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MicroRNA primary transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.)

Journal of Integrative Agriculture 2013年第9期12卷 1522-1529页

作者： LI Jing LIU Yong-xin HAN Ying-peng LI Yong-guang GUO Mao-zu LI Wen-bin Key Laboratory of Soybean Biology Ministry of Education/Northeast Agricultural University Department of Computer Science and Technology Harbin Institute of Technology

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.

关键词： soybean miRNA primary transcript RACE TATA box motif promoter cis-acting element

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miRT:A Database of Validated transcription Start Sites of Human MicroRNAs

引用

Genomics, Proteomics & Bioinformatics 2012年第5期10卷 310-316页

作者： Malay Bhattacharyya Manali Das Sanghamitra Bandyopadhyay Machine Intelligence Unit Indian Statistical Institute Department of Bioinformatics West Bengal University of Technology

MicroRNAs （miRNAs） are small endogenous non-coding RNAs of about 22 nt in length that take crucial roles in many biological pro cesses. These short RNAs regulate the expression of mRNAs by binding to their 3＇-UTRs or by translational repression. Many of the current studies focus on how mature miRNAs regulate mRNAs, however, very limited knowledge is available regarding their transcrip- tional loci. It is known that primary miRNAs （pri-miRs） are first transcribed from the DNA, followed by the formation of precursor miRNAs （pre-miRs） by endonuclease activity, which finally produces the mature miRNAs. Till date, many of the pre-miRs and mature miRNAs have been experimentally verified. But unfortunately, identification of the loci of pri-miRs, promoters and associated transcrip- tion start sites （TSSs） are still in progress. TSSs of only about 40% of the known mature miRNAs in human have been reported. This information, albeit limited, may be useful for further study of the regulation of miRNAs. In this paper, we provide a novel database of validated miRNA TSSs, miRT, by collecting data from several experimental studies that validate miRNA TSSs and are available for full download. We present miRT as a web server and it is also possible to convert the TSS loci between different genome built, miRT might be a valuable resource for advanced research on miRNA regulation, which is freely accessible at： http：//***/~bioinfo_miu/ miRT/***.

关键词： MicroRNA transcription start site primary transcript transcriptional regulation Database

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