• Molecules and Cells
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• 제46권1호
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• pp.57-64
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• 2023

In eukaryotic cells, a key RNA processing step to generate mature mRNA is the coupled reaction for cleavage and polyadenylation (CPA) at the 3' end of individual transcripts. Many transcripts are alternatively polyadenylated (APA) to produce mRNAs with different 3' ends that may either alter protein coding sequence (CDS-APA) or create different lengths of 3'UTR (tandem-APA). As the CPA reaction is intimately associated with transcriptional termination, it has been widely assumed that APA is regulated cotranscriptionally. Isoforms terminated at different regions may have distinct RNA stability under different conditions, thus altering the ratio of APA isoforms. Such differential impacts on different isoforms have been considered as post-transcriptional APA, but strictly speaking, this can only be considered "apparent" APA, as the choice is not made during the CPA reaction. Interestingly, a recent study reveals sequential APA as a new mechanism for post-transcriptional APA. This minireview will focus on this new mechanism to provide insights into various documented regulatory paradigms.

• Molecules and Cells
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• 제39권4호
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• pp.281-285
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• 2016

Almost all of eukaryotic mRNAs are subjected to polyadenylation during mRNA processing. Recent discoveries showed that many of these mRNAs contain more than one polyadenylation sites in their 3' untranslated regions (UTR) and that alternative polyadenylation (APA) is prevalent among these genes. Many biological processes such as differentiation, proliferation, and tumorigenesis have been correlated to global APA events in the 3' UTR of mRNAs, suggesting that these APA events are tightly regulated and may play important physiological roles. In this review, recent discoveries in the physiological roles of APA events, as well as the known and proposed mechanisms are summarized. Perspective for future directions is also discussed.

• BMB Reports
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• 제50권4호
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• pp.201-207
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• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• Molecules and Cells
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• 제46권1호
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• pp.48-56
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• 2023

Genomic information stored in the DNA is transcribed to the mRNA and translated to proteins. The 3' untranslated regions (3'UTRs) of the mRNA serve pivotal roles in post-transcriptional gene expression, regulating mRNA stability, translation, and localization. Similar to DNA mutations producing aberrant proteins, RNA alterations expand the transcriptome landscape and change the cellular proteome. Recent global analyses reveal that many genes express various forms of altered RNAs, including 3'UTR length variants. Alternative polyadenylation and alternative splicing are involved in diversifying 3'UTRs, which could act as a hidden layer of eukaryotic gene expression control. In this review, we summarize the functions and regulations of 3'UTRs and elaborate on the generation and functional consequences of 3'UTR diversity. Given that dynamic 3'UTR length control contributes to phenotypic complexity, dysregulated 3'UTR diversity might be relevant to disease development, including cancers. Thus, 3'UTR diversity in cancer could open exciting new research areas and provide avenues for novel cancer theragnostics.

• Genomics & Informatics
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• 제5권4호
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• pp.174-178
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• 2007

The earliest stages of mammalian embryogenesis are governed by the activity of maternally inherited transcripts and proteins. Cytoplasmic polyadenylation of selected maternal mRNA has been reported to be a major control mechanism of delayed translation during preimplantation embryogenesis in mice. The presence of cis-elements required for cytoplasmic polyadenylation (e.g., CPE) can serve as a useful tag in the screening of maternal genes partaking in key functions in the transcriptionally dormant egg and early embryo. However, due to its relative simplicity, UA-rich sequences satisfying the canonical rule of known CPE consensus sequences are often found in the 3'-UTR of maternal transcripts that do not actually undergo cytoplasmic polyadenylation. In this study, we developed a method to confirm the validity of candidate CPE sequences in a given gene by a multiplex comparison of 3'-UTR sequences between mammalian homologs. We found that genes undergoing cytoplasmic polyadenylation tend to create a conserved block around the CPE, while CPE-like sequences in the 3'-UTR of genes lacking cytoplasmic polyadenylation do not exhibit such conservation between species. Through this cross-species comparison, we also identified an alternative CPE in the 3'-UTR of tissue-type plasminogen activator (tPA), which is more likely to serve as a functional element. We suggest that verification of CPEs based on sequence conservation can provide a convenient tool for mass screening of factors governing the earliest processes of mammalian embryogenesis.

• 한국동물학회지
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• 제39권1호
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• pp.115-121
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• 1996

임신중기에서 발기에 이르는 흰쥐의 태반에서 Placental Lactogen I (PL-I), II 그리고 Pit-1 의 유전자 발현 변화를 Northern blot hybridization으로 조사하였다. 그 결과, 임신시기에 따라 PL-I과 PL-II의 mRNA 양과 크기에 변화가 나타났다. 이들 유전자 발현에 미치는 에스트로겐의 영향을 조사하기 위하여, 임신 14일째 쥐의 난소를 제거하고(OVX), 이후 매일 에스트로겐을 투여한 후 (OVX+E), 임신 18일째 태반을 회수하여 PL-I, II 그리고 Pit-1의 유전자 발현을 Northern blot hybridization으로 조사하였다. OVX 군의 경우, PL-I의 mRNA 크기는 1 kb에서 1.3 kb로 PL-II의 mRNA는 0.6kb에서 1 kb로 변화하였다. OVX+E 군에서는 PL-I과 PL-II의 mRNA가 정상대조군과 같은 상태로 환원하였다. 정상대조군에 비하여 OVX와 OVX+E 군에서 PL-I과 PL-II의 mRNA 크기에는 영향을 미치지 못한 반면, mRNA 양은 난소제거시 감소하였다가, 에스트로겐을 투여하면, 부분적으로 회복되는 경향을 보였다. 이러한 본 실험의결과는 에스트로겐이 PL-I과 PL-II의 RNA splicing이나 polyadenylation 등을 포함한 유전자 발현에 영향을 미치며, Pit-1이 이 과정에 개입하는 것을 시사하는 것이다.

• Journal of Microbiology
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• 제34권1호
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• pp.25-29
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• 1996

Since sequencing of randomly selected cDNA clones has been known to be a powerful approach to obtain information on gene expression pattern in specific cells or tissues, we have analyzed a 3'-directed cDNA library of vegetative mycelia of A. nidulans by single-pass sequencing of hundreds of randomly selected clones. Sequencing of 292 cDNA clones yielded 209 gene signatures (GSs) probably representing highly or lesser expressed genes in the vegetative mycelia. Among the 209 GSs, 25 (79 cDNA clones) appeared more than once and 184 only once. One GS appeared at a highest frequency of 6 times, 2 GSs5 times, 4 GSs 4 times, a GSs 3 times and 16 GSs twice. About 6.6% GSs comprizing of 13 GSs showed alternative polyadenylation. Among 23 redundant GSs, three were common in both mycelia and sexual organs, and 22 were probably mycelia-specific. Out of 209 GSs, 36 were identified in GenBank showing of 70% or greater similaritis. Only six GSs were for A. nidulans genes, and 13 GSs were of DNA or genes encoding cytoplasmic or organellar proteins. This pattern is similar to those in the human HepG2 cell line and in human colonic mucosa, although very few genes for nuclear proteins and for protein synthesis were in A. nidulans.

• KSBB Journal
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• 제18권4호
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• pp.329-334
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• 2003

Insulin-like growth factor-I (IGF-I) 유전자의 발현은 사람 및 쥐에서 두 개의 promoters (P1과 P2)로부터의 전사와 alternative RNA splicing 및 differential RNA polyadenylation과 같은 복잡한 기전들에 의하여 조절되는데 조직에 따라 성장호르몬을 포함한 여러 요소들이 관여하는 것으로 알려져 있다. 또한 사람의 IGF-I 유전자 exon 1의 upstream에 존재하는 P1에 hepatocyte nuclear factor l$\alpha$와 CAAT/enhancer-binding protein (C/EBP) isoform 들이 결합하여 조직 및 발달단계 특이한 발현에 중요한 역할을 할 것으로 제안되었지만, exon 1의 downstream sequence가 IGF-I 유전자의 조직 특이적 발현을 조절하는 지에 대하여는 연구되어 있지 않다. 연령이 다른 쥐의 간 및 뇌 조직에서 total RNA를 분리하고 solution hybridization/RNase protection 방법으로 분석하여 IGF-I 유전자의 발현이 태어난 후 간 조직에서는 점차적으로 증가하였지만 뇌조직에서는 감소하여 발달단계에 따라 조직 특이하게 발현되는 것을 확인하였다. IGF-I exon 1의 주요한 전사 개시점으로부터 아래쪽에 존재하는 C/EBP 결합부위를 포함하고 있는 cis-acting element에 해당하는 oligonucleotide들과 간 및 뇌조직에서 분리한 핵단백질들을 이용하여 DNA-결합 활성을 가진 분자량이 다른 C/EBP$\alpha$나 C/EBP$\beta$ 단백질들을 확인하였으며 southwestern 및 western immnoblotting 분석을 하여 간 조직의 핵 추출물에서는 42$^{C}$EBP$\alpha$/, 와 p38$^{C}$EBP$\alpha$/, p35$^{C}$EBP$\alpha$/, p38$^{C}$EBP$\beta$/, 그리고 p35$^{C}$EBP$\beta$/가 IGF-I exon 1 oligonucleotide와 복합체를 형성하고 뇌 조직에서는 p42$^{C}$EBP$\alpha$과 p38$^{C}$EBP$\beta$가 복합체 형성에 관여하는 것으로 나타났다. 이러한 결과들은 FRE-C/EBP isoform 복합체 형성이 IGF-I 유전자 발현의 조직 특이적 조절에 중요한 역할을 할 것으로 제안한다.할을 할 것으로 제안한다.