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Imprinted genes in mouse
Libo Wang1, Yanjun Wei1, Hongbo Liu1, Jingyuan Fu2, Yan Zhang2
1. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
2. The Northeast Agricultural University, Harbin, 150031, China
[email protected] (YZ)
Abstract
Genomic imprinting is an important mechanism of epigenetic regulation. It only
expresses the genetic information one of the parent, the other part is silence.
Numerous studies have shown that Imprinted Genes play an important role in
regulating the growth and development of mammals, and its abnormal
expression may lead to diseases. After many years of studies, so far more than
100 imprinted genes in mice have been identified, they play an important role in
the regulation of growth and development. However, biological function of
imprinted genes still requires us to conduct more in-depth exploration. It has
important implications for theoretical research of Biological Evolution and Genes
and Development. With the continuous development of high-throughput
sequencing, it provides a convenient analytical tool for us to study the complex
Imprinted genes. It allows us to explore the dynamic of genomic imprinting
between different tissues and cell.
Keywords：imprinted gene，DNA methylation，High throughput sequencing，
Tissue-specific
1. The Characteristics of imprinted genes
Imprinted genes usually cluster in its chromosome, and they can span millions
of bases or more(Yang, Adamson et al. 1998).For example, there are two large
clusters of imprinted genes on chromosome 7 in the mouse, and there are at
least 35 imprinted genes have been discovered on it. The phenomenon of
Imprinted genes existing in clusters on chromosome is considered to be due to
the co-regulation of genes within the same chromosome(Reik and Walter
2001).Each cluster of imprinted genes is regulated by Imprinting
Control
Elements, also known as imprinting control region. In the mammals, many male
parent or female parent allele expression are clustered near the ICRs, this
illustrates the important role of ICRs in gene imprinting.
The vast majority of imprinted genes have CPG Island (Yang, Adamson et al.
1998), and it can occur DNA methylation. It has a differentially methylated
region (DMRs) in allele. Differential methylation occurs mainly in the gene
promoter region. Most imprinted genes being found have DMR or regulated by
the DMR, and it is an important condition that Imprinted genes reflect genetic
difference.
Also, the occurrence of imprinted genes has the specificity of tissue and
developmental stage. For example, The Grb10 is paternally imprinted in various
tissues in the mouse, but it is biallelic in the brain. In the adult brain it tends to
express paternal allele (Hikichi, Kohda et al. 2003).
2. The Progress of Imprinted Genes
For the study of gene imprinting, we generally look for a new candidate
imprinted genes, and we analyze and identify its imprint. And then we study the
physiological function of imprinted genes in the growth and development of
mammals. We study the gene expression regulation. Of course, the premise of
this work is to find a candidate imprinted genes.
We are looking for imprinted genes around the known imprinted genes by its
occurring in clusters. Now a large part of imprinted genes have been found in
this way. Such as imprinted genes Peg10, Neurabin, Pon2 and Pon3 are to be
identified by this method(Ono, Shiura et al. 2003).
It can also be judged by the allele-specific expression of imprinted genes. Use of
experimental methods, we make the genome in a zygote come from same-sex
parents, and it becomes parthenogenetic (or andrenogenetic) embryo. By
analyzing the parthenogenetic (or andrenogenetic) embryos and normal
embryos phenotype, we determined the genetic which causing of differences.
On this basis, we developed a number of experimental methods. Such as, Ishino
et al. managed to isolate the Peg1/Mest imprinted genes cluster by Suppression
Subtractive Hybridization. the Peg1/Mest imprinted genes cluster includes three
paternal genes which are Mest (Peg1), Pw1 (Peg3) and Nnat (Peg5)
(Kaneko-Ishino, Kuroiwa et al. 1995; Kuroiwa, Kaneko-Ishino et al. 1996;
Kagitani, Kuroiwa et al. 1997), and two maternal genes which are Grb10 (Meg1)
and Gtl2 (Meg3) (Miyoshi, Kuroiwa et al. 1998).
We distinguish the difference of parental origin on parental alleles of imprinted
genes existing various epigenetic modifications. This modification often occur
on differentially methylated region. We can obtain the candidate imprinted
genes by comparing analysis the differentially methylated region in allele. For
example, Smith et al. retrieved within a genome-wide and identified 3 new
imprinted genes which are Nap1l5, Peg13 and Slc38a4 by the method of
Methylated-sensitive
Representational Difference Analysis in 2003(Smith,
Dean et al. 2003).
However, so far the number of imprinted genes has been identified is very
limited. The study of imprinted genes is based on looking for new imprinted
genes. It is obviously a complex and lengthy process via theoretical basis
searching for new imprinted genes. At this time, the development of high
throughput sequencing data, finding a candidate imprinted genes by the
method of bioinformatics emerge. It can be more accurately refine the
candidate genes range。
3. High throughput sequencing to help identify the novel tissue-specific
imprinting
With the development of high throughout sequencing technology, it provides
new insights for exploring the genomic imprinting. RNA-seq data and BS-seq
data can be accurately defined that the levels of imprinted gene expression and
methylation at different stages of development of various tissues and cell
types(Prickett and Oakey 2012). High-throughput sequencing technology has
significant progress in elucidating epigenetic markers, and this is the key of
genomic imprinting during oogenesis(Smallwood, Tomizawa et al. 2011).The
analysis of
tissue-specific imprinting in genome-wide
understand
the
changes
of
epigenetic
marks
in
enables us to
the
growth
and
development ,and We can directly analyze that allele is silent or active in imprint
and non-imprint tissue. For further, RNA-seq data can quantitatively measure
the expression levels of parental alleles. It allows us to determine that the gene
is monoallelic expression or biallelic expression in the different tissue types, so
that we can identify tissue-specific imprint. So far RNA-seq data has been to a
useful tools to recognize the new tissue-specific imprint(Gregg, Zhang et al.
2010; Gregg, Zhang et al. 2010).However, The method used by Gregg et al.
assumes no experimental error in lirbary
construction, sequencing and
genomic alignments time, and each sequencing read independently of the other
reads. Unfortunately, it is clear that these assumptions are violated. In
allele-specific
expression,
there
is
a
systematic
error
for
RNA-seq
obviously(DeVeale, van der Kooy et al. 2012). As the complexity of biological
phenomena, it is a big challenge for filtrating imprinted genes through
high-throughput data(Baran, Subramaniam et al. 2015).This requires us to use
more complex and accurate method to study RNA-seq data, so that we can
more accurately identify imprinted genes.
The differentially methylated of parents allelic is known to control the
expression
of
imprinted
genes(Engemann,
Strodicke
et
al.
2000).The
development of BS-seq technology allows us to obtain the methylation levels of
a single base resolution in Genome-wide. This enables us check the
parent-of-origin specific manner methylation. In the field of imprinted genes
found allele-specific methylation area.
Summary
Currently, the study of genomic imprinting has become an important area in
epigenetics .It is closely related to the growth and development of the organism.
The changes of the normal pattern of imprinting can cause many diseases, but
its mechanisms haven’t been researched thoroughly. This need us use
constantly produce high-throughput data as an analytical tool, more accurate
identification of new imprinted genes, and then continue its in-depth exploration,
to contribute to the study of biological function。
Acknowledgments
Funding for this work provided by the National Natural Science Foundation of China
(grant numbers 31371334, 61403112), the Natural Scientific Research Fund of
Heilongjiang Provincial (grant number ZD2015003).
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