The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans
- *Wadsworth Center, David Axelrod Institute, Albany, NY 12208; and
- ‡Birth Defects Laboratories, Division of Medical Genetics, Department of Pediatrics, Children's Hospital of Pittsburgh, and
- §Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213
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Edited by Stanley M. Gartler, University of Washington, Seattle, WA, and approved June 22, 2006 (received for review March 17, 2006)
Abstract
A recently promoted genome evolution model posits that mammalian pseudogenes can regulate their founding source genes, and it thereby ascribes an important function to “junk DNA.” This model arose from analysis of a serendipitous mouse mutant in which a transgene insertion/deletion caused severe polycystic kidney disease and osteogenesis imperfecta with ≈80% perinatal lethality, when inherited paternally [Hirotsune, S., et al. (2003) Nature 423, 91–96]. The authors concluded that the transgene reduced the expression of a nearby transcribed and imprinted pseudogene, Mkrn1-p1. This reduction in chromosome 5-imprinted Mkrn1-p1 transcripts was proposed to destabilize the cognate chromosome 6 Mkrn1 source gene mRNA, with a partial reduction in one Mkrn1 isoform leading to the imprinted phenotype. Here, we show that 5’ Mkrn1-p1 is fully methylated on both alleles, a pattern indicative of silenced chromatin, and that Mkrn1-p1 is not transcribed and therefore cannot stabilize Mkrn1 transcripts in trans. A small, truncated, rodent-specific Mkrn1 transcript explains the product erroneously attributed to Mkrn1-p1. Additionally, Mkrn1 expression is not imprinted, and 5’ Mkrn1 is fully unmethylated. Finally, mice in which Mkrn1 has been directly disrupted show none of the phenotypes attributed to a partial reduction of Mkrn1. These data contradict the previous suggestions that Mkrn1-p1 is imprinted, and that either it or its source Mkrn1 gene relates to the original imprinted transgene phenotype. This study invalidates the data upon which the pseudogene trans-regulation model is based and therefore strongly supports the view that mammalian pseudogenes are evolutionary relics.
Footnotes
- †To whom correspondence may be addressed. E-mail: gray{at}wadsworth.org or robert.nicholls{at}chp.edu
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Author contributions: T.A.G. and R.D.N. designed research; T.A.G., A.W., P.J.F., and R.D.N. performed research; T.A.G. contributed new reagents/analytic tools; T.A.G. and R.D.N. analyzed data; and T.A.G. and R.D.N. wrote the paper.
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Conflict of interest statement: No conflicts declared.
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This paper was submitted directly (Track II) to the PNAS office.
- © 2006 by The National Academy of Sciences of the USA
