Promoter, alternative splice forms, and genomic structure of protocadherin 15

Kumar N Alagramam; Nathaniel D Miller; Nithin D Adappa; Darrell R Pitts; John C Heaphy; Huijun Yuan; Richard J Smith

doi:10.1016/j.ygeno.2007.06.007

Back

Promoter, alternative splice forms, and genomic structure of protocadherin 15

Journal article

Open access

Peer reviewed

Promoter, alternative splice forms, and genomic structure of protocadherin 15

Kumar N Alagramam, Nathaniel D Miller, Nithin D Adappa, Darrell R Pitts, John C Heaphy, Huijun Yuan and Richard J Smith

Genomics (San Diego, Calif.), Vol.90(4), pp.482-492

2007

DOI: 10.1016/j.ygeno.2007.06.007

PMCID: PMC2043478

PMID: 17706913

Files and links (1)

url

https://doi.org/10.1016/j.ygeno.2007.06.007View

Published (Version of record) Open Access

Abstract

We originally showed that the protocadherin 15 gene ( Pcdh15) is necessary for hearing and balance functions; mutations in Pcdh15 affect hair cell development in Ames waltzer ( av) mice. Here we extend that study to understand better how Pcdh15 operates in a cell. The original report identified 33 exons in Pcdh15, with exon 1 being noncoding; additional exons of Pcdh15 have since been reported. The 33 exons of Pcdh15 described originally are embedded in 409 kb of mouse genomic sequence, while the corresponding exons of human PCDH15 are spread over 980 kb of genomic DNA; the exons in Pcdh15/PCDH15 range in size from 9 to ∼ 2000 bp. The genomic organization of Pcdh15/PCDH15 bears similarity to that of cadherin 23, but differs significantly from other protocadherin genes, such as Pcdhα, β, or γ. A CpG island is located ∼ 2900 bp upstream of the PCDH15 transcriptional start site. The Pcdh15/PCDH15 promoter lacks TATAA or CAAT sequences within 100 bases upstream of the transcription start site; deletion mapping showed that Pcdh15 harbors suppressor and enhancer elements. Preliminary searches for alternatively spliced transcripts of Pcdh15 identified novel splice variants not reported previously. Results from our study show that both mouse and human protocadherin 15 genes have complex genomic structures and transcription control mechanisms.

Protocadherin 15

Genomic structure

Promoter elements

Alternate splicing

Details

Title: Subtitle: Promoter, alternative splice forms, and genomic structure of protocadherin 15
Creators: Kumar N Alagramam - Department of Otolaryngology–Head and Neck Surgery, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH 44106, USA
Nathaniel D Miller - Department of Biochemistry, Miami University, Miami, OH 44904, USA
Nithin D Adappa - Department of Otolaryngology–Head and Neck Surgery, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH 44106, USA
Darrell R Pitts - Department of Otolaryngology–Head and Neck Surgery, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH 44106, USA
John C Heaphy - Department of Otolaryngology–Head and Neck Surgery, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH 44106, USA
Huijun Yuan - Molecular Otolaryngology Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA 52242, USA
Richard J Smith - Molecular Otolaryngology Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA 52242, USA
Resource Type: Journal article
Publication Details: Genomics (San Diego, Calif.), Vol.90(4), pp.482-492
DOI: 10.1016/j.ygeno.2007.06.007
PMID: 17706913
PMCID: PMC2043478
NLM abbreviation: Genomics
ISSN: 0888-7543
eISSN: 1089-8646
Publisher: Elsevier Inc
Language: English
Date published: 2007
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Molecular Physiology and Biophysics; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Otolaryngology; Internal Medicine
Record Identifier: 9984006401302771

Metrics

15 Record Views

19 Times Cited - Web of Science

See more details