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MiRNAs are derived from single-stranded RNA precursors that are transcribed by RNA polymerase II to generate self-complementary fold-back structures (stem-loop or hairpin) processed subsequently by DICER-like 1 (DCL1) in association with other protein factors. These regulatory sRNAs have been classified into at least six groups, including microRNAs (miRNAs), heterochromatic small interfering RNAs (hc-siRNAs), trans-acting small interfering RNAs (tasiRNAs), natural antisense small interfering RNAs (nat-siRNAs), repeat-associated small interfering RNAs (ra-siRNAs), and in metazoans, the piwi-interacting RNAs (piRNAs). In eukaryotes, sRNAs have been found to control cellular metabolism, growth and differentiation, to maintain genome integrity, and to combat viruses and mobile genetic elements. ![]() The discovery of RNA interference in the late 1990s prompted a revolution in RNA biology, and the unveiling of small RNA (sRNA)-mediated gene regulatory pathways has profoundly shaped our understanding of the complexity of gene regulation. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family. Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. Finally, we found that 10 of the 19 miR828-targeted MYBs undergo small interfering RNA (siRNA) biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. Apple also conserves two TAS gene families with similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profiles and target specificities. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. We performed deep small RNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. For geneticists, biologists, and especially students, however, it's a versatile, compatible lab-grade research tool.MicroRNAs (miRNAs) and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown. It's easy to use, but it requires specific knowledge to make proper use of it. #CLC SEQUENCE VIEWER COLOR CODE SELECTED RESIDUE WINDOWS#Sequence Viewer is freeware that works with all recent versions of Windows up to Vista. Sophisticated reporting features simplify publishing data in papers. Sequence Viewer's standout feature is its views, which clearly depict the results of complex genetic sequences, statistics, and enzyme analysis in colorful graphics that can be exported into a staggering array of formats. There's a main pane view and left-hand side panes with tree views of the Navigation Area and Toolbox. The program's main interface features the familiar businesslike Windows layout, with a toolbar that lists common menu items such as File, Edit, and Help as well as program-specific menus like Workspace. It offers a continuously evolving lab-grade application in a compact, easy-to-use format that can access many integrated research tools and databases. It also carries over the premium utilities' sophisticated data management and exporting capabilities as well as compatibility with a wide range of platforms and file formats. It offers many of the features and capabilities of the publisher's high-end science software, such as the ability to perform many bioinformatics analyses, including interactive restriction site analysis, creating and editing alignments, phylogenetics, integrated GenBank searches, and advanced DNA to protein translation. #CLC SEQUENCE VIEWER COLOR CODE SELECTED RESIDUE FREE#CLC bio's Sequence Viewer is a free tool for basic bioinformatics analysis. ![]()
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