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CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation.
Brief Bioinform
September 2023
Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Shenzhen University, 1066 Xueyuan Street, Nanshan District, Shenzhen 518055, Guangdong, China.
Dynamic tuning of the poly(A) tail is a crucial mechanism for controlling translation and stability of eukaryotic mRNA. Achieving a comprehensive understanding of how this regulation occurs requires unbiased abundance quantification of poly(A)-tail transcripts and simple poly(A)-length measurement using high-throughput sequencing platforms. Current methods have limitations due to complicated setups and elaborate library preparation plans.
View Article and Find Full Text PDFmiR-RACE: an effective approach to accurately determine the sequence of computationally identified miRNAs.
Methods Mol Biol
December 2015
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
Computational prediction of microRNAs (miRNAs) is one of the most important approaches in microRNA studies. While validation of the predicted microRNAs' precise sequences is essential for further studies on their biogenesis, evolution, and functions, computational miRNA prediction methods, however, often fail to predict the accurate sequence of the mature miRNA within the precursor at the nucleotide precision level. Here, we depict a highly efficient method for determining the precise sequences of computationally predicted miRNAs.
View Article and Find Full Text PDFOligo-dT anchored cDNA-SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.).
Gene
September 2014
College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China.
Differential display is a powerful technique for analyzing differences in gene expression. Oligo-dT cDNAstart codon targeted marker (cDNA-SCoT) technique is a novel, simple, cheap, rapid, and efficient method for differential gene expression research. In the present study, the oligo-dT anchored cDNA-SCoT technique was exploited to identify differentially expressed genes during several stress treatments in mango.
View Article and Find Full Text PDFPreparation of fluorescent-dye-labeled cDNA from RNA for microarray hybridization.
Cold Spring Harb Protoc
January 2014
This protocol describes how to prepare fluorescently labeled cDNA for hybridization to microarrays. It consists of two steps: first, a mixture of anchored oligo(dT) and random hexamers is used to prime amine-modified cDNA synthesis by reverse transcriptase using a modified deoxynucleotide with a reactive amine group (aminoallyl-dUTP) and an RNA sample as a template. Second, the cDNA is purified and exchanged into bicarbonate buffer so that the amine groups in the cDNA react with the dye N-hydroxysuccinimide (NHS) esters, covalently joining the dye to the cDNA.
View Article and Find Full Text PDFHigh throughput characterizations of poly(A) site choice in plants.
Methods
May 2014
Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA. Electronic address:
The polyadenylation of mRNA in eukaryotes is an important biological process. In recent years, significant progress has been made in the field of mRNA polyadenylation owing to the advent of the next generation DNA sequencing technologies. The high-throughput sequencing capabilities have resulted in the direct experimental determinations of large numbers of polyadenylation sites, analysis of which has revealed a vast potential for the regulation of gene expression in eukaryotes.
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