Mol. Cells 2015; 38(11): 950-958
Published online November 4, 2015
https://doi.org/10.14348/molcells.2015.0121
© The Korean Society for Molecular and Cellular Biology
Correspondence to : *Correspondence: huhjw@kribb.re.kr (JWH); changkt@kribb.re.kr (KTC)
Keywords alternative splicing, AluYRa2, BCS1L, exonization, transposable element
Alternative splicing (AS) is an important molecular mechanism that regulates genes and increases genome diversity and complexity without increasing genome size in eukaryotes (Kim et al., 2014). In the case of humans, high-throughput sequencing data revealed that approximately 95% of multi-exon genes undergo AS (Pan et al., 2008). AS events are classified into four main types, including exon skipping, alternative 5′ splice sites, alternative 3′ splice sites, and intron retention, as well as other less frequent types, such as mutual exclusion, alternative promoter usage, and alternative polyadenylation (Ast, 2004; Keren et al., 2010). The exon skipping mechanism accounts for nearly 40% of AS events and is conserved in higher eukaryotes genomes. This mechanism could produce specific exon-skipped mRNA transcripts (Alekseyenko et al., 2007). Alternative 5′ splice sites and alternative 3′ splice sites account for nearly 18% and 8% of AS events, respectively. Additionally, these events are conserved in higher eukaryote genomes. Specifically, these events could occur when two or more splice sites are recognized at one end of an exon (Ast, 2004). Therefore, different sized exons are transcribed as different mRNA transcripts. Intron retention accounts for less than 5% of all AS events in vertebrate and invertebrate genomes (Park et al., 2012); in this case, intron sequences remain in the mature mRNA transcript without being spliced out.
A previous comparative analysis between human and mouse genomes indicated that AS is often associated with recent exon creation and/or loss (Lev-Maor et al., 2003). Three mechanisms, including exon shuffling, transition of a constitutive exon to an alternative exon, and exonization of intronic sequences, have been identified as causes of the production of alternatively spliced new exons (Corvelo and Eyras, 2008). In mammals, most newly exonized intronic sequences are generated by transposable elements (TEs) (Almeida et al., 2007; Amit et al., 2007; DeBarry et al., 2006; Huh et al., 2009; 2010; Piriyapongsa et al., 2007). In particular,
The BC1 (ubiquinol-cytochrome c reductase) synthesis-like (
In our analysis, we focused on the identification and molecular characterization of
Animal preparation and study design were conducted in accordance with the Guidelines of the Institutional Animal Care and Use Committee (KRIBB-AEC-15031) of the Korea Research Institute of Bioscience and Biotechnology (KRIBB).
Total RNA from humans (
We used a standard protocol to isolate genomic DNA from heparinized blood samples from the following species: (1) HU: humans (
Following the protocols of the CapFishingTM Full-length cDNA Premix kit (Seegene), about 1?3 μg of total RNA from placental tissues of rhesus monkeys were reverse transcribed with the CapFishingTM adaptor for 5′ RACE and the Oligo dT adaptor for 3′ RACE. The first round of PCR was performed with either of the following primer combinations: 5′-RACE primer and 5′-target site primer (TSP; the target is the well-conserved region of
PCR products were separated on a 1.2% agarose gel, purified with the Gel SV Extraction kit (GeneAll), and cloned into the pGEM-T-easy vector (Promega). The cloned DNA was isolated using the Plasmid DNA Mini-prep kit (GeneAll). Sequencing of primate DNA samples and alternative transcripts was performed by a commercial sequencing company (Macrogen).
To estimate the integration time of
In our previous study, we constructed and sequenced a full-length cDNA library as well as conducted a comparative gene analysis with humans to identify numerous full-length gene transcripts using the placental tissue of rhesus monkeys (Kim et al., 2010). A rhesus monkey-specific AS event was identified on the
Comparative structure analysis revealed that the integrated
To estimate the integration time of
In order to understand the expression features of the
To demonstrate the transcriptional start site (TSS) and polyadenylation sequence of the
More than 40% of the human genome is comprised of TEs. According to previous studies, TEs can influence transcription and biological function of genes via various mechanisms (Gogvadze and Buzdin, 2009; Han et al., 2007b; Park et al., 2012). For these reasons, TEs play an important role in evolutionary processes and genome diversification. Moreover, about 90% of TEs are retroelements in the human genome (Bannert and Kurth, 2004). Of the retroelements, about 8% are human endogenous retrovirus (HERV), 20% are long interspersed elements (LINEs), and 13% are short interspersed elements (SINEs) (Schmitz and Brosius, 2011).
In our previous study, we identified an
Our genomic sequence analysis demonstrated integration of an antisense-oriented
RT-PCR experiments showed that the
Integration of
Rhesus and crab-eating monkeys are the most valuable non-human primate animal model species for biomedical research, particularly in the fields of microbiology, neuroscience, and biochemistry (Gibbs et al., 2007; Lee et al., 2014; Park et al., 2013; 2015). The genus
Mol. Cells 2015; 38(11): 950-958
Published online November 30, 2015 https://doi.org/10.14348/molcells.2015.0121
Copyright © The Korean Society for Molecular and Cellular Biology.
Sang-Je Park1,4, Young-Hyun Kim1,2,4, Sang-Rae Lee1,2,4, Se-Hee Choe1,2, Myung-Jin Kim1, Sun-Uk Kim1, Ji-Su Kim1, Bo-Woong Sim1, Bong-Seok Song1, Kang-Jin Jeong1, Yeung-Bae Jin1, Youngjeon Lee1, Young-Ho Park1, Young Il Park3, Jae-Won Huh1,2,*, and Kyu-Tae Chang1,2,*
1National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883, Korea, 2University of Science & Technology, National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 363-883, Korea, 3Graduate School Department of Digital Media, Ewha Womans University, Seoul 120-750, Korea, 4These authors contributed equally to this work.
Correspondence to:*Correspondence: huhjw@kribb.re.kr (JWH); changkt@kribb.re.kr (KTC)
Keywords: alternative splicing, AluYRa2, BCS1L, exonization, transposable element
Alternative splicing (AS) is an important molecular mechanism that regulates genes and increases genome diversity and complexity without increasing genome size in eukaryotes (Kim et al., 2014). In the case of humans, high-throughput sequencing data revealed that approximately 95% of multi-exon genes undergo AS (Pan et al., 2008). AS events are classified into four main types, including exon skipping, alternative 5′ splice sites, alternative 3′ splice sites, and intron retention, as well as other less frequent types, such as mutual exclusion, alternative promoter usage, and alternative polyadenylation (Ast, 2004; Keren et al., 2010). The exon skipping mechanism accounts for nearly 40% of AS events and is conserved in higher eukaryotes genomes. This mechanism could produce specific exon-skipped mRNA transcripts (Alekseyenko et al., 2007). Alternative 5′ splice sites and alternative 3′ splice sites account for nearly 18% and 8% of AS events, respectively. Additionally, these events are conserved in higher eukaryote genomes. Specifically, these events could occur when two or more splice sites are recognized at one end of an exon (Ast, 2004). Therefore, different sized exons are transcribed as different mRNA transcripts. Intron retention accounts for less than 5% of all AS events in vertebrate and invertebrate genomes (Park et al., 2012); in this case, intron sequences remain in the mature mRNA transcript without being spliced out.
A previous comparative analysis between human and mouse genomes indicated that AS is often associated with recent exon creation and/or loss (Lev-Maor et al., 2003). Three mechanisms, including exon shuffling, transition of a constitutive exon to an alternative exon, and exonization of intronic sequences, have been identified as causes of the production of alternatively spliced new exons (Corvelo and Eyras, 2008). In mammals, most newly exonized intronic sequences are generated by transposable elements (TEs) (Almeida et al., 2007; Amit et al., 2007; DeBarry et al., 2006; Huh et al., 2009; 2010; Piriyapongsa et al., 2007). In particular,
The BC1 (ubiquinol-cytochrome c reductase) synthesis-like (
In our analysis, we focused on the identification and molecular characterization of
Animal preparation and study design were conducted in accordance with the Guidelines of the Institutional Animal Care and Use Committee (KRIBB-AEC-15031) of the Korea Research Institute of Bioscience and Biotechnology (KRIBB).
Total RNA from humans (
We used a standard protocol to isolate genomic DNA from heparinized blood samples from the following species: (1) HU: humans (
Following the protocols of the CapFishingTM Full-length cDNA Premix kit (Seegene), about 1?3 μg of total RNA from placental tissues of rhesus monkeys were reverse transcribed with the CapFishingTM adaptor for 5′ RACE and the Oligo dT adaptor for 3′ RACE. The first round of PCR was performed with either of the following primer combinations: 5′-RACE primer and 5′-target site primer (TSP; the target is the well-conserved region of
PCR products were separated on a 1.2% agarose gel, purified with the Gel SV Extraction kit (GeneAll), and cloned into the pGEM-T-easy vector (Promega). The cloned DNA was isolated using the Plasmid DNA Mini-prep kit (GeneAll). Sequencing of primate DNA samples and alternative transcripts was performed by a commercial sequencing company (Macrogen).
To estimate the integration time of
In our previous study, we constructed and sequenced a full-length cDNA library as well as conducted a comparative gene analysis with humans to identify numerous full-length gene transcripts using the placental tissue of rhesus monkeys (Kim et al., 2010). A rhesus monkey-specific AS event was identified on the
Comparative structure analysis revealed that the integrated
To estimate the integration time of
In order to understand the expression features of the
To demonstrate the transcriptional start site (TSS) and polyadenylation sequence of the
More than 40% of the human genome is comprised of TEs. According to previous studies, TEs can influence transcription and biological function of genes via various mechanisms (Gogvadze and Buzdin, 2009; Han et al., 2007b; Park et al., 2012). For these reasons, TEs play an important role in evolutionary processes and genome diversification. Moreover, about 90% of TEs are retroelements in the human genome (Bannert and Kurth, 2004). Of the retroelements, about 8% are human endogenous retrovirus (HERV), 20% are long interspersed elements (LINEs), and 13% are short interspersed elements (SINEs) (Schmitz and Brosius, 2011).
In our previous study, we identified an
Our genomic sequence analysis demonstrated integration of an antisense-oriented
RT-PCR experiments showed that the
Integration of
Rhesus and crab-eating monkeys are the most valuable non-human primate animal model species for biomedical research, particularly in the fields of microbiology, neuroscience, and biochemistry (Gibbs et al., 2007; Lee et al., 2014; Park et al., 2013; 2015). The genus
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