• BMB Reports
• /
• 제45권3호
• /
• pp.133-140
• /
• 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.

• Molecules and Cells
• /
• 제46권1호
• /
• pp.10-20
• /
• 2023

Antisense oligonucleotide (ASO) technology has become an attractive therapeutic modality for various diseases, including Mendelian disorders. ASOs can modulate the expression of a target gene by promoting mRNA degradation or changing pre-mRNA splicing, nonsense-mediated mRNA decay, or translation. Advances in medicinal chemistry and a deeper understanding of post-transcriptional mechanisms have led to the approval of several ASO drugs for diseases that had long lacked therapeutic options. For instance, an ASO drug called nusinersen became the first approved drug for spinal muscular atrophy, improving survival and the overall disease course. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Although Trikafta and other CFTR-modulation therapies benefit most CF patients, there is a significant unmet therapeutic need for a subset of CF patients. In this review, we introduce ASO therapies and their mechanisms of action, describe the opportunities and challenges for ASO therapeutics for CF, and discuss the current state and prospects of ASO therapies for CF.

• 한국동물학회:뉴스레터
• /
• 제17권1호
• /
• pp.22-30
• /
• 2000

• 미생물학회지
• /
• 제27권1호
• /
• pp.1-9
• /
• 1989

SV40 바이러스가 원숭이 세포(CVIP)에 감염한 후기에 생기는 poly A(-) 19S RNA의 5'끝과 splicing 유형을 알아보기 위하여 primer extension 및 그 변형방법을 행하였다. 이 RNA의 5' 끝은 SV40 후가 RNA들이 가장 많이 사용하는 cap 자리 인 잔기 325 위치임이 밝혀졌다. 또한 splicing 유형도 세포질의 polyA(+)인 19S RNA와 같은 잔기 373에서 잔기 5581까지의 intron이 제거된 형태이었다. Sl 뉴클리아제에 의한 분석결과 이 RNA의 3' 끝은 polyadenylation 위치로부터 상위로 약11kb에 걸쳐 다양하게 존재함을 알았다. 정상적인 cap 자리와 splicing 형태를 지닌 이 RNA가 왜 핵에 축적되는지의 이유를 조사하였다. 이 RNA상에 사용되지 못한채로 남아있는 3' splice 부위가 핵내 편재를 유발했는지의 여부를 알아보기 위하여, 3' splice 부위를 결손시킨 돌연변이 SV 40 pNA를 세포에 도입시켰다.. 그 결과 3'splice 자리가 없는 RNA는 세포질에 많이 축적됨을 관찰하였다. 이 결손 RNA의 세포질내 축적은 결손으로 인해 RNA의 안정성이 증가함으로써 비롯된 것이 아니라는 것을 actinomycin D 추적실험을 통해 밝혔다. 따라서 정상적인 19S spliced RNA가 세포질로 이동되는 과정을 방해하는 것은 사용되지 않은 3' splice 부위에 형성된 pre-splicing 복합체 때문인 것으로 여겨진다.

• BMB Reports
• /
• 제49권8호
• /
• pp.405-413
• /
• 2016

Tau proteins, which stabilize the structure and regulate the dynamics of microtubules, also play important roles in axonal transport and signal transduction. Tau proteins are missorted, aggregated, and found as tau inclusions under many pathological conditions associated with neurodegenerative disorders, which are collectively known as tauopathies. In the adult human brain, tau protein can be expressed in six isoforms due to alternative splicing. The aberrant splicing of tau pre-mRNA has been consistently identified in a variety of tauopathies but is not restricted to these types of disorders as it is also present in patients with non-tau proteinopathies and RNAopathies. Tau mis-splicing results in isoform-specific impairments in normal physiological function and enhanced recruitment of excessive tau isoforms into the pathological process. A variety of factors are involved in the complex set of mechanisms underlying tau mis-splicing, but variation in the cis-element, methylation of the MAPT gene, genetic polymorphisms, the quantity and activity of spliceosomal proteins, and the patency of other RNA-binding proteins, are related to aberrant splicing. Currently, there is a lack of appropriate therapeutic strategies aimed at correcting the tau mis-splicing process in patients with neurodegenerative disorders. Thus, a more comprehensive understanding of the relationship between tau mis-splicing and neurodegenerative disorders will aid in the development of efficient therapeutic strategies for patients with a tauopathy or other, related neurodegenerative disorders.

• BMB Reports
• /
• 제50권8호
• /
• pp.423-428
• /
• 2017

SRSF2, a Serine-Arginine rich (SR) protein, is a splicing activator that mediates exon inclusion and exclusion events equally well. Here we show SRSF2 directly suppresses intron splicing to suppress cassette exon inclusion in SMN pre-mRNA. Through a serial mutagenesis, we demonstrate that a 10 nt RNA sequence surrounding the branch-point (BP), is important for SRSF2-mediated inhibition of cassette exon inclusion through directly interacting with SRSF2. We conclude that SRSF2 inhibits intron splicing to promote exon exclusion.

• Animal cells and systems
• /
• 제1권1호
• /
• pp.87-91
• /
• 1997

Effects of divalent cations such as $Mg^{2+}$, $Mn^{2+}$, $Ca^{2+}$, and $Zn^2$ on splicing activity of phage T4 thymidylate synthase intron RNA have been investigated. At the concentration of 0.5 mM, $Mn^{2+}$ in the absence of $Mg^{2+}$, a very small amount of pre-RNA was cleaved into ligation products (El-E2) but no circular or linear intron was produced. As the concentration of $Mn^{2+}$ was increased from 1 to 5 mM the pre-RNA was completely hydrolyzed. In the presence of 5 mM $Mg^{2+}$, both the linear intron and circular intron were produced but no El-E2 ligation product was produced. At both 3 and 5 mM $Mn^{2+}$ the RNA was hydrolyzed completely as observed with no $Mg^2+$ being present. In the case of $Zn^{2+}$, even at 0.5 mM concentration, the pre-RNA was completely hydrolyzed. This observation suggested that $Zn^{2+}$ facilitates RNA hydrolysis more rapidly than $Mn^{2+}$ does. at 5mM $Ca^{2+}$, the RNA was not hydrolyzed and remained intact as a primary transcript.

• Molecules and Cells
• /
• 제40권10호
• /
• pp.714-730
• /
• 2017

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

• Genomics & Informatics
• /
• 제4권1호
• /
• pp.33-39
• /
• 2006

Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.

• Journal of Applied Biological Chemistry
• /
• 제58권3호
• /
• pp.201-208
• /
• 2015

RNA 결합 단백질들이 유전자 조절의 다양한 범위에 작용한다는 사실이 아주 중요하다. 유전자의 전사에 관련된 유전자 조절이 많이 연구가 되었어도 RNA의 조절에 관한 연구는 상대적으로 부진한 편이다. RNA 결합 단백질들은 RNA와 관련되는 각종 과정, 예를 들면 전사, pre-mRNA splicing, polyadenylation, 수송, 위치화, 번역, 분해 및 구조의 유지 등 다양한 범위에서 작용을 하고 있다. RNA 결합 단백질들의 많은 부분들이 아직 잘 알려지지 않고 있으며 유전자 발현에 대해 더 잘 이해하기 위해 이러한 부분의 연구가 더 수행되어야 한다. 최근에 유전학, 생화 학, 및 유전자들의 생물정보학의 발달 등으로 인하여. RNA 결합 단백질들의 다양한 분야들이 알려지고 있으며 이러한 부분들이 많은 관심을 받고 있다.