al. (2014) Human active X-specific DNA methylation events showing stability across time and tissues. Eur J Hum Genet 22(12):1376-1381.
25. Wamstad JA, Corcoran CM, Keating AM, Bardwell VJ (2008) Role of the transcriptional corepressor Bcor in embryonic stem cell differentiation and early embryonic development. PLoS One 3(7):e2814.
26. Cotton AM, et al. (2015) Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation. Hum Mol Genet 24(6):1528-1539.
27. Kinde B, Gabel HW, Gilbert CS, Griffith EC, Greenberg ME (2015) Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2. Proc Natl Acad Sci USA 112(22):6800-6806.
28. Hon GC, et al. (2013) Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet 45(10):1198-1206.
29. Lingenfelter PA, et al. (1998) Escape from X inactivation of Smcx is preceded by silencing during mouse development. Nat Genet 18(3):212-213.
30. Nugent BM, et al. (2015) Brain feminization requires active repression of masculinization via DNA methylation. Nat Neurosci 18(5):690-697.
31. McCarthy MM, et al. (2009) The epigenetics of sex differences in the brain. J Neurosci 29(41):12815-12823.
32. Clayton JA, Collins FS (2014) Policy: NIH to balance sex in cell and animal studies. Nature 509(7500):282-283.
33. Yang F, Babak T, Shendure J, Disteche CM (2010) Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res 20(5):614-622.
34. Keane TM, et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477(7364):289-294.
35. Kim D, et al. (2013) TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):R36.
36. Lister R, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315-322.
37. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324(5929):929-930.
38. Yu M, et al. (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149(6):1368-1380.
39. Trapnell C, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511-515.
40. Karolchik D, et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32(Database issue):D493-D496.
41. Williamson CM, Skinner JA, Kelsey G, Peters J (2002) Alternative non-coding splice variants of Nespas, an imprinted gene antisense to Nesp in the Gnas imprinting cluster. Mamm Genome 13(2):74-79.
42. Tian D, Sun S, Lee JT (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143(3):390-403.