Comparative genomic sequence analysis coupled to chromatin immunoprecipitation: A screening procedure applied to search for regulatory elements at the RET locus

Physiological Genomics

Volumn 23, Issue 3, 2005, Pages 269-274

  Puppo, Francesca ^a,b   Musso, Marco ^a   Pirulli, Doroti ^c   Griseri, Paola ^a   Bachetti, Tiziana ^a,b   Crovella, Sergio ^c   Patrone, Giovanna ^a   Ceccherini, Isabella ^a   Ravazzolo, Roberto ^a,b  

^a G GASLINI INSTITUTE   (Italy)

^b UNIVERSITY OF GENOA   (Italy)

^c INSTITUTE FOR MATERNAL AND CHILD HEALTH IRCCS BURLO GAROFOLO   (Italy)

Author keywords

Comparative sequence analysis; Hirschsprung disease; Histone acetylation; Real time quantitative PCR; Transcriptional regulation

Indexed keywords

HISTONE; PROTEIN RET; PRIMER DNA; RET PROTEIN, HUMAN; RET PROTEIN, MOUSE;

ACETYLATION; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC SCREENING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REPORTER GENE; SEQUENCE ANALYSIS; ANIMAL; GENE EXPRESSION REGULATION; GENETICS; HIRSCHSPRUNG DISEASE; METABOLISM; MOUSE; NEUROBLASTOMA; RAT; THYROID TUMOR; TUMOR CELL LINE;

ACETYLATION; ANIMALS; CELL LINE, TUMOR; DNA PRIMERS; GENE EXPRESSION REGULATION, NEOPLASTIC; HIRSCHSPRUNG DISEASE; HISTONES; HUMANS; MICE; NEUROBLASTOMA; POLYMERASE CHAIN REACTION; PROTO-ONCOGENE PROTEINS C-RET; RATS; THYROID NEOPLASMS; TRANSCRIPTION, GENETIC;

EID: 31744441602     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00036.2005     Document Type: Article

References (26)

1. Andrew SD, Delhanty PJ, Mulligan LM, and Robinson BG. Sp1 and Sp3 transactivate the RET proto-oncogene promoter. Gene 256: 283-291, 2000.
2. Attie-Bitach T, Abitbol M, Gerard M, Delezoide AL, Auge J, Pelet A, Amiel J, Pachnis V, Munnich A, Lyonnet S, and Vekemans M. Expression of the RET proto-oncogene in human embryos. Am J Med Genet 80: 481-486, 1998.
3. Burzynski GM, Nolte IM, Osinga J, Ceccherini I, Twigt B, Maas S, Brooks A, Verheij J, Menacho IP, Buys CH, and Hofstra RM. Localizing a putative mutation as the major contributor to the development of sporadic Hirschsprung disease to the RET genomic sequence between the promoter region and exon 2. Eur J Hum Genet 12: 604-612, 2004.
4. Burzynski GM, Nolte IM, Bronda A, Bos KK, Osinga J, Plaza Menacho I, Twigt B, Maas S, Brooks AS, Verheij JB, Buys CH, and Hofstra RM. Identifying candidate Hirschsprung disease-associated RET variants. Am J Hum Genet 76: 850-858, 2005.
5. Chakravarti A and Lyonnet S. Hirschsprung disease. In: The Metabolic and Molecular Bases of Inherited Disease, edited by Scriver C, Beaudet AL, Sly WS, and Valle D. New York: McGraw-Hill, 2001, p. 6231-6255.
6. Emison ES, McCallion AS, Kashuk CS, Bush RT, Grice E, Lin S, Portnoy ME, Cutler DJ, Green ED, and Chakravarti A. A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk. Nature 434: 857-863, 2005.
7. Ge B, Li O, Wilder P, Rizzino A, and McKeithan TW. NF-κB regulates BCL3 transcription in T lymphocytes through an intronic enhancer. J Immunol 171: 4210-4218, 2003.
8. Griseri P, Bachetti T, Puppo F, Lantieri F, Ravazzolo R, Devoto M, and Ceccherini I. A common haplotype at the 5′ end of the RET proto-oncogene, over-represented in Hirschsprung patients, is associated with reduced gene expression. Hum Mutat 25: 189-195, 2005.
9. Hahn M and Bishop J. Expression pattern of Drosophila ret suggests a common ancestral origin between the metamorphosis precursors in insect endoderm and the vertebrate enteric neurons. Proc Natl Acad Sci USA 98: 1053-1058, 2001.
10. Hardison RC, Oeltjen J, and Miller W. Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res 7: 959-966, 1997.
11. Honda T, Yokota S, Gang FG, Takahashi M, and Sugiura Y. Evidence for the c-ret protooncogene product (c-Ret) expression in the spinal tanycytes of adult rat. J Chem Neuroanat 17: 163-168, 1999.
12. Ichihara M, Murakumo Y, and Takahashi M. RET and neuroendocrine tumors. Cancer Lett 204: 197-211, 2004.
13. Kawakami T, Wakabayashi Y, Aimi Y, Isone T, and Okada Y. Developmental expression of glia cell-line derived neurotrophic factor, neurturin, and their receptor mRNA in the rat urinary bladder. Neurourol Urodyn 22: 83-88, 2003.
14. Lang D, Chen F, Milewski F, Li J, Lu MM, and Epstein J. Pax3 is required for enteric ganglia formation and functions with Sox10 to modulate expression of c-Ret. J Clin Invest 106: 963-971, 2000.
15. Lang D and Epstein J. Sox10 and Pax3 physically interact to mediate activation of a conserved c-RET enhancer. Hum Mol Genet 12: 937-945, 2003.
16. Majumdar A, Vainio S, Kispert A, McMahon J, and McMahon AP. Wnt11 and Ret/Gdnf pathways cooperate in regulating ureteric branching during metanephric kidney development. Development 130: 3175-3185, 2003.
17. Marcos-Gutierrez CV, Wilson SW, Holder N, and Pachnis V. The zebrafish homologue of the ret receptor and its pattern of expression during embryogenesis. Oncogene 14: 879-889, 1997.
18. Miller W. So many genomes, so little time. Nat Biotechnol 18: 148-149, 2000.
19. Munnes M, Patrone G, Schmitz B, Romeo G, and Doerfler W. A 5′-CG-3′-rich region in the promoter of the transcriptionally frequently silenced RET protooncogene lacks methylated cytidine residues. Oncogene 17: 2573-2583, 1998.
20. Natarajan D, Marcos-Gutierrez C, Pachnis V, and deGraaff E. Requirement of signalling by receptor tyrosine kinase RET for the directed migration of enteric nervous system progenitor cells during mammalian embryogenesis. Development 129: 5151-5160, 2002.
21. Patrone G, Puliti A, Bocciardi R, Ravazzolo R, and Romeo G. Sequence and characterisation of the RET proto-oncogene 5′ flanking region: analysis of retinoic acid responsiveness at the transcriptional level. FEBS Lett 419: 76-82, 1997.
22. Patrone G, Puppo F, Scaranari M, Cusano R, Griseri P, Romeo G, Ceccherini I, Puliti A, and Ravazzolo R. Cell-line specific transcription rates of the RET gene and functional domains in its minimal promoter. Gene Funct Dis 3: 145-153, 2000.
23. Puppo F, Griseri P, Fanelli M, Schena F, Romeo G, Pelicci PG, Ceccherini I, Ravazzolo R, and Patrone G. Cell-line specific chromatin acetylation at the Sox10-Pax3 enhancer site modulates the RET protooncogene expression. FEBS Lett 523: 123-127, 2002.
24. Sancandi M, Griseri P, Pesce B, Patrone G, Puppo F, Lerone M, Martucciello G, Romeo G, Ravazzolo R, Devoto M, and Ceccherini I. Single nucleotide polymorphic alleles in the 5′ region of the RET protooncogene define a risk haplotype in Hirschsprung's disease. J Med Genet 40: 714-718, 2003.
25. Schuchardt A, D'Agati V, Pachnis V, and Costantini F. Renal agenesis and hypodysplasia in ret-k-mutant mice result from defects in ureteric bud development. Development 122: 1919-1929, 1996.
26. Touchman JW, Dehejia A, Chiba-Falek O, Cabin DE, Schwartz JR, Orrison BM, Polymeropoulos MH, and Nussbaum RL. Human and mouse α-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element. Genome Res 11: 78-86, 2001.