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Characterization of the ovine ribosomal protein SA gene and its pseudogenes

Alice Van den Broeke UGent, Mario Van Poucke UGent, Ane Marcos-Carcavilla, Karine Hugot, Helene Hayes, Maud Bertaud, Alex Van Zeveren UGent and Luc Peelman UGent (2010) BMC GENOMICS. 11(179).
abstract
Background: The ribosomal protein SA (RPSA), previously named 37-kDa laminin receptor precursor/67-kDa laminin receptor (LRP/LR) is a multifunctional protein that plays a role in a number of pathological processes, such as cancer and prion diseases. In all investigated species, RPSA is a member of a multicopy gene family consisting of one full length functional gene and several pseudogenes. Therefore, for studies on RPSA related pathways/pathologies, it is important to characterize the whole family and to address the possible function of the other RPSA family members. The present work aims at deciphering the RPSA family in sheep. Results: In addition to the full length functional ovine RPSA gene, 11 other members of this multicopy gene family, all processed pseudogenes, were identified. Comparison between the RPSA transcript and these pseudogenes shows a large variety in sequence identities ranging from 99% to 74%. Only one of the 11 pseudogenes, i.e. RPSAP7, shares the same open reading frame (ORF) of 295 amino acids with the RPSA gene, differing in only one amino acid. All members of the RPSA family were annotated by comparative mapping and fluorescence in situ hybridization (FISH) localization. Transcription was investigated in the cerebrum, cerebellum, spleen, muscle, lymph node, duodenum and blood, and transcripts were detected for 6 of the 11 pseudogenes in some of these tissues. Conclusions: In the present work we have characterized the ovine RPSA family. Our results have revealed the existence of 11 ovine RPSA pseudogenes and provide new data on their structure and sequence. Such information will facilitate molecular studies of the functional RPSA gene taking into account the existence of these pseudogenes in the design of experiments. It remains to be investigated if the transcribed members are functional as regulatory non-coding RNA or as functional proteins.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
VECTORS, CARCINOMA, PATHWAY, IDENTIFICATION, SHEEP, PRION PROTEIN, MAMMALIAN GENOMES, PROCESSED PSEUDOGENES, -KDA LAMININ RECEPTOR, SCRAPIE-INFECTED MICE
journal title
BMC GENOMICS
BMC Genomics
volume
11
issue
179
Web of Science type
article
Web of Science id
000276365100001
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
4.206 (2010)
JCR rank
24/158 (2010)
JCR quartile
1 (2010)
ISSN
1471-2164
DOI
10.1186/1471-2164-11-179
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
996817
handle
http://hdl.handle.net/1854/LU-996817
alternative location
http://www.biomedcentral.com/1471-2164/11/179
date created
2010-06-29 16:15:36
date last changed
2010-07-01 12:07:01
@article{996817,
  abstract     = {Background: The ribosomal protein SA (RPSA), previously named 37-kDa laminin receptor precursor/67-kDa laminin receptor (LRP/LR) is a multifunctional protein that plays a role in a number of pathological processes, such as cancer and prion diseases. In all investigated species, RPSA is a member of a multicopy gene family consisting of one full length functional gene and several pseudogenes. Therefore, for studies on RPSA related pathways/pathologies, it is important to characterize the whole family and to address the possible function of the other RPSA family members. The present work aims at deciphering the RPSA family in sheep.
Results: In addition to the full length functional ovine RPSA gene, 11 other members of this multicopy gene family, all processed pseudogenes, were identified. Comparison between the RPSA transcript and these pseudogenes shows a large variety in sequence identities ranging from 99\% to 74\%. Only one of the 11 pseudogenes, i.e. RPSAP7, shares the same open reading frame (ORF) of 295 amino acids with the RPSA gene, differing in only one amino acid. All members of the RPSA family were annotated by comparative mapping and fluorescence in situ hybridization (FISH) localization. Transcription was investigated in the cerebrum, cerebellum, spleen, muscle, lymph node, duodenum and blood, and transcripts were detected for 6 of the 11 pseudogenes in some of these tissues.

Conclusions: In the present work we have characterized the ovine RPSA family. Our results have revealed the existence of 11 ovine RPSA pseudogenes and provide new data on their structure and sequence. Such information will facilitate molecular studies of the functional RPSA gene taking into account the existence of these pseudogenes in the design of experiments. It remains to be investigated if the transcribed members are functional as regulatory non-coding RNA or as functional proteins.},
  author       = {Van den Broeke, Alice and Van Poucke, Mario and Marcos-Carcavilla, Ane and Hugot, Karine and Hayes, Helene and Bertaud, Maud and Van Zeveren, Alex and Peelman, Luc},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {VECTORS,CARCINOMA,PATHWAY,IDENTIFICATION,SHEEP,PRION PROTEIN,MAMMALIAN GENOMES,PROCESSED PSEUDOGENES,-KDA LAMININ RECEPTOR,SCRAPIE-INFECTED MICE},
  language     = {eng},
  number       = {179},
  title        = {Characterization of the ovine ribosomal protein SA gene and its pseudogenes},
  url          = {http://dx.doi.org/10.1186/1471-2164-11-179},
  volume       = {11},
  year         = {2010},
}

Chicago
Van den Broeke, Alice, Mario Van Poucke, Ane Marcos-Carcavilla, Karine Hugot, Helene Hayes, Maud Bertaud, Alex Van Zeveren, and Luc Peelman. 2010. “Characterization of the Ovine Ribosomal Protein SA Gene and Its Pseudogenes.” Bmc Genomics 11 (179).
APA
Van den Broeke, A., Van Poucke, M., Marcos-Carcavilla, A., Hugot, K., Hayes, H., Bertaud, M., Van Zeveren, A., et al. (2010). Characterization of the ovine ribosomal protein SA gene and its pseudogenes. BMC GENOMICS, 11(179).
Vancouver
1.
Van den Broeke A, Van Poucke M, Marcos-Carcavilla A, Hugot K, Hayes H, Bertaud M, et al. Characterization of the ovine ribosomal protein SA gene and its pseudogenes. BMC GENOMICS. 2010;11(179).
MLA
Van den Broeke, Alice, Mario Van Poucke, Ane Marcos-Carcavilla, et al. “Characterization of the Ovine Ribosomal Protein SA Gene and Its Pseudogenes.” BMC GENOMICS 11.179 (2010): n. pag. Print.