• BMB Reports
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• v.42 no.4
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• pp.185-188
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• 2009

Transcripts contain introns that are usually removed from premessenger RNA (MRNA) in the process of pre-mRNA splicing. After splicing, the mature RNA is exported from the nucleus to the cytoplasm. The splicing and export processes are coupled. UAP56 protein, which is ubiquitously present in organisms from yeasts to humans, is a DExD/H-box family RNA helicase that is an essential splicing factor with various functions in the prespliceosome assembly and mature spliceosome assembly. Collective evidence indicates that UAP56 has an essential role in mRNA nuclear export. This mini-review summarizes recent evidence for the role of UAP56 in pre-mRNA splicing and nuclear export.

• Molecules and Cells
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• v.27 no.6
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• pp.657-665
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• 2009

The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature mRNA. The spatial arrangements are, in average, 16 nucleotides per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.7 nt in the inter-hairpin spacer. The constitutive splicing system of ovomucoid-pre-mRNA is characterized by preferred order of intron removal of 5/6 > 7/4 > 2/1 > 3. The 5' splice sites (5'SS), branch point sequences (BPS) and 3' splice sites (3'SS) were identified and free energies involved have been estimated in 7 splice sites. Thermodynamic barriers for splice sites from the least (|lowest| -Kcal) were 5, 4, 7, 6, 2, 1, and 3; i.e., -18.7 Kcal, -20.2 Kcal, -21.0 Kcal, -24.0 Kcal, - 25.4 Kcal, -26.4 Kcal and -28.2 Kcal respectively. These are parallel to the kinetic data of splicing order reported in the literature. As a result, the preferred order of intron removals can be described by a consideration of free energy changes involved in the spliceosomal assembly pathway. This finding is consistent with the validity of hnRNP formation mechanisms in previous reports.

• BMB Reports
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• v.49 no.11
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• pp.612-616
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• 2016

CD44 pre-mRNA includes 20 exons, of which exons 1-5 ($C_1-C_5$) and exons 16-20 ($C_6-C_{10}$) are constant exons, whereas exons 6-15 ($V_1-V_{10}$) are variant exons. $V_6$-exon-containing isoforms have been known to be implicated in tumor cell invasion and metastasis. In the present study, we performed a SR protein screen for CD44 $V_6$ splicing using overexpression and lentivirus-mediated shRNA treatment. Using a CD44 $V_6$ minigene, we demonstrate that increased SRSF3 and SRSF4 expression do not affect $V_6$ splicing, but increased expression of SRSF1, SRSF6 and SRSF9 significantly inhibit $V_6$ splicing. In addition, using a constitutive exon-specific primer set, we could not detect alterations of CD44 splicing after SR protein-targeting shRNA treatment. However, using a $V_6$ specific primer, we identified that reduced SRSF2 expression significantly reduced the $V_6$ isoform, but increased $V_{6-10}$ and $V_{6,8-10}$ isoforms. Our results indicate that SR proteins are important regulatory proteins for CD44 $V_6$ splicing.

• BMB Reports
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• v.54 no.3
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• pp.176-181
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• 2021

Bcl-x, a member of the Bcl-2 family, plays a key role in apoptosis. Alternative splicing of Bcl-x pre-mRNA through alternative 5' splice-site selection produces an anti-apoptotic mRNA isoform that includes exon 2b and a pro-apoptotic Bcl-x mRNA isoform that excludes exon 2b. Here we used Bcl-x minigene and identified SRSF2 and SRSF6 as two regulatory factors of 5' splice-site selection of Bcl-x pre-mRNA. We selected binding clusters closer to 5' splice-sites from multiple potential binding sites of SRSF2 and SRSF6 to perform loss of functions analysis through site-directed mutagenesis. Our results demonstrated that these mutations did not abolish regulatory functions of SRSF2 or SRSF6, indicating that a single binding motif or a cluster was not a functional target of these proteins in Bcl-x pre-mRNA splicing. Random deletion mutagenesis did not disrupt the role of SRSF2 and SRSF6. Importantly, mutagenesis of 5' splice-site to a conserved or a weaker score demonstrated that the weaker strength of the target 5' splice-site or higher strength of the other 5' splice-site strength limited the role of SRSF2 and SRSF6 in 5' splice-site activation.

• BMB Reports
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• v.52 no.11
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• pp.641-646
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• 2019

The Ron proto-oncogene is a human receptor for macrophage-stimulating protein (MSP). The exclusion of exon 11 in alternative splicing generates ${\Delta}RON$ protein that is constitutively activated. Heterogenous ribonucleaoprotein (hnRNP) $C_1/C_2$ is one of the most abundant proteins in cells. In this manuscript, we showed that both hnRNP $C_1$ and $C_2$ promoted exon 11 inclusion of Ron pre-mRNA and that hnRNP $C_1$ and hnRNP $C_2$ functioned independently but not cooperatively. Moreover, hnRNP $C_1$ stimulated exon 11 splicing through intron 10 activation but not through intron 11 splicing. Furthermore, we showed that, whereas the RRM domain was required for hnRNP $C_1$ function, the Asp/Glu domain was not. In conclusion, hnRNP $C_1/C_2$ promoted exon 11 splicing independently by stimulating intron 10 splicing through RRM but not through the Asp/Glu domain.

• The Journal of the Korea Contents Association
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• v.10 no.10
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• pp.102-110
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• 2010

Alternative splicing is an important process in gene expression. Alternative Splicing can lead to mutations and diseases. Most studies detect alternatively spliced genes with ESTs (Expressed Sequence Tags). However, reliance on ESTs might have some weaknesses in predicting alternative splicing. ESTs have been stored in the libraries. The EST libraries are often not clearly organized and annotated. We can pick erroneous ESTs. It is also difficult to predict whether or not alternative splicing exists for those genes where ESTs are not available. To address these issues and to improve the quality of detection and prediction for alternative splicing, we propose the One-leaf One-node Tree Algorithm that uses pre-mRNAs. It is achieved by codons, three nucleotides, as attributes for each chromosome in Arabidopsis thaliana. The proposed decision tree shows that alternative and normal splicing have different splicing patterns according to triplet nucleotides in each chromosome. Based on the patterns, alternative splicing of unlabeled genes can also be predicted.

• Journal of Life Science
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• v.30 no.6
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• pp.570-579
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• 2020

Pre-mRNA splicing is a crucial step for the expression of information encoded in eukaryotic genomes. Alternative splicing occurs when splice sites are differentially recognized and more than one transcript and potentially multiple proteins are generated from the same pre-mRNA. The decision on which splice sites are selected under particular cellular conditions is determined by the interaction of proteins, globally designated as splicing factors, that guide spliceosomal components, and thereby the spliceosome, to their respective splice sites. Abiotic stresses such as heat, cold, salt, drought, and hypoxia markedly alter alternative splicing patterns in plants, and these splicing events implement changes in gene expression for adaptive responses to adverse environments. Alteration of the expression or activity of splicing factors results in alternative splicing under cold, heat, salt, or drought conditions, and alternatively spliced isoforms respond distinctly in several aspects such as expression in different tissues or degradation via nonsense-mediated decay. Spliced isoforms may vary in their subcellular localization or have different biological functions under stress conditions. Despite numerous studies, functional analyses of alternative splicing have been limited to particular abiotic stresses; the molecular mechanism of alternative splicing in abiotic stress response remains uncovered which suggests that further studies are needed in this area.

• Proceedings of the Korean Information Science Society Conference
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• 2011.06a
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• pp.37-40
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• 2011

선택 스플라이싱 (alternative splicing)은 mRNA (messenger RNA)의 전구체인 pre-mRNA가 mRNA로 전사될 때 pre-mRNA의 엑손 영역들 (exons)이 여러 가지 유형 (pattern)으로 다시 연결되는 과정을 말한다. 선택 스플라이싱에 의해 하나의 유전자로부터 서로 다른 mRNA가 만들어 지고 서로 다른 이소형의 단백질 (protein isoforms)이 생성된다. 현재까지 알려진 선택 스플라이싱의 유형은 약 7가지 종류가 있으며, 유전자의 돌연변이 및 질병과 밀접한 연관성을 가지고 있는 것으로 알려져 있다. 본 연구에서는 차세대 시퀀싱 (Next Generation Sequencing : NGS) 기술로 생성된 RNA-Seq 데이터로부터 각 유전자 영역에 대한 선택 스플라이싱 유형을 분류/추출하는 새로운 알고리즘을 제안한다. 제안된 알고리즘에서는 RNA-Seq 데이터를 DNA 시퀀스와 mRNA 트랜스크립트 시퀀스에 동시 매핑하고, 각 엑손 영역에 정렬된 RNA-Seq 데이터의 커버리지 정보 및 엑손의 접합 (junction) 정보를 이용하여 발현된 트랜스크립트 (transcript)의 종류와 양을 측정한다. 알고리즘의 유효성을 보이기 위하여 시뮬레이션 데이터를 이용한 인간 유전자 영역에서의 선택 스플라이싱 유형 추출 실험을 수행하였으며, 검증된 선택 스플라이싱 DB와 비교, 검증하였다.

• Molecules and Cells
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• v.37 no.1
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• pp.1-8
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• 2014

Mammalian-cell messenger RNAs (mRNAs) are generated in the nucleus from precursor RNAs (pre-mRNAs, which often contain one or more introns) that are complexed with an array of incompletely inventoried proteins. During their biogenesis, pre-mRNAs and their derivative mRNAs are subject to extensive cis-modifications. These modifications promote the binding of distinct polypeptides that mediate a diverse array of functions needed for mRNA metabolism, including nuclear export, inspection by the nonsense-mediated mRNA decay (NMD) quality-control machinery, and synthesis of the encoded protein product. Ribonucleoprotein complex (RNP) remodeling through the loss and gain of protein constituents before and after pre-mRNA splicing, during mRNA export, and within the cytoplasm facilitates NMD, ensuring integrity of the transcriptome. Here we review the mRNP rearrangements that culminate in detection and elimination of faulty transcripts by mammalian-cell NMD.

• BMB Reports
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• v.45 no.3
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• pp.133-140
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• 2012

Cancers claim millions of lives each year. Early detection that can enable a higher chance of cure is of paramount importance to cancer patients. However, diagnostic tools for many forms of tumors have been lacking. Over the last few years, studies of chimeric RNAs as biomarkers have emerged. Numerous reports using bioinformatics and screening methodologies have described more than 30,000 expressed sequence tags (EST) or cDNA sequences as putative chimeric RNAs. While cancer cells have been well known to contain fusion genes derived from chromosomal translocations, rearrangements or deletions, recent studies suggest that trans-splicing in cells may be another source of chimeric RNA production. Unlike cis-splicing, trans-splicing takes place between two pre-mRNA molecules, which are in most cases derived from two different genes, generating a chimeric non-co-linear RNA. It is possible that trans-splicing occurs in normal cells at high frequencies but the resulting chimeric RNAs exist only at low levels. However the levels of certain RNA chimeras may be elevated in cancers, leading to the formation of fusion genes. In light of the fact that chimeric RNAs have been shown to be overrepresented in various tumors, studies of the mechanisms that produce chimeric RNAs and identification of signature RNA chimeras as biomarkers present an opportunity for the development of diagnoses for early tumor detection.