Developmental Xist Induction is Mediated by Enhanced Splicing

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2018 Nov 30

PMID 30496473

Citations 3

Authors

Cheryl Stork

Zhelin Li

Lin Lin

Sika Zheng

Affiliations

Soon will be listed here.

Abstract

X-inactive-specific transcript (Xist) is a long noncoding RNA (lncRNA) essential for inactivating one of the two X chromosomes in mammalian females. Random X chromosome inactivation is mediated by Xist RNA expressed from the inactive X chromosome. We found that Xist RNA is unspliced in naïve embryonic stem (ES) cells. Upon differentiation, Xist splicing becomes efficient across all exons independent of transcription, suggesting interdependent or coordinated removal of Xist introns. In female cells with mutated polypyrimidine tract binding protein 1 (Ptbp1), differentiation fails to substantially upregulate mature Xist RNA because of a defect in Xist splicing. We further found both Xist129 and XistCAS RNA are unspliced in Mus musculus 129SvJ/Mus castaneous (CAS) hybrid female ES cells. Upon differentiation, Xist129 exhibits a higher splicing efficiency than XistCAS, likely contributing to preferential inhibition of the X129 chromosome. Single cell analysis shows that the allelic choice of Xist splicing is linked to the inactive X chromosome. We conclude post-transcriptional control of Xist RNA splicing is an essential regulatory step of Xist induction. Our studies shed light on the developmental roles of splicing for nuclear-retained Xist lncRNA and suggest inefficient Xist splicing is an additional fail-safe mechanism to prevent Xist activity in ES cells.

Citing Articles

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Real-time PCR quantification of spliced X-box binding protein 1 (XBP1) using a universal primer method.

Yoon S, Park Y, Choi S, Yang H, Jeong P, Cha J PLoS One. 2019; 14(7):e0219978.

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References

Zheng S . Alternative splicing and nonsense-mediated mRNA decay enforce neural specific gene expression. Int J Dev Neurosci. 2016; 55:102-108. PMC: 5016260. DOI: 10.1016/j.ijdevneu.2016.03.003. View

McHugh C, Chen C, Chow A, Surka C, Tran C, McDonel P . The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015; 521(7551):232-6. PMC: 4516396. DOI: 10.1038/nature14443. View

Kafasla P, Mickleburgh I, Llorian M, Coelho M, Gooding C, Cherny D . Defining the roles and interactions of PTB. Biochem Soc Trans. 2012; 40(4):815-20. DOI: 10.1042/BST20120044. View

Stegle O, Teichmann S, Marioni J . Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. 2015; 16(3):133-45. DOI: 10.1038/nrg3833. View

Moindrot B, Cerase A, Coker H, Masui O, Grijzenhout A, Pintacuda G . A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing. Cell Rep. 2015; 12(4):562-72. PMC: 4534822. DOI: 10.1016/j.celrep.2015.06.053. View

Augui S, Nora E, Heard E . Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet. 2011; 12(6):429-42. DOI: 10.1038/nrg2987. View

Herzel L, Straube K, Neugebauer K . Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res. 2018; 28(7):1008-1019. PMC: 6028129. DOI: 10.1101/gr.232025.117. View

Chen L, Zheng S . BCseq: accurate single cell RNA-seq quantification with bias correction. Nucleic Acids Res. 2018; 46(14):e82. PMC: 6101504. DOI: 10.1093/nar/gky308. View

Heard E, Mongelard F, Arnaud D, Avner P . Xist yeast artificial chromosome transgenes function as X-inactivation centers only in multicopy arrays and not as single copies. Mol Cell Biol. 1999; 19(4):3156-66. PMC: 84109. DOI: 10.1128/MCB.19.4.3156. View

10.

Royce-Tolland M, Andersen A, Koyfman H, Talbot D, Wutz A, Tonks I . The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation. Nat Struct Mol Biol. 2010; 17(8):948-54. PMC: 4336797. DOI: 10.1038/nsmb.1877. View

11.

Brockdorff N, Ashworth A, Kay G, McCabe V, Norris D, Cooper P . The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell. 1992; 71(3):515-26. DOI: 10.1016/0092-8674(92)90519-i. View

12.

Navarro P, Chambers I, Karwacki-Neisius V, Chureau C, Morey C, Rougeulle C . Molecular coupling of Xist regulation and pluripotency. Science. 2008; 321(5896):1693-5. DOI: 10.1126/science.1160952. View

13.

da Rocha S, Heard E . Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. Nat Struct Mol Biol. 2017; 24(3):197-204. DOI: 10.1038/nsmb.3370. View

14.

Keppetipola N, Sharma S, Li Q, Black D . Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol. 2012; 47(4):360-78. PMC: 3422667. DOI: 10.3109/10409238.2012.691456. View

15.

Cattanach B, Isaacson J . Controlling elements in the mouse X chromosome. Genetics. 1967; 57(2):331-46. PMC: 1211730. DOI: 10.1093/genetics/57.2.331. View

16.

Brown C, Willard H . The human X-inactivation centre is not required for maintenance of X-chromosome inactivation. Nature. 1994; 368(6467):154-6. DOI: 10.1038/368154a0. View

17.

Beard C, Li E, Jaenisch R . Loss of methylation activates Xist in somatic but not in embryonic cells. Genes Dev. 1995; 9(19):2325-34. DOI: 10.1101/gad.9.19.2325. View

18.

Mak W, Nesterova T, de Napoles M, Appanah R, Yamanaka S, Otte A . Reactivation of the paternal X chromosome in early mouse embryos. Science. 2004; 303(5658):666-9. DOI: 10.1126/science.1092674. View

19.

Czechanski A, Byers C, Greenstein I, Schrode N, Donahue L, Hadjantonakis A . Derivation and characterization of mouse embryonic stem cells from permissive and nonpermissive strains. Nat Protoc. 2014; 9(3):559-74. PMC: 4112089. DOI: 10.1038/nprot.2014.030. View

20.

Csankovszki G, Panning B, Bates B, Pehrson J, Jaenisch R . Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation. Nat Genet. 1999; 22(4):323-4. DOI: 10.1038/11887. View