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PubMed2007

Evolution of plant microRNA gene families.

MicroRNAs (miRNAs) are important post-transcriptional regulators of their target genes in plants and animals. miRNAs are usually 20-24 nucleotides long. Despite their unusually small sizes, the evolutionary history of miRNA gene families seems to be similar to their protein-coding counterparts. In contrast to the small but abundant miRNA families in the animal genomes, plants have fewer but larger miRNA gene families. Members of plant miRNA gene families are often highly similar, suggesting recent expansion via tandem gene duplication and segmental duplication events. Although many miRNA genes are conserved across plant species, the same gene family varies significantly in size and genomic organization in different species, which may cause dosage effects and spatial and temporal differences in target gene regulations. In this review, we summarize the current progress in understanding the evolution of plant miRNA gene families.

Animals↗

PubMed2004

Profile-based detection of microRNA precursors in animal genomes.

MOTIVATION: MicroRNAs (miRNA) are essential 21-22 nt regulatory RNAs produced from larger hairpin-like precursors. Local sequence alignment tools such as BLAST are able to identify new members of known miRNA families, but not all of them. We set out to estimate how many new miRNAs could be recovered using a profile-based strategy such as that implemented in the ERPIN program. RESULTS: We constructed alignments for 18 miRNA families and performed ERPIN searches on animal genomes. Results were compared to those of a WU-BLAST search at the same E-value cutoff. The two combined approaches produced 265 new miRNA candidates that were not found in miRNA databases. About 17% of hits were ERPIN specific. They showed better structural characteristics than BLAST-specific hits and included interesting candidates such as members of the miR-17 cluster in Tetraodon. Profile-based RNA detection will be an important complement of similarity search programs in the completion of miRNA collections.

Algorithms↗

PubMed2004

Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs.

The factors regulating the expression of microRNAs (miRNAs), a ubiquitous family of approximately 22-nt noncoding regulatory RNAs, remain undefined. However, it is known that miRNAs are first transcribed as a largely unstructured precursor, termed a primary miRNA (pri-miRNA), which is sequentially processed in the nucleus, to give the approximately 65-nt pre-miRNA hairpin intermediate, and then in the cytoplasm, to give the mature miRNA. Here we have sought to identify the RNA polymerase responsible for miRNA transcription and to define the structure of a full-length human miRNA. We show that the pri-miRNA precursors for nine human miRNAs are both capped and polyadenylated and report the sequence of the full-length, approximately 3433-nt pri-miR-21 RNA. This pri-miR-21 gene sequence is flanked 5' by a promoter element able to transcribe heterologous mRNAs and 3' by a consensus polyadenylation sequence. Nuclear processing of pri-miRNAs was found to be efficient, thus largely preventing the nuclear export of full-length pri-miRNAs. Nevertheless, an intact miRNA stem-loop precursor located in the 3' UTR of a protein coding gene only moderately inhibited expression of the linked open reading frame, probably because the 3' truncated mRNA could still be exported and expressed. Together, these data show that human pri-miRNAs are not only structurally similar to mRNAs but can, in fact, function both as pri-miRNAs and mRNAs.

Base Sequence↗

PubMed2006

An approach for the identification of microRNA with an application to Anopheles gambiae.

MicroRNAs (miRNAs) are an abundant class of 20-27 nt long noncoding RNAs, involved in post-transcriptional regulation of genes in eukaryotes. These miRNAs are usually highly conserved between the genomes of related organisms and their pre-miRNA transcript, about 60-120 nt long, forms extended stem-loop structure. Keeping these facts in mind miRsearch is developed which relies on searching the homologues of all known miRNAs of one organism in the genome of a related organism allowing few mismatches depending on the phylogenetic distance between them, followed by assessing for the capability of formation of stem-loop structure. The precursor sequences so obtained were then screened through the RNA folding program MFOLD selecting the cut-off values on the basis of known Drosophila melanogaster pre-miRNAs. With this approach, about 91 probable candidate miRNAs along with pre-miRNAs were identified in Anopheles gambiae using known D. melanogaster miRNAs. Out of these, 41 probable miRNAs have 100% similarity with already known D. melanogaster miRNAs and others were found to be at least 85% similar to the miRNAs of various other organisms.

Animals↗

PubMed2025

Discovering diabetes complications-related microRNAs: meta-analyses and pathway modeling approach.

PURPOSE: MicroRNAs(miRNA) play an important role in the pathogenesis of diabetic complications by regulating gene expression. The objective of this paper is to investigate micoRNA expression in diabetic nephropathy (DN), diabetic retinopathy (DR), diabetic neuropathy (DNP), and diabetic cardiopathy (DC). METHODS: We conducted this systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement and retrieved eligible microRNA-related studies of diabetic complications from PubMed, Embase, and Web of science databases. We enriched pathways corresponding to differentially expressed miRNAs using the miRPath tool on the DIANA website, and predicted their target genes with DIANA microT-CDS and TargetScan. RESULTS: Although many of the selected studies were of high scientific quality, the results were heterogeneous. Among the 71 selected articles, 79 miRNAs were differentially expressed in various complications of diabetes, of which miRNA126, miRNA192 and 17 others were reported in at least two or more studies. A total of 156 target genes were predicted and 103 pathways were obtained by KEGG enrichment analysis. CONCLUSION: This comprehensive systematic evaluation provides experimental evidence statistics for miRNAs as circulating biomarkers and highlights promising biomarkers. These results provide preliminary data to further investigate the role of miRNAs in the diagnosis and therapeutic targets of human diabetic complications and support future broader longitudinal studies to better substantiate the role of dysregulated miRNAs as potential biomarkers and therapeutic targets of diabetic complications.

Humans↗

PubMed2006

Identification of 188 conserved maize microRNAs and their targets.

MicroRNAs (miRNAs) represent a newly identified class of non-protein-coding approximately 20nt small RNAs which play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. After searching a genomic survey sequence database using homologs and secondary structures, we found 188 maize miRNAs belonging to 29 miRNA families. Of the 188 maize miRNA genes, 28 (15%) were found in at least one EST. A total of 115 potential targets were identified for 26 of the miRNA families based on the fact that miRNAs exhibit perfect or nearly perfect complementarity with their target sequences. A majority of the targets are transcription factors which play important roles in maize development, including leaf, shoot, and root development. Additionally, these maize miRNAs are also involved in other cellular processes, such as signal transduction, stress response, sucrose and cellulose synthesis, and ubiquitin protein degradation pathway. Some of the newly identified miRNA targets may be unique to maize.

Base Sequence↗

PubMed2005

Camels and zebrafish, viruses and cancer: a microRNA update.

MicroRNAs (miRNAs) form an extensive class of RNA molecules that regulate gene expression at post-transcriptional level. In recent years, much progress has been made in dissection of biogenesis and functions of miRNAs. There are at least several hundred miRNA genes in the human genome, and the emerging evidence suggests that miRNAs are broadly implicated in gene regulation. Here, we review some recent advances, and particularly we discuss how comparative genomics helps to identify novel miRNA genes, how studies in zebrafish reveal roles of miRNAs in morphogenesis, how changes in miRNA expression patterns are connected with cancer and how host-virus coevolution exploits miRNA regulatory pathways.

Animals↗

PubMed2006

Cloning and detection of HIV-1-encoded microRNA.

MicroRNAs (miRNAs) are 21-to 25-nucleotides (nt) long and interact with messenger RNAs to trigger either translational repression or RNA cleavage through RNA interference (RNAi). We have shown that HIV-1 nef double-stranded RNA from AIDS patients who are long-term nonprogressors, inhibits HIV-1 transcription; and that nef-derived miRNA, miR-N367, is produced in human T-cells persistently infected with HIV-1. The miR-N367 can block HIV-1 Nef expression and long terminal repeat (LTR) transcription, suggesting that miR-N367 might suppress both Nef function and HIV-1 transcription through the RNAi pathway. Protocols are presented here for cloning HIV-1-encoded miRNA and confirming miRNA expression by Northern blot hybridization.

Blotting, Northern↗

PubMed2006

Isolation and identification of gene-specific microRNAs.

Prediction of microRNA (miRNA) candidates using computer programming has identified hundreds and hundreds of genomic hairpin sequences, of which, the functions remain to be determined. Because direct transfection of hairpin-like miRNA precursors (pre)-miRNAs in mammalian cells is not always sufficient to trigger effective RNA-induced gene-silencing complex (RISC) assembly, a key step for RNA interference (RNAi)-related gene silencing, we developed an intronic miRNA-expressing system to overcome this problem, and successfully increased the efficiency and effectiveness of miRNA-associated RNAi induction in vitro and in vivo. By insertion of a hairpin-like pre-miRNA structure into the intron region of a gene, this intronic miRNA biogenesis system has been found to depend on a coupled interaction of nascent precursor messenger RNA transcription and intron excision within a specific nuclear region proximal to genomic perichromatin fibrils. The intronic miRNA was transcribed by RNA type II polymerases, coexpressed with a primary gene transcript, and excised out of its encoding gene transcript by intracellular RNA splicing and processing mechanisms. Currently, some ribonuclease III endonucleases have been found to be involved in the processing of spliced introns and probably facilitating the intronic miRNA maturation. Using this miRNA-expressing system, we have shown for the first time that the intron-derived miRNAs were able to induce strong RNAi effects in not only human and mouse cells but also zebrafish, chicken embryos, and adult mice. Based on the strand complementarity between the designed miRNA and its target gene sequence, we have also developed a miRNA isolation protocol to purify and identify the mature miRNAs generated by the intronic miRNA-expressing system. Several intronic miRNA identities and structures are currently confirmed to be active in vitro and in vivo. According to this proof- of-principle method, we now have the knowledge to design pre-miRNA inserts that are more efficient and effective for the intronic miRNA-expressing system.

Animals↗

PubMed2006

Recognition and cleavage of primary microRNA transcripts.

MicroRNAs (miRNAs) are approx 22-nucleotide (nt)-long, single-stranded, endogenous, noncoding RNAs that are widely expressed in multicellular organisms. This chapter describes methods that allow the overexpression of human miRNAs and also discusses how primary miRNAs (pri-miRNAs), the much longer precursors of mature miRNAs, are processed in human cells, as well as in vitro.

Humans↗

PubMed2006

MicroRNAs and messenger RNA turnover.

Although initially believed to act exclusively as translational repressors, microRNAs (miRNAs) are now known to target complementary messenger RNA (mRNA) transcripts for either translational repression or cleavage via the RNA-induced silencing complex (RISC) ([1], reviewed in ref. 2). The current model postulates that mature miRNAs are incorporated into the RISC, bind target mRNAs based on complementarity, and guide cleavage of mRNA targets with perfect or nearly perfect complementarity and translational repression of targets with lower complementarity (2). The translational repression mechanism of miRNA-mediated gene regulation, which is common in animals but also exists in plants, is not well understood mechanistically. Conversely, miRNA-directed mRNA cleavage by RISC is common in plants, but also occurs in animals (3). This chapter focuses on the mRNA cleavage by miRNA-programmed RISC, and, specifically, on characterizing the products of such cleavage.

Animals↗

PubMed2006

MicroRNAs 143 and 145 are possible common onco-microRNAs in human cancers.

MicroRNAs (miRNAs) are endogenously expressed RNAs 18-24 nucleotides in length that regulate gene expression through translational repression by binding to a target mRNA. It is thought that the expression level of miRNAs, which act like antioncogenes, is frequently reduced in cancers because of chromosome deletion and epigenetic changes. Since the processing of miRNAs has been characterized to be enzymatic in nature, the expression levels of miRNAs are closely associated with the activity and levels of such enzymes. Here, we found that miRNA 143 and 145 expression levels were extremely reduced in colon cancer cells and commonly in the other kinds of cancer cells tested. The transfection of each precursor miRNA into the cells demonstrated a significant growth inhibition in human colon cancer DLD-1 and SW480 cells, and ERK5 was determined to be the target gene of miRNA 143. Since the presence of genomic loci of the miRNAs was confirmed by PCR in the cell lines and the precursor miRNAs exhibited a growth inhibitory effect in DLD-1 and SW480 cells, the early processes such as transcription and enzymatic modification from primary miRNAs to precursor miRNAs seemed to be commonly disturbed. These findings indicate that the miRNAs 143 and 145 could become good tumor markers and provide an important clue in the study of the mechanism of oncogenesis involving miRNAs.

Cell Line, Tumor↗

PubMed2004

The functions of animal microRNAs.

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.

Animals↗

PubMed2004

Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.

MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were discovered in Caenorhabditis elegans, >300 miRNAs were recently documented in animals and plants, both by cloning methods and computational predictions. We present a genome-wide computational approach to detect miRNA genes in the Arabidopsis thaliana genome. Our method is based on the conservation of short sequences between the genomes of Arabidopsis and rice (Oryza sativa) and on properties of the secondary structure of the miRNA precursor. The method was fine-tuned to take into account plant-specific properties, such as the variable length of the miRNA precursor sequences. In total, 91 potential miRNA genes were identified, of which 58 had at least one nearly perfect match with an Arabidopsis mRNA, constituting the potential targets of those miRNAs. In addition to already known transcription factors involved in plant development, the targets also comprised genes involved in several other cellular processes, such as sulfur assimilation and ubiquitin-dependent protein degradation. These findings considerably broaden the scope of miRNA functions in plants.

Arabidopsis↗

PubMed2004

Uridine addition after microRNA-directed cleavage.

One of the important roles of microRNA (miRNA) is to direct the cleavage of messenger RNA (mRNA). However, the mechanisms of decay of the cleaved mRNA products is not well understood. We show that miRNA-directed cleavage products in organisms as diverse as Arabidopsis, mouse, and Epstein-Barr virus have at their 3' ends a stretch (1 to 24 nucleotides) of oligouridine posttranscriptionally added downstream of the cleavage site. This 3' uridine addition, as shown for Arabidopsis, is correlated with decapping and 5' shortening of the cleaved products, suggesting a mechanistic step in the miRNA-directed mRNA decay mechanism.

Animals↗

PubMed2006

Identification of messenger RNAs and microRNAs associated with fragile X mental retardation protein.

Fragile X syndrome, a common form of inherited mental retardation, is caused by the loss of the Fragile X mental retardation protein (FMRP). FMRP, which may regulate translation in neurons, not only associates with specific messenger RNAs (mRNAs) and with microRNAs (miRNAs), but also associates with the components of the miRNA pathway, including the Dicer and Argonaute proteins. It has been proposed that FMRP regulates the translation of its mRNA targets through miRNAs. In this chapter, we describe the protocol to identify the mRNAs and miRNAs associated with FMRP in vivo. The same method could also be applied to other RNA-binding proteins interacting with specific mRNAs or miRNAs.

Animals↗

PubMed2004

Profiling microRNA expression using sensitive cDNA probes and filter arrays.

MicroRNAs (miRNAs) are small noncoding RNAs (approximately 22 nucleotides) that have recently emerged as important regulators of gene expression in both plants and animals. With few exceptions, however, the target genes and the expression levels of most miRNAs are unknown. Here we show that direct random-primed cDNA synthesis on either chemically synthesized small RNAs (21-22 nucleotides) or gel-purified mature miRNAs from human cells can produce specific and sensitive full-length cDNA probes. Using oligonucleotide filter arrays, we demonstrate that the internally labeled cDNA probes are sensitive for detecting differential miRNA expression between untreated and O-tetradecanoylphorbol-13-acetate (TPA)-treated HL60 cells. The present study should facilitate a high-throughput analysis of miRNA expression between samples.

DNA Probes↗

PubMed2003

siRNAs can function as miRNAs.

With the discovery of RNA interference (RNAi) and related phenomena, new regulatory roles attributed to RNA continue to emerge. Here we show, in mammalian tissue culture, that a short interfering RNA (siRNA) can repress expression of a target mRNA with partially complementary binding sites in its 3' UTR, much like the demonstrated function of endogenously encoded microRNAs (miRNAs). The mechanism for this repression is cooperative, distinct from the catalytic mechanism of mRNA cleavage by siRNAs. The use of siRNAs to study translational repression holds promise for dissecting the sequence and structural determinants and general mechanism of gene repression by miRNAs.

3' Untranslated Regions↗