> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
>
http://people.math.sc.edu/nyikos/
>
Evolutionary direction of processed pseudogenes
By: Liu, Guoqing; Cui, Xiangjun; Li, Hong; et al.
SCIENCE CHINA-LIFE SCIENCES Volume: 59 Issue: 8 Pages: 839-849
Published: AUG 2016
While some pseudogenes have been reported to play important roles in
gene regulation, little is known about the possible relationship between
pseudogene functions and evolutionary process of pseudogenes, or about
the forces responsible for the pseudogene evolution. In this study, we
characterized human processed pseudogenes in terms of evolutionary
dynamics. Our results show that pseudogenes tend to evolve toward: lower
GC content, strong dinucleotide bias, reduced abundance of transcription
factor binding motifs and short palindromes, and decreased ability to
form nucleosomes. We explored possible evolutionary forces that shaped
the evolution pattern of pseudogenes, and concluded that mutations in
pseudogenes are likely determined, at least partially, by
neighbor-dependent mutational bias and recombination-associated selection.
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Noise-induced multistability in the regulation of cancer by genes and
pseudogenes
By: Petrosyan, K. G.; Hu, Chin-Kun
JOURNAL OF CHEMICAL PHYSICS Volume: 145 Issue: 4 Article Number:
045102 Published: JUL 28 2016
By: Petrosyan, K. G.; Hu, Chin-Kun
JOURNAL OF CHEMICAL PHYSICS Volume: 145 Issue: 4 Article Number:
045102 Published: JUL 28 2016
We extend a previously introduced model of stochastic gene regulation of
cancer to a nonlinear case having both gene and pseudogene messenger
RNAs (mRNAs) self-regulated. The model consists of stochastic Boolean
genetic elements and possesses noise-induced multistability
(multimodality). We obtain analytical expressions for probabilities for
the case of constant but finite number of microRNA molecules which act
as a noise source for the competing gene and pseudogene mRNAs. The
probability distribution functions display both the global bistability
regime as well as even-odd number oscillations for a certain range of
model parameters. Statistical characteristics of the mRNA's level
fluctuations are evaluated. The obtained results of the extended model
advance our understanding of the process of stochastic gene and
pseudogene expressions that is crucial in regulation of cancer.
Published by AIP Publishing.
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HMGA1-pseudogenes and cancer
By: De Martino, Marco; Forzati, Floriana; Arra, Claudio; et al.
ONCOTARGET Volume: 7 Issue: 19 Pages: 28724-28735 Published: MAY
10 2016
Abstract
Pseudogenes are DNA sequences with high homology to the corresponding
functional gene, but, because of the accumulation of various mutations,
they have lost their initial functions to code for proteins.
Consequently, pseudogenes have been considered until few years ago
dysfunctional relatives of the corresponding ancestral genes, and then
useless in the course of genome evolution. However, several studies have
recently established that pseudogenes are owners of key biological
functions. Indeed, some pseudogenes control the expression of functional
genes by competitively binding to the miRNAs, some of them generate
small interference RNAs to negatively modulate the expression of
functional genes, and some of them even encode functional mutated
proteins. Here, we concentrate our attention on the pseudogenes of the
HMGA1 gene, that codes for the HMGA1a and HMGA1b proteins having a
critical role in development and cancer progression. In this review, we
analyze the family of HMGA1 pseudogenes through three aspects:
classification, characterization, and their possible function and
involvement in cancer.
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Pseudogenes: a novel source of trans-acting antisense RNAs.
By:Johnsson, Per; Morris, Kevin V; Grander, Dan
Methods in molecular biology (Clifton, N.J.)
Volume:1167 Pages:213-26
DOI:10.1007/978-1-4939-0835-6_14
Published:2014
While long thought to represent only "junk" DNA, several recent studies
support a functional role for pseudogenes. Several hundreds of
pseudogenes have been reported as transcribed into RNA in a large
variety of tissues and tumors. Most studies have focused on pseudogenes
expressed in the sense direction, but some reports suggest that
pseudogenes can be also transcribed as antisense RNAs (asRNAs). A few
examples of key regulatory genes, such as PTEN and OCT4, have in fact
been reported to be under the regulation of pseudogene-expressed asRNAs.
Here, we review what is known about pseudogene-expressed asRNAs and we
discuss the functional role that these transcripts may have in gene
regulation. Finally, we discuss some technical challenges when
characterising the function of pseudogene asRNAs.
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Four products from Escherichia coli pseudogenes increase hydrogen production
By:Yusoff, MZM (Yusoff, Mohd Zulkhairi Mohd)[ 1,2,3,4 ] ; Hashiguchi, Y
(Hashiguchi, Yuya)[ 1 ] ; Maeda, T (Maeda, Toshinari)[ 1 ] ; Wood, TK
(Wood, Thomas K.)[ 2,3 ]
View ResearcherID and ORCID
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Volume: 439 Issue: 4 Pages: 576-579
DOI: 10.1016/j.bbrc.2013.09.016
Published: OCT 4 2013
Pseudogenes are considered to be nonfunctional genes that lack a
physiological role. By screening 3985 Escherichia coli mutants using
chemochromic membranes, we found four pseudogenes involved in hydrogen
metabolism. Knockouts of pseudogenes ydfW and ypdJ had a defective
hydrogen phenotype on glucose and formate, respectively. Also, the
knockout of pseudogene yqiG formed hydrogen from formate but not from
glucose. For the yqiG mutant, 100% hydrogen recovery was obtained by the
complementation of YqiG via a plasmid. The knockout of pseudogene ylcE
showed hydrogen deficiency in minimal media which suggested that the
role of YlcE is associated with cell growth. Hence, the products of
these four pseudogenes play an important physiological role in hydrogen
production in E. coli. (C) 2013 The Authors. Published by Elsevier Inc.
All rights reserved.