Loss of RNA expression and allele-specific expression associated with congenital heart disease

Nature Communications

Volumn 7, Issue , 2016, Pages

  McKean, David M ^a,b   Homsy, Jason ^a,b,c   Wakimoto, Hiroko ^a   Patel, Neil ^d   Gorham, Joshua ^a   Depalma, Steven R ^a,b   Ware, James S ^a,e,f   Zaidi, Samir ^g   Ma, Wenji ^h   Patel, Nihir ^d   Lifton, Richard P ^g,i   Chung, Wendy K ^h   Kim, Richard ^j   Shen, Yufeng ^h   Brueckner, Martina ^g   Goldmuntz, Elizabeth ^k   Sharp, Andrew J ^d   Seidman, Christine E ^a,b   Gelb, Bruce D ^d   Seidman, J G ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD UNIVERSITY   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

^d MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^e ROYAL BROMPTON HOSPITAL   (United Kingdom)

^f NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

^g YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h NewYork Presbyterian Hospital   (United States)

ⁱ YALE UNIVERSITY   (United States)

^j UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^k UNIVERSITY OF PENNSYLVANIA   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALLELE; CARDIOVASCULAR DISEASE; DISEASE INCIDENCE; GENE EXPRESSION; MUTATION; PROTEIN; RNA;

ADULT; ALLELE; ARTICLE; CARDIOVASCULAR TISSUE; CONGENITAL HEART DISEASE; CONTROLLED STUDY; FETUS; FGFBP2 GENE; GENE; GENE EXPRESSION; GENE MUTATION; GENETIC IDENTIFICATION; GENETIC PARAMETERS; HUMAN; HUMAN TISSUE; LBH GENE; LOSS OF EXPRESSION; MAJOR CLINICAL STUDY; NULL ALLELE; RBFOX2 GENE; RNA SEQUENCE; SEQUENCE ANALYSIS; SGSM1 GENE; ZBTB16 GENE; ADOLESCENT; AGED; AORTA; CARDIAC MUSCLE; CASE CONTROL STUDY; CHILD; CONGENITAL HEART MALFORMATION; GENETIC ASSOCIATION STUDY; GENETICS; GENOME IMPRINTING; INFANT; METABOLISM; MIDDLE AGED; NEWBORN; PRESCHOOL CHILD; PULMONARY ARTERY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; ALLELES; AORTA; CASE-CONTROL STUDIES; CHILD; CHILD, PRESCHOOL; FETUS; GENE EXPRESSION; GENETIC ASSOCIATION STUDIES; GENOMIC IMPRINTING; HEART DEFECTS, CONGENITAL; HUMANS; INFANT; INFANT, NEWBORN; MIDDLE AGED; MYOCARDIUM; PULMONARY ARTERY; RNA; YOUNG ADULT;

EID: 84989211595     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12824     Document Type: Article

References (39)

1. Gelb, B. D. & Chung, W. K. Complex genetics and the etiology of human congenital heart disease. Cold Spring Harb. Perspect. Med. 4, a013953 (2014).
2. Fahed, A. C, Gelb, B. D, Seidman, J. G. & Seidman, C. E. Genetics of congenital heart disease: the glass half empty. Circ. Res. 112, 707-720 (2013).
3. Glessner, J. T. et al. Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ. Res. 115, 884-896 (2014).
4. Zaidi, S. et al. De novo mutations in histone-modifying genes in congenital heart disease. Nature 498, 220-223 (2013).
5. Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249 (2010).
6. Vissers, L. E. et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat. Genet. 36, 955-957 (2004).
7. Ng, S. B. et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790-793 (2010).
8. Homsy, J. et al. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science 350, 1262-1266 (2015).
9. Lyon, M. F. X chromosomes and dosage compensation. Nature 320, 313. (1986).
10. Peters, J. The role of genomic imprinting in biology and disease: an expanding view. Nat. Rev. Genet. 15, 517-530 (2014).
11. Chotalia, M. et al. Transcription is required for establishment of germline methylation marks at imprinted genes. Genes Dev. 23, 105-117 (2009).
12. Lee, J. T. & Bartolomei, M. S. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152, 1308-1323 (2013).
13. Fu, X. et al. Loss-of-function mutation in the X-linked TBX22 promoter disrupts an ETS-1 binding site and leads to cleft palate. Hum. Genet. 134, 147-158 (2015).
14. Kim, J. K, Kolodziejczyk, A. A, Illicic, T, Teichmann, S. A. & Marioni, J. C. Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat. Commun. 6, 8687. (2015).
15. Consortium, G.T. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648-660 (2015).
16. Deng, Q, Ramskold, D, Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193-196 (2014).
17. Pediatric Cardiac Genomics Consortium et al. The Congenital Heart Disease Genetic Network Study: rationale, design, and early results. Circ. Res. 112, 698-706 (2013).
18. Consortium, G.T. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580-585 (2013).
19. Morison, I. M, Paton, C. J. & Cleverley, S. D. The imprinted gene and parent-of-origin effect database. Nucleic Acids Res. 29, 275-276 (2001).
20. Matsuoka, S. et al. Imprinting of the gene encoding a human cyclin-dependent kinase inhibitor, p57KIP2, on chromosome 11p15. Proc. Natl Acad. Sci. USA 93, 3026-3030 (1996).
21. Kalscheuer, V. M, Mariman, E. C, Schepens, M. T, Rehder, H. & Ropers, H. H. The insulin-like growth factor type-2 receptor gene is imprinted in the mouse but not in humans. Nat. Genet. 5, 74-78 (1993).
22. Muller, B. et al. Evidence that paternal expression of the epsilon-sarcoglycan gene accounts for reduced penetrance in myoclonus-dystonia. Am. J. Hum. Genet. 71, 1303-1311 (2002).
23. MacArthur, D. G. et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828 (2012).
24. Morcos, L. et al. Genome-wide assessment of imprinted expression in human cells. Genome Biol. 12, R25 (2011).
25. Seitz, H. et al. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat. Genet. 34, 261-262 (2003).
26. Baran, Y. et al. The landscape of genomic imprinting across diverse adult human tissues. Genome Res. 25, 927-936 (2015).
27. Blagitko, N. et al. Human GRB10 is imprinted and expressed from the paternal and maternal allele in a highly tissue- and isoform-specific fashion. Hum. Mol. Genet. 9, 1587-1595 (2000).
28. Zhang, J. et al. The FGF-BMP signaling axis regulates outflow tract valve primordium formation by promoting cushion neural crest cell differentiation. Circ. Res. 107, 1209-1219 (2010).
29. Jain, R. et al. Cardiac neural crest orchestrates remodeling and functional maturation of mouse semilunar valves. J. Clin. Invest. 121, 422-430 (2011).
30. Phillips, H. M. et al. Neural crest cells are required for correct positioning of the developing outflow cushions and pattern the arterial valve leaflets. Cardiovasc. Res. 99, 452-460 (2013).
31. Briegel, K. J, Baldwin, H. S, Epstein, J. A. & Joyner, A. L. Congenital heart disease reminiscent of partial trisomy 2p syndrome in mice transgenic for the transcription factor Lbh. Development 132, 3305-3316 (2005).
32. Lindley, L. E. & Briegel, K. J. Generation of mice with a conditional Lbh null allele. Genesis 51, 491-497 (2013).
33. Wang, N. et al. Promyelocytic leukemia zinc finger protein activates GATA4 transcription and mediates cardiac hypertrophic signaling from angiotensin II receptor 2. PLoS ONE 7, e35632 (2012).
34. Laforest, B. & Nemer, M. GATA5 interacts with GATA4 and GATA6 in outflow tract development. Dev. Biol. 358, 368-378 (2011).
35. Bonnard, C. et al. Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1. Nat. Genet. 44, 709-713 (2012).
36. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
37. Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80-92 (2012).
38. Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46, 310-315 (2014).
39. Muehlschlegel, J. D. et al. Using next-generation RNA sequencing to examine ischemic changes induced by cold blood cardioplegia on the human left ventricular myocardium transcriptome. Anesthesiology 122, 537-550 (2015).