MicroRNAs （miRNAs） are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. Th...MicroRNAs （miRNAs） are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. The miRNAs are approximately 21 nucleotides long and code for the complementary strand to a larger genic mRNA. They are often found within the complementary primary transcript （pri-miRNAs）. In the past few years, a growing number of soybean miRNAs have been discovered, however, little is known about the transcriptional regulation of these miRNAs. In this study, promoters and cis-acting elements of soybean miRNAs were analyzed using the genomic data for the first time. A total of 82 miRNAs were located among 122 loci in genome, some were present as double or multiple copies. Five clusters that included ten miRNAs were found in genome, and only one cluster share the same promoter. A total of 191 promoters from 122 loci of the soybean miRNA sequences were found and further analyzed. The results indicated that the conserved soybean miRNA genes had a greater proportion of promoters than that of non-conserved ones, and the distribution of the transcript start sites （TSSs） and TATA-boxes found had different motif styles between conserved and non-conserved miRNA genes. Furthermore, the cis-acting elements 5＇ of the TSSs were analyzed to obtain potential function and spatiotemporal expression pattern of miRNAs. The data obtained here may lead to the identification of specific sequences upstream of pre-miRNAs and the functional annotation of miRNAs in soybean.展开更多
The importance of microRNA （miRNA） at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and funct...The importance of microRNA （miRNA） at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites （TSSs） for 11 miRNA primary transcripts of soybean from 11 miRNA loci （of 50 loci tested） were cloned by a 5＂ rapid amplification of cDNA ends （5＂ RACE） procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 （76%） of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5＂ to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNA-mediated regulatory pathways and networks in soybean.展开更多
Abstract Leaves of melon were collected and extracted by the CTAB method for total DNA which was used for PCR amplification, obtaining the gene sequence of cucumisin promoter. The sequence results were processed and a...Abstract Leaves of melon were collected and extracted by the CTAB method for total DNA which was used for PCR amplification, obtaining the gene sequence of cucumisin promoter. The sequence results were processed and analyzed with DNAman, DNAstar and other softwares, and bioinformatic element analysis was performed with PlantCARE and PLACE. The analysis results showed that the cucumisin promoter shared 100%, 99% and 99% homology with AY055805, LN713264 and LN681897, respectively. The promoter sequence contains a variety of c/s-acting elements common in fruit promoters of higher plants such as TATA-Box and CAAT-Box, and light-responsive elements, some of which involved in ABA and VP1 responsiveness and salicylic acid responsiveness. This study provides a scien- tific basis for further research on genetic engineering of fruits.展开更多
The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the las...The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the last decade, acquisition of a controllable regulatory element from a random library has been established and applied to control the protein expression and metabolic flux in different chassis cells. However, more rational strategies are still urgently needed to improve the efficiency and reduce the laborious screening and multifaceted characterizations. Building precise computational models that can predict the activity of regulatory elements and quantitatively design elements with desired strength have been demonstrated tremendous potentiality. Here, recent progress on construction of cis- acting regulatory element library and the quantitative predicting models for design of such elements are reviewed and discussed in detail.展开更多
基金supported by the National High-Tech R&D Program of China (863 Program,2006AA100104-4)the Project of 948 from Ministryof Agriculture of China (2006-G5)+5 种基金the National Nature Science Foundation of China (30971810,60932008)the National Basic Research Program ofChina (973 Program, 2009CB118400)the Postdoctoral Fund in Heilongjiang Province, China (LBH-Z07228)the Foundation Projects of Northeast Agricultural University, Chinathe Technology Project of Education Ministry of Heilongjiang Province, China(11541025)the Technology Project of Harbin,China (2009RFQXN085)
文摘MicroRNAs （miRNAs） are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. The miRNAs are approximately 21 nucleotides long and code for the complementary strand to a larger genic mRNA. They are often found within the complementary primary transcript （pri-miRNAs）. In the past few years, a growing number of soybean miRNAs have been discovered, however, little is known about the transcriptional regulation of these miRNAs. In this study, promoters and cis-acting elements of soybean miRNAs were analyzed using the genomic data for the first time. A total of 82 miRNAs were located among 122 loci in genome, some were present as double or multiple copies. Five clusters that included ten miRNAs were found in genome, and only one cluster share the same promoter. A total of 191 promoters from 122 loci of the soybean miRNA sequences were found and further analyzed. The results indicated that the conserved soybean miRNA genes had a greater proportion of promoters than that of non-conserved ones, and the distribution of the transcript start sites （TSSs） and TATA-boxes found had different motif styles between conserved and non-conserved miRNA genes. Furthermore, the cis-acting elements 5＇ of the TSSs were analyzed to obtain potential function and spatiotemporal expression pattern of miRNAs. The data obtained here may lead to the identification of specific sequences upstream of pre-miRNAs and the functional annotation of miRNAs in soybean.
基金supported by the National High-Tech R&D Program of China (2006AA10Z1F1)the National Core Soybean Genetic Engineering Project, China(2011ZX08004-002)+3 种基金the National Natural Science Foundation of China (60932008, 30971810)the National Basic Research Program of China (2009CB118400)the Ministry of Education Innovation Team of Soybean Molecular Design,Chinathe Innovation Team of the Education Bureau of Heilongjiang Province, China
文摘The importance of microRNA （miRNA） at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites （TSSs） for 11 miRNA primary transcripts of soybean from 11 miRNA loci （of 50 loci tested） were cloned by a 5＂ rapid amplification of cDNA ends （5＂ RACE） procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 （76%） of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5＂ to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNA-mediated regulatory pathways and networks in soybean.
基金Supported by Fund of Education Department of Yunnan Province(2013Y251)Characteristic Biological Resource Development and Utilization Key Laboratory Open Fund of Kunming University(GXKJ201612)Fund for Introduction of Doctors(YJL11015)
文摘Abstract Leaves of melon were collected and extracted by the CTAB method for total DNA which was used for PCR amplification, obtaining the gene sequence of cucumisin promoter. The sequence results were processed and analyzed with DNAman, DNAstar and other softwares, and bioinformatic element analysis was performed with PlantCARE and PLACE. The analysis results showed that the cucumisin promoter shared 100%, 99% and 99% homology with AY055805, LN713264 and LN681897, respectively. The promoter sequence contains a variety of c/s-acting elements common in fruit promoters of higher plants such as TATA-Box and CAAT-Box, and light-responsive elements, some of which involved in ABA and VP1 responsiveness and salicylic acid responsiveness. This study provides a scien- tific basis for further research on genetic engineering of fruits.
基金This work was supported by the National Basic Research Program of China （973 Program, grant No. 2012CB721104）, the National High Technology Research and Development Program （863 Program, grant No. 2012AA02A701）, the National Natural Science Foundation of China （grant Nos. 31170101 and 31301017）, and the Natural Science Foundation of Guangdong Province, China （grant No. 2015A030310317）.
文摘The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the last decade, acquisition of a controllable regulatory element from a random library has been established and applied to control the protein expression and metabolic flux in different chassis cells. However, more rational strategies are still urgently needed to improve the efficiency and reduce the laborious screening and multifaceted characterizations. Building precise computational models that can predict the activity of regulatory elements and quantitatively design elements with desired strength have been demonstrated tremendous potentiality. Here, recent progress on construction of cis- acting regulatory element library and the quantitative predicting models for design of such elements are reviewed and discussed in detail.
