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Author Topic:   Role discovered for a pseudogene"
judge
Member (Idle past 6465 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 1 of 7 (39462)
05-08-2003 7:54 PM


I don't think this got a run here yet (apologies if I missed it), but I wuld be interested to hear any comments
Researchers in Japan and UCSD Discover Novel Role For Pseudogenes
The mantra of molecular biology — DNA makes RNA, which makes protein* — has pretty much ignored pseudogenes. Considered defective copies of DNA segments, the 20,000 pseudogenes in the human genome are thought to be non-participants in the protein-production assembly line.
A comparison of normal mice, left, to mice with a defective pseudogene shows the resulting bone deformities.
Now, scientists in Japan and at the University of California, San Diego (UCSD) School of Medicine have discovered a novel regulatory role for one pseudogene, showing that it stabilizes a similar protein-coding gene on another chromosome. When the pseudogene was disabled, protein-production was compromised, with resulting abnormal kidneys and bones in laboratory mice. When a functioning pseudogene was re-introduced into mouse embryos, the mice developed normally.
From......
http://health.ucsd.edu/news/2003/04_30_Boris.html

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Coragyps
Member (Idle past 756 days)
Posts: 5553
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 2 of 7 (39467)
05-08-2003 8:49 PM
Reply to: Message 1 by judge
05-08-2003 7:54 PM


And the abstract:
A pseudogene is a gene copy that does not produce a functional, full-length protein. The human genome is estimated to contain up to 20,000 pseudogenes. Although much effort has been devoted to understanding the function of pseudogenes, their biological roles remain largely unknown. Here we report the role of an expressed pseudogeneregulation of messenger-RNA stabilityin a transgene-insertion mouse mutant exhibiting polycystic kidneys and bone deformity. The transgene was integrated into the vicinity of the expressing pseudogene of Makorin1, called Makorin1-p1. This insertion reduced transcription of Makorin1-p1, resulting in destabilization of Makorin1 mRNA in trans by way of a cis-acting RNA decay element within the 5' region of Makorin1 that is homologous between Makorin1 and Makorin1-p1. Either Makorin1 or Makorin1-p1 transgenes could rescue these phenotypes. Our findings demonstrate a specific regulatory role of an expressed pseudogene, and point to the functional significance of non-coding RNAs.
from Nature 423, 91 - 96 (2003).
And the conclusion of a companion commentary:
Whatever the underlying mechanism, the work of Hirotsune et al.5 is provocative for revealing the first biological function of any pseudogene. It challenges the popular belief that pseudogenes are simply molecular fossils the evidence of Mother Nature's experiments gone awry. Indeed, it suggests that evolutionary forces can work in both directions. The forward direction is driven by pressures to create new genes from existing ones, an imperfect process that often generates defective copies of the original. But these defective copies need not be evolutionary dead ends, because pressures in the reverse direction could modify them for specific tasks. In the case of Makorin1 and Makorin1-p1, the result of bidirectional selection is that one gene cannot exist without the other an example of functional complicity between a perfected product of evolution and its derivative castaway. Might the pseudogene copies of other functional genes be similarly useful?
J T Lee, Nature 423, 26 - 28 (2003)

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judge
Member (Idle past 6465 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 3 of 7 (39496)
05-09-2003 5:48 AM
Reply to: Message 1 by judge
05-08-2003 7:54 PM


Definition of pseudogene?
I notice in the glossary here there is no definition of "pseudogene".There is a brief definition in coragyps post above (thank you). Can anyone add to this?
I understand it is a "gene" which is apparently deficient in some way, thus not enabling it to function as a gene.
Is this accurate?
Does this mean that any gene which appears this way is labelled as a pseudogene?
Are there different kinds of pseudogenes/
Thanks in advance to anyone who gives their time with an answer.
[This message has been edited by judge, 05-09-2003]
[This message has been edited by judge, 05-09-2003]

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 Message 1 by judge, posted 05-08-2003 7:54 PM judge has not replied

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 4 of 7 (39499)
05-09-2003 6:19 AM
Reply to: Message 1 by judge
05-08-2003 7:54 PM


I brought this up in a different thread. I dont see what it has to do with the central dogma though, it is still DNA>RNA, there are so many non coding RNAs with functions nowadays that one more is hardly news.
[This message has been edited by Wounded King, 05-09-2003]

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 Message 1 by judge, posted 05-08-2003 7:54 PM judge has not replied

  
Mammuthus
Member (Idle past 6497 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 5 of 7 (39502)
05-09-2003 8:13 AM
Reply to: Message 3 by judge
05-09-2003 5:48 AM


Re: Definition of pseudogene?
http://bioinfo.mbb.yale.edu/genome/pseudogene/#what
Hi Judge,
The above link should help a bit and describes generally the different kinds of pseudogenes.
cheers,
M

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 6 of 7 (338368)
08-07-2006 11:34 AM


Makorin1-p1 really is non-functional
Research recently published in PNAS suggests that in fact the model Hirotsune, et al. put forward to explain the effect is quite wrong (Gray et al., 2006). They detected no mRNA for the Makorin1-p1pseudogene and found the locus to be fully methylated. direct diruption of the Makrin1 gene prodced a completely different phenotype to that seen in the original study.
so it seems in fact that this really is a pseudogene, and not a functional one either, ho hum.
TTFN,
WK

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mick
Member (Idle past 5008 days)
Posts: 913
Joined: 02-17-2005


Message 7 of 7 (339923)
08-14-2006 3:20 AM
Reply to: Message 6 by Wounded King
08-07-2006 11:34 AM


Re: Makorin1-p1 really is non-functional
qk writes:
They detected no mRNA for the Makorin1-p1pseudogene and found the locus to be fully methylated... so it seems in fact that this really is a pseudogene, and not a functional one either
Of course even non-coding pseudogenes might have some kind of "function" in a structural sense. For example I can imagine that an upstream pseudogene might protect a gene from being affected by the promoters of other nearby loci by putting physical distance between exons of different genes. Plenty of non-coding sequences are functional, the stop codon being probably the most obvious example.
Does anybody know if a possible structural role for pseudogenes has been explored in the literature?
mick

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