MicroRNAs: Genomics, Biogenesis, Mechanism, and Function

http://bartellab.wi.mit.edu/publication_reprints/Bartel_Cell09.pdf

MicroRNAs: Target Recognition and Regulatory Functions

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

MicroRNAs (miRNAs) are small RNAs that regulate the expression of complementary messenger RNAs. Hundreds of miRNA genes have been found in diverse animals, and many of these are phylogenetically conserved. With miRNA roles identified in developmental timing, cell death, cell proliferation, haematopoiesis and patterning of the nervous system, evidence is mounting that animal miRNAs are more numerous, and their regulatory impact more pervasive, than was previously suspected.

The functions of animal microRNAs

MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. The two founding members of the microRNA family were originally identified in Caenorhabditis elegans as genes that were required for the timed regulation of developmental events. Since then, hundreds of microRNAs have been identified in almost all metazoan genomes, including worms, flies, plants and mammals. MicroRNAs have diverse expression patterns and might regulate various developmental and physiological processes. Their discovery adds a new dimension to our understanding of complex gene regulatory networks.

/pdf/micrornas-small-rnas-with-a-big-role-in-gene-regulation-3a05xihg95.pdf

MicroRNAs: small RNAs with a big role in gene regulation

http://bartellab.wi.mit.edu/publication_reprints/Rhoades_Cell02.pdf

Prediction of Plant MicroRNA Targets

The present invention generally relates to the production and expression of microRNA (miRNA) in plants. In some cases, production and expression of miRNA can be used to at least partially inhibit or alter gene expression in plants. For instance, in some embodiments, a nucleotide sequence, which may encode a sequence substantially complementary to a gene to be inhibited or otherwise altered, may be prepared and inserted into a plant cell. Expression of the nucleotide sequence may cause the formation of precursor miRNA, which may, in turn, be cleaved (for example, with Dicer or other nucleases, including, for example, nucleases associated with RNA interference), to produce an miRNA sequence substantially complementary to the gene. The miRNA sequence may then interact with the gene (e.g., complementary binding) to inhibit the gene. In some cases, the nucleotide sequence may be an isolated nucleotide sequence. Other embodiments of the invention are directed to the precursor miRNA and/or the final miRNA sequence, as well as methods of making, promoting, and use thereof.

http://genesdev.cshlp.org/content/16/13/1616.full.pdf

MicroRNAs in plants

MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.

/pdf/the-micrornas-of-caenorhabditis-elegans-2jk0ln0n7y.pdf

Matthew W. Rhoades

Papers

Prediction of Plant MicroRNA Targets

MicroRNAs in plants

The microRNAs of Caenorhabditis elegans