In silico identification of microRNAs from expressed sequence tags of three earthworm species
ABSTRACT MicroRNAs are a newly identified class of small regulatory RNAs that target more than 30% protein-coding genes. Elevating evidence shows that miRNA play a critical role in many biological and metabolic processes, including developmental timing, tissue differentiation, and response to chemical exposure. In this study, we applied a computational approach to analyze expressed sequence tags (ESTs), and identified 32 miRNA belonging to 22 miRNA families, in three earthworm species Eisenia fetida, Eisenia andrei, and Lumbricus rubellus. Some of the newly identified miRNAs putatively play important roles in animal growth and development as well as in disease and response to environmental stresses, including chemical exposure. They also share similar features with known animal miRNAs, for instance, the nucleotide U being dominant in both mature and pre-miRNA sequences, particularly in the first position of mature miRNA sequence at the 5' end.
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ABSTRACT: microRNAs (miRNAs) are a large family of small regulatory RNA molecules found in all multicellular organisms. Since their discovery in 2001, there has been impressive progress in miRNA research, and a great deal is now known about the biosynthesis of miRNAs and their regulatory role in translation. It is becoming increasingly clear that miRNAs have fundamental roles to play in cellular responses to xenobiotic stress, the development of pathophysiological changes and other toxicological phenomenon such as susceptibility and resistance. Furthermore, the expression of miRNAs, like many of the genes important in toxicology, can be regulated by xenobiotics and DNA methylation. In this article we review the present understanding of the miRNA field with particular reference to toxicology. We also give an insight into our current projects within this exciting area and highlight some of the new challenges that now face miRNA research.Toxicology 05/2008; 246(1):34-9. DOI:10.1016/j.tox.2007.12.030 · 3.62 Impact Factor
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ABSTRACT: microRNAs (miRNAs) are approximately 22-nucleotide noncoding RNA regulatory genes that are key players in cellular differentiation and homeostasis. They might also play important roles in shaping metazoan macroevolution. Previous studies have shown that miRNAs are continuously being added to metazoan genomes through time, and, once integrated into gene regulatory networks, show only rare mutations within the primary sequence of the mature gene product and are only rarely secondarily lost. However, because the conclusions from these studies were largely based on phylogenetic conservation of miRNAs between model systems like Drosophila and the taxon of interest, it was unclear if these trends would describe most miRNAs in most metazoan taxa. Here, we describe the shared complement of miRNAs among 18 animal species using a combination of 454 sequencing of small RNA libraries with genomic searches. We show that the evolutionary trends elucidated from the model systems are generally true for all miRNA families and metazoan taxa explored: the continuous addition of miRNA families with only rare substitutions to the mature sequence, and only rare instances of secondary loss. Despite this conservation, we document evolutionary stable shifts to the determination of position 1 of the mature sequence, a phenomenon we call seed shifting, as well as the ability to post-transcriptionally edit the 5' end of the mature read, changing the identity of the seed sequence and possibly the repertoire of downstream targets. Finally, we describe a novel type of miRNA in demosponges that, although shows a different pre-miRNA structure, still shows remarkable conservation of the mature sequence in the two sponge species analyzed. We propose that miRNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation.Evolution & Development 01/2009; 11(1):50-68. DOI:10.1111/j.1525-142X.2008.00302.x · 2.72 Impact Factor
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ABSTRACT: No study has been performed on identifying microRNAs (miRNAs) and their targets in cotton although cotton is one of the most important fiber and economic crops around the world. In this study, we found 30 potential cotton miRNAs using a comparative genomic approach based on genomic survey sequence analysis and miRNA secondary structure. These cotton miRNAs belong to 22 miRNA families. Expressed sequence tag (EST) analysis indicated that the predicted miRNAs were expressed in cotton plants. Based on the characteristic that miRNAs exhibit perfect or nearly perfect complementarity with their targeted mRNA sequences, a total of 139 potential miRNA targets were identified in cotton genome. A majority of these targets belong to transcriptional factors which regulate cotton growth and development, including leaf, root, stem, flower, and even fiber development. Those miRNAs may also be involved in other cellular and metabolic processes, such as stress response, signal transduction, and secondary wall synthesis and deposition. Some of the newly identified miRNA targets may be unique to cotton species. In this study, we found that at least 3 miRNA families (miR 396, 414, and 782) target callous synthase, fiber protein Fb23, and fiber quinone-oxidoreductase, suggesting that miRNAs play an important role in cotton fiber differentiation and development.Gene 09/2007; 397(1-2):26-37. DOI:10.1016/j.gene.2007.03.020 · 2.14 Impact Factor