Genome wide identification and functional prediction of long non-coding RNAs in Brassica rapa

임용표,Parameswari Paul,Vignesh Dhandapani,최수련 한국유전학회 2016 Genes & Genomics Vol.38 No.6

Long non-coding RNAs (LncRNAs) are a large, diverse class of RNA molecules that has garnered attention for their potential to regulate gene expression and been identified in various organisms. Here we report the first prediction of lncRNAs in Brassica rapa (B. rapa) genome using computational method. We subjected the publicly available full length cDNA sequences and identified 2237 candidate lncRNAs, characterized their functions based on insilico methods. Housekeeping and small regulatory non-coding RNAs (ncRNAs) were removed from the pool. Although 14–15 % of the total sequences were predicted to be non-coding initially, on filtering only 4.6 % of the total sequences were predicted as lncRNAs carrying a large number of simple repeats. The lncRNAs had an average length of 497 bp and were mapped on each chromosome of B. rapa. They were classified to 4 groups based on their origin. Thirty six motifs involving transcription related activities, signaling mechanism and stress response were identified in the lncRNAs. Repeat elements and neighboring genes of the lncRNAs were analyzed since they were associated in function and regulating the expression of these long non-coding RNAs. We believe that this study would be an initial and reference for any further studies regarding long non-coding RNAs in B. rapa and other Brassica crops.

한-중 유채를 통한 농민들의 소득증대 방안과 실증재배

임용표 한국로고스경영학회 2007 한국로고스경영학회 학술발표대회논문집 Vol.2007 No.7월

고려인삼의 미토콘드리아 DNA의 분자생물학적 특성연구 ( The Characterization of Mitochondrial DNA of Korean Ginseng ( Panax ginseng C. A. Meyer ) )

임용표,최광태 고려인삼학회 1990 Journal of Ginseng Research Vol.14 No.2

Bacterial Artificial Chromosome(BAC)을 이용한 Genomic Library 작성과 최근동향

임용표 한국분자생물학회 1996 분자생물학뉴스 Vol.8 No.2

한국 생명공학과 종자산업의 미래혁신 방향

임용표 한국종자연구회 2021 한국종자연구회 심포지엄 Vol.2021 No.12

배추 유전체연구의 현황과 전망

임용표,최수련,박지영,박범석,김호일 한국식물생명공학회 2006 JOURNAL OF PLANT BIOTECHNOLOGY Vol.33 No.3

Brassica rapa is an important species used as a vegetable, oil, and fodder worldwide. It is related phylogenically to Arabidopsis thaliana, which has already been fully sequenced as a model plant. The ‘Multinational Brassica Genome Project (MBGP)’ was launched by the international Brassica community with the aim of sequencing the whole genome of B. rapa in 2003 on account of its value and the fact that it has the smallest genome among the diploid Brassica. The genome study was carried out not only to know the structure of genome but also to understand the function and the evolution of the genes comprehensively. There are two mapping populations, over 1,000 molecular markers and a genetic map, 2 BAC libraries, physical map, a 22 cDNA libraries as suitable genomic materials for examining the genome of B. rapa ssp. pekinensis Chinese cabbage. As the first step for whole genome analysis, 220,000 BAC-end sequences of the KBrH and KBrB BAC library are achieved by cooperation of six countries. The results of BAC-end sequence analysis will provide a clue in understanding the structure of the genome of Brassica rapa by analyzing the gene sequence, annotation and abundant repetitive DNA. The second stage involves sequencing of the genetically mapped seed BACs and identifying the overlapping BACs for complete genome sequencing. Currently, the second stage is comprises of process genetic anchoring using communal populations and maps to identify more than 1,000 seed BACs based on a BAC-to-BAC strategy. For the initial sequencing, 629 seed BACs corresponding to the minimum tiling path onto Arabidopsis genome were selected and fully sequenced. These BACs are now anchoring to the genetic map using the development of SSR markers. This information will be useful for identifying near BAC clones with the seed BAC on a genome map. From the BAC sequences, it is revealed that the Brassica rapa genome has extensive triplication of the DNA segment coupled with variable gene losses and rearrangements within the segments. This article introduces the current status and prospective of Korea Brassica Genome Project and the bioinformatics tools possessed in each national team. In the near future, data of the genome will contribute to improving Brassicas for their economic use as well as in understanding the evolutional process.

진주조 미토콘드리아 용성분획의 신종 토포아이소머레이즈 그의 분리와 동정

임용표,김병동 ( Yong Pyo Lim,Byung Dong Kim ) 생화학분자생물학회 1988 BMB Reports Vol.21 No.4

A unique DNA-modifying enzyme has been isolated from pearl millet (Pennisetum typhoides) mitochondria. The enzyme relaxes negatively supercoiled pBR322 into an open circular DNA as a major product and also produces a linear DNA and high molecular weight multimer complexes as minor products. The enzyme was isolated from the soluble fraction of mitochondria by DEAE-cellulose and Sephacryl S200 SF column chromatography steps and polyacrylamide gel electrophoresis. The enzyme is dependent on divalent cations (Mg^(++), Mn^(++), Zn^(++), Co^(++), and Ca^(++)), and is independent of ATP. The enzyme is inhibited by high concentrations of monovalent and divalent cations, EDTA, SDS, and spermidine. The molecular weight of this protein is estimated to be about 70,000. The new enzyme, unlike the bacterial topoisomerase I, does not produce ladder intermediate, but also produces high molecular weight multimers. This suggests that the new protein is a mixed functional enzyme of topoisomerase and recombinase. We tentatively call this unique enzyme a novel class of topoisomerase.

진주조 미토콘드리아로 부터 DNA 결합 단백질의 분리와 동정

임용표,김병동 ( Yong Pyo Lim,Byung Dong Kim ) 생화학분자생물학회 1988 BMB Reports Vol.21 No.4

A DNA-binding protein was isolated from pearl millet (Pennisetum typhoides) mitochondrial DNA. The DNA-binding protein transformed negatively supercoiled pBR322 DNA into an open circle DNA as a major product, and a linear DNA and a high molecular weight multimer as minor products. The reaction was dependent on divalent cations (Mg ^(++), Mn^(++), Zn^(++), and Co^(++), but was independent of ATP. The enzyme reaction was inhibited by high concentrations of monovalent and divalent cations, EDTA, SDS, and spermidine. The putative multifunctional enzyme is tentatively designated as a new class of topoisomerase, since, unlike the bacterial topoisomerase I, it does not produce the ladder intermediates.

한국 금잔디(Zoysia Japonica Steud)의 콜히친 처리에 의한 돌연변이유기

임용표,Skogley, Conrad R,Yeam, Do Yi 한국유전학회 1990 Genes & Genomics Vol.12 No.3

Colchicine-induced mutants of Zoysia japonica STEUD here investigated to compare morphological and cytological characters. The pregerminated seeds were treated with colchicine in the combination of various concentrations and soaking durations. From the treatment, nine mutants, different from another in morphology, were selected. The diploid and tetraploid gametes were observed together in the colchicine-treated clone 11-4. When the twenty five subclones isolated from the node of mixoploid clone 11-4 were transplanted, the significant variations were observed in the cotton hair number, stomata number, internode length, rhizome diameter, leaf width, and total rhizome length. It seemed that these morphological variations were related to the various polyploid levels as tetraploid, octaploid, or mixoploid. From these studies, it has been shown that colchcine treatment significantly increases the genetic variability in Zoysiagrass, and that chlchicine be a valuable agent for induction of genetic variability in Zoysia genetic and breeding programs.

Isolation and Characterization of a DNA-binding Protein from Pearl Millet Mitochondria

임용표,김병동,Lim, Yong-Pyo,Kim, Byung-Dong 생화학분자생물학회 1988 한국생화학회지 Vol.21 No.4

한 DNA-결합 단백질이 진주조 (Pennisetum typhoides)의 미토콘드리아 DNA로부터 분리되었다. 그 DNA결함 단백질은 negatively supercoiled pBR322 DNA를 open circle DNA를 주산물로, linear DNA와 고분자량 multimer를 부산물로 전환시켰다. 반응은 이가 양이온 ($Mg^{++}$, $Mn^{++}$, $Zn^{++}$, $Co^{++}$)을 필요하였으나 ATP를 필요로 하지 않았다. 효소반응은 고농도의 일가 및 이가 양이온, EDTA, SDS, 그리고 spermidine에 의하여 억제되었다. 이 다기능 효소 (topoisomerase, recombinase)는 박테리아 topoisomerase I과는 달리 사다리 중간물질을 만들지 않으므로 잠정적으로 신종의 topoisomerase로 명명한다. A DNA-binding protein was isolated from pearl millet (Pennisetum typhoides) mitochondrial DNA. The DNA-binding protein transformed negatively supercoiled pBR322 DNA into an open circle DNA as a major product, and a linear DNA and a high molecular weight multimer as minor products. The reaction was dependent on divalent cations ($Mg^{++}$, $Mn^{++}$, $Zn^{++}$, $Co^{++}$), but was independent of ATP. The enzyme reaction was inhibited by high concentrations of monovalent and divalent cations, EDTA, SDS, and spermidine. The putative multifunctional enzyme is tentatively designated as a new class of topoisomerase, since, unlike the bacterial topoisomerase I. it does not produce the ladder intermediates