Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development

Neurogenetics

Volumn 17, Issue 1, 2016, Pages 1-9

  Haliburton, Genevieve D E ^a,b   McKinsey, Gabriel L ^c   Pollard, Katherine S ^a,b  

^a GLADSTONE INSTITUTES   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Development; Enhancer; Gene regulation; Transcription factor

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXC1; TRANSCRIPTION FACTOR GMDS; TRANSCRIPTION FACTOR ZIC; UNCLASSIFIED DRUG; FORKHEAD TRANSCRIPTION FACTOR; FOXC1 PROTEIN, HUMAN; GDPMANNOSE 4,6-DEHYDRATASE; HYDROLYASE; ZIC1 PROTEIN, HUMAN;

ANIMAL TISSUE; ARTICLE; BINDING SITE; BRAIN DEVELOPMENT; CONTROLLED STUDY; EMBRYO; ENHANCER REGION; FEMALE; GENE CLUSTER; GENE EXPRESSION; GENE LOCUS; HUMAN; HUMAN TISSUE; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; ANIMAL; BIOLOGY; BRAIN; DEVELOPMENTAL GENE; EMBRYOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MULTIGENE FAMILY; MUTAGENESIS; PHYSIOLOGY; TRANSGENIC MOUSE; VALIDATION STUDY;

ANIMALS; BINDING SITES; BRAIN; COMPUTATIONAL BIOLOGY; ENHANCER ELEMENTS, GENETIC; FORKHEAD TRANSCRIPTION FACTORS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, DEVELOPMENTAL; HUMANS; HYDRO-LYASES; MICE; MICE, TRANSGENIC; MULTIGENE FAMILY; MUTAGENESIS; TRANSCRIPTION FACTORS;

EID: 84941670430     PISSN: 13646745     EISSN: 13646753     Source Type: Journal    
DOI: 10.1007/s10048-015-0458-9     Document Type: Article

References (18)

1. Noonan JP, McCallion AS (2010) Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet 11:1–23. doi:10.1146/annurev-genom-082509-141651
2. Maas SA, Fallon JF (2005) Single base pair change in the long-range Sonic hedgehog limb-specific enhancer is a genetic basis for preaxial polydactyly. Dev Dyn 232(2):345–348. doi:10.1002/dvdy.20254
3. Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Pollard KS, Ahituv N, Capra JA (2014) Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol 10(6):e1003677. doi:10.1371/journal.pcbi.1003677
4. Aldinger KA, Lehmann OJ, Hudgins L, Chizhikov VV, Bassuk AG, Ades LC, Krantz ID, Dobyns WB, Millen KJ (2009) FOXC1 is required for normal cerebellar development and is a major contributor to chromosome 6p25.3 Dandy-Walker malformation. Nat Genet 41(9):1037–1042. doi:10.1038/ng.422
5. Song Y, Willer JR, Scherer PC, Panzer JA, Kugath A, Skordalakes E, Gregg RG, Willer GB, Balice-Gordon RJ (2010) Neural and synaptic defects in slytherin, a zebrafish model for human congenital disorders of glycosylation. PLOS One 5(10):e13743. doi:10.1371/journal.pone.0013743
6. Ohata S, Kinoshita S, Aoki R, Tanaka H, Wada H, Tsuruoka-Kinoshita S, Tsuboi T, Watabe S, Okamoto H (2009) Neuroepithelial cells require fucosylated glycans to guide the migration of vagal motor progenitors in the developing zebrafish hindbrain. Development 136(10):1653–63. doi:10.1242/dev.033290
7. Visel A, Minovitsky S, Dubchak I, Pennacchio LA (2007) VISTA enhancer browser—a database of tissue-specific human enhancers. Nucleic Acids Res 35(Database issue):D88–D92. doi:10.1093/nar/gkl822
8. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28(5):495–501. doi:10.1038/nbt.1630
9. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380. doi:10.1038/nature11082
10. Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27(7):1017–1018. doi:10.1093/bioinformatics/btr064
11. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28(1):316–319
12. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842. doi:10.1093/bioinformatics/btq033
13. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101(16):6062–6067. doi:10.1073/pnas.0400782101
14. BrainSpan (2013) Transcriptome profiling by RNA sequencing and exon microarray. Technical White Paper
15. Rossant J, Tam PPL (2002) Mouse development: patterning, morphogenesis, and organogenesis. Academic, San Diego
16. Blank MC, Grinberg I, Aryee E, Laliberte C, Chizhikov VV, Henkelman RM, Millen KJ (2011) Multiple developmental programs are altered by loss of Zic1 and Zic4 to cause Dandy-Walker malformation cerebellar pathogenesis. Development 138(6):1207–1216. doi:10.1242/dev.054114
17. Panzer, JA, Gibbs SM, Dosch R, Wagner D, Mullins MC, Granato M, Balice-Gordon RJ (2005) Neuromuscular synaptogenesis in wild-type and mutant zebrafish. Develop Biol 285(2):340–57. doi:10.1016/j.ydbio.2005.06.027
18. Grinberg I, Northrup H, Ardinger H, Prasad C, Dobyns WB, Millen KJ (2004) Heterozygous deletion of the linked genes ZIC1 and ZIC4 is involved in Dandy-Walker malformation. Nat Genet 36:153–1055