Expanding the microRNA targeting code: functional sites with centered pairing

신찬석 생화학분자생물학회 (구 한국생화학분자생물학회) 2010 생화학분자생물학회 소식 Vol.30 No.4

식물분자육종에의 non-coding RNA의 적용 가능성

신찬석 한국종자연구회 2014 종자과학과 산업 Vol.11 No.1

Cleavage of the Star Strand Facilitates Assembly of Some MicroRNAs into Ago2-containing Silencing Complexes in Mammals

신찬석 한국분자세포생물학회 2008 Molecules and cells Vol.26 No.3

In animals, microRNAs (miRNAs) and small interfering RNAs (siRNAs) repress expression of protein coding genes by assembling distinct RNA-induced silencing complexes (RISCs). It has previously been shown that passenger-strand cleavage is the predominant mechanism when siRNA duplexes are loaded into Argonaute2 (Ago2)-containing RISC, while an unwinding bypass mechanism is favored for miRNA duplexes with mismatches. Here I present experimental data indicating that some mammalian miRNAs are assembled into Ago2-containing RISC by cleaving their corresponding miRNA star strands. This phenomenon may depend on the secondary structure near the scissile phosphate of the miRNA duplex. In addition, I show that ATP is not required for star-strand cleavage in this process. Taken together, the data here provide insight into the miRNA-loading mechanisms in mammals.

벼의 질소 결핍 스트레스 관련 유전자, microRNA 및 lincRNA 대량 발굴

신상윤,이두영,오규진,신찬석 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

LincRNA (long intergenic noncoding RNA)란 단백질을 coding하지 않으며 genome 상의 intergenic region으로부터 전사되는 200 nucleotide 이상으로 이루어진 RNA를 총칭하는 용어이다. Whole-genome tiling array나 transcriptome sequencing 등에 의해 여러 모델 생물종에서 lincRNA의 존재가 확인되어 왔으며, 이들은 microRNA나 단백질과는 달리 매우 다양한 방식으로 유전자 발현을 조절하는 것으로 보인다. 최근 동물에서는 생물학적으로 중요한 의미를 가지는 몇몇 lincRNA가 발견되었고 이들이 세포 사멸‧세포 주기‧줄기 세포의 전분화능 등의 다양한 생물학적 과정에 관여할 것이라는 증거가 포착되었다. 이에 비하여 식물의 lincRNA에 대한 이해는 아직 초보적인 수준이다. 그러나 최근 들어 애기장대를 중심으로 최적 생장 조건에서와 각종 스트레스를 유도한 조건에서 lincRNA의 발현 양상을 비교함으로써 식물의 스트레스 저항성에 있어 lincRNA의 역할을 규명하려는 시도가 있어 왔다. 이들 연구에 의하면 한발‧냉해‧염해 등의 스트레스 조건 하에서 lincRNA의 pool에 상당한 변화가 일어나는 것으로 보인다. 이에 본 연구에서는 벼의 질소 결핍 스트레스 관련 lincRNA를 오믹스 기법을 이용한 대량 발굴 및 이에 대한 기능적 연구를 수행하고자 한다. 이를 위해 질소 결핍 조건에서 생장시킨 벼 샘플에 대해 RNA-Seq을 실시하였으며, 이에 대한 분석을 통해 질소 결핍 스트레스에 반응하는 다수의 질소 대사 관련 유전자, microRNA 및 lincRNA 후보들을 선정하였다. 앞으로는 qRT-PCR 등의 기법을 통해 lincRNA의 발현 및 기능에 대한 추가적인 연구를 진행함으로써 이들이 질소 결핍 스트레스에 대한 벼의 반응과 어떻게 연관되어 있는지를 확인할 것이다.

Regulatory non-coding RNAs in plants: potential gene resources for the improvement of agricultural traits

신상윤,신찬석 한국식물생명공학회 2016 Plant biotechnology reports Vol.10 No.2

Plant regulatory non-coding RNAs (ncRNAs) are known as important ‘‘top tier’’ regulators in gene regulatory networks. They modulate various biological processes and responses to surrounding environments by directly regulating their target genes which are involved in growth and product yield of crop plants from transcription to translation steps. Due to their agricultural importance of regulatory ncRNAs in plants, they are now spotlighted as potential targets for molecular breeding of agricultural trait-improved crop plants. In this review, we will discuss the agricultural importance of these plant regulatory ncRNAs, and review recent progresses in understanding their functions and molecular mechanisms in regulating their target genes. In addition, we will discuss the application of next generation sequencing (NGS) methodologies on regulatory ncRNA researches in plants, and candidate selection strategy using those NGS-derived dataset and preexisting genetic materials.

벼의 스트레스 저항성에 관여하는 LincRNA 발굴 및 작용 기작 연구

이두영,신찬석 한국육종학회 2011 한국육종학회 학술발표회 발표요지 Vol.43 No.-

miRAuto: An Automated User-Friendly MicroRNA Prediction Tool Utilizing Plant Small RNA Sequencing Data

이정수,신찬석,김동인,박준현,최익영 한국분자세포생물학회 2013 Molecules and cells Vol.35 No.4

MicroRNAs (miRNAs) are a class of small RNAs that post-transcriptionally regulate gene expression in ani-mals and plants. The recent rapid advancement in miRNA biology, including high-throughput sequencing of small RNA libraries, inspired the development of a bioinformatics software, miRAuto, which predicts puta-tive miRNAs in model plant genomes computationally. Furthermore, miRAuto enables users to identify miRNAs in non-model plant species whose genomes have yet to be fully sequenced. miRAuto analyzes the expression of the 5-end position of mapped small RNAs in reference sequences to prevent the possibility of mRNA fragments being included as candidate miRNAs. We validated the utility of miRAuto on a small RNA dataset, and the results were compared to other publicly available miRNA prediction programs. In conclusion, miRAuto is a fully automated user-friendly tool for predicting miRNAs from small RNA sequencing data in both model and non-model plant species. miRAuto is available at http://nature.snu.ac.kr/software/miRAuto.htm.

Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling

임종성,최익영,최범순,이정수,신찬석,양태진,이재성,이재성 한국유전체학회 2012 Genomics & informatics Vol.10 No.1

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

RNA Interference-Mediated Simultaneous Silencing of Four Genes Using Cross-Shaped RNA

이태연,이동기,장찬일,이두영,홍선우,신찬석,Chiang J. Li,김소연,Dirk Haussecker 한국분자세포생물학회 2013 Molecules and cells Vol.35 No.4

The structural flexibility of RNA interference (RNAi)-trig-gering nucleic acids suggests that the design of uncon-ventional RNAi trigger structures with novel features is possible. Here, we report a cross-shaped RNA duplex structure, termed quadruple interfering RNA (qiRNA), with multiple target gene silencing activity. qiRNA trig-gers the simultaneous down-regulation of four cellular target genes via an RNAi mechanism. In addition, qiRNA shows enhanced intracellular delivery and target gene silencing over conventional siRNA when complexed with jetPEI, a linear polyethyleneimine (PEI). We also show that the long antisense strand of qiRNA is incorporated intact into an RNA-induced silencing complex (RISC). This novel RNA scaffold further expands the repertoire of RNAi-triggering molecular structures and could be used in the development of therapeutics for various diseases including viral infections and cancer.

Small RNA Transcriptome of Hibiscus Syriacus Provides Insights into the Potential Influence of microRNAs in Flower Development and Terpene Synthesis

김태욱,박준현,이상길,김소영,김지현,이정호,신찬석 한국분자세포생물학회 2017 Molecules and cells Vol.40 No.8

MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. We employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissue-specific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in H. syriacus. Collectively, this study provides the first reliable draft of the H. syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in H. syriacus.