Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage

Long noncoding RNAs (lncRNAs) have been shown to play important roles in gene regulatory networks acting in early development. There has been rapid turnover of lncRNA loci during vertebrate evolution, with few human lncRNAs conserved beyond mammals. The sequences of these rare deeply conserved lncRNAs are typically not similar to each other. Here, we characterize HOXA-AS3 and HOXB-AS3, lncRNAs produced from the central regions of the HOXA and HOXB clusters. Sequence-similar orthologs of both lncRNAs are found in multiple vertebrate species and there is evident sequence similarity between their promoters, suggesting that the production of these lncRNAs predates the duplication of the HOX clusters at the root of the vertebrate lineage. This conservation extends to similar expression patterns of the two lncRNAs, in particular in cells transiently arising during early development or in the adult colon. Functionally, the RNA products of HOXA-AS3 and HOXB-AS3 regulate the expression of their overlapping HOX5–7 genes both in HT-29 cells and during differentiation of human embryonic stem cells. Beyond production of paralogous protein-coding and microRNA genes, the regulatory program in the HOX clusters therefore also relies on paralogous lncRNAs acting in restricted spatial and temporal windows of embryonic development and cell differentiation.     

A morphologically conserved nonapoptotic program promotes linker cell death in Caenorhabditis elegans

Apoptosis, cell death characterized by stereotypical morphological features, requires caspase proteases. Nonapoptotic, caspase-independent cell death pathways have been postulated; however, little is known about their molecular constituents or in vivo functions. Here, we show that death of the Caenorhabditis elegans linker cell during development is independent of the ced-3 caspase and all known cell death genes. The linker cell employs a cell-autonomous death program, and a previously undescribed engulfment program is required for its clearance. Dying linker cells display nonapoptotic features, including nuclear crenellation, absence of chromatin condensation, organelle swelling, and accumulation of cytoplasmic membrane-bound structures. Similar features are seen during developmental death of neurons in the vertebrate spinal cord and ciliary ganglia. Linker cell death is controlled by the microRNA let-7 and Zn-finger protein LIN-29, components of the C. elegans developmental timing pathway. We propose that the program executing linker cell death is conserved and used during vertebrate development.     

Prediction of personalized microRNA activity

MicroRNAs have been known to regulate almost all physiological and pathological processes by suppressing their target genes. In humans, more than 1000 microRNAs have been identified, each of which targets dozens or even hundreds of genes. Facing this huge repertoire of microRNA targeting, it is important to identify which microRNAs are active, i.e., down-regulating their targets, in specific physiological or pathological conditions. Predicting active microRNAs is different from predicting microRNA targets because the authentic target genes of a microRNA are often not directly and solely regulated by that microRNA, leading to inconsistent expression changes between the microRNA and its true targets. Several computational programs have been proposed to predict the activity of a microRNA from the expressions of its target genes. These programs performed well when being applied on the expression data obtained from distinct tissue types or from experiments that transfect a microRNA into cells (i.e., non-physiological). But the performance of microRNA activity prediction is not clear on the expression data from the same tissue type in two physiological conditions, e.g., liver tissues from cancer patients and healthy people. In this work, we evaluate the performance of two microRNA activity prediction programs using seven expression data sets, all of which compare samples in two physiological conditions, as well as propose a new approach that predicts microRNA activity with an accuracy of over 80%. Unlike current methods, which predict active microRNAs by comparing two groups of samples, e.g., tumor versus normal, our new approach compares each diseased sample with all the samples in the control group. In other words, it can predict the microRNA activity of a person. In this work, this new application is named to predict “personalized microRNA activity”.     

Computational identification of microRNA targets

Recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of microRNA genes. Many of these microRNAs are thought to regulate the translational expression of other genes by binding to partially complementary sites in messenger RNAs. Phenotypic and expression analysis suggests an important role of microRNAs during development. Therefore, it is of fundamental importance to identify microRNA targets. However, no experimental or computational high-throughput method for target site identification in animals has been published yet. Our main result is a new computational method that is designed to identify microRNA target sites. This method recovers with high specificity known microRNA target sites that have previously been defined experimentally. Based on these results, we present a simple model for the mechanism of microRNA target site recognition. Our model incorporates both kinetic and thermodynamic components of target recognition. When we applied our method to a set of 74 Drosophila melanogaster microRNAs, searching 3'UTR sequences of a predefined set of fly mRNAs for target sites which were evolutionary conserved between D. melanogaster and Drosophila pseudoobscura, we found that many key developmental body patterning genes such as hairy and fushi-tarazu are likely to be translationally regulated by microRNAs.     

Establishment of cells to monitor Microprocessor through fusion genes of microRNA and GFP

Microprocessor, the complex of Drosha and DGCR8, promotes the processing of primary microRNA to precursor microRNA, which is a crucial step for microRNA maturation. So far, no convenient assay systems have been developed for observing this step in vivo.Here we report the establishment of highly sensitive cellular systems where we can visually monitor the function of Microprocessor. During a series of screening of transfectants with fusion genes of the EGFP cDNA and primary microRNA genes, we have obtained certain cell lines where introduction of siRNA against DGCR8 or Drosha strikingly augments GFP signals. In contrast, these cells have not responded to Dicer siRNA; thus they have a unique character that GFP signals should be negatively and specifically correlated to the action of Microprocessor among biogenesis of microRNA.These cell lines can be useful tools for real-time analysis of Microprocessor action in vivo and identifying its novel modulators.     

TGF-beta family factors in Drosophila morphogenesis.

Many Drosophila genes have now been identified with substantial sequence similarity to vertebrate protooncogenes and growth factors. Some of these have been isolated directly by cross-hybridization with vertebrate probes and some have been recognized in the sequences of genes cloned because of their intiguing mutant phenotypes. An example of a gene isolated for its interesting development functions but with homology to a vertebrate growth factor is the Drosophila decapentaplegic gene (dpp). An example of a Drosophila gene isolated by virtue of its sequence conservation is the vgr/60A gene. Both dpp and vgr/60A are members of the transforming growth factor-beta family and are most similar to the human bone morphogenetic proteins. The regulation of the dpp gene by several different groups of pattern formation genes including the dorsal/ventral group, the terminal group, the segment polarity genes, and the homeotic genes indicates that many events in embryogenesis require the cell to cell communication mediated by the secreted dpp protein. The temporal and spatial pattern of vgr/60A expression differs from that of dpp indicating that it may be regulated by different pattern information genes. The experimental advantages of the Drosophila system should permit a better understanding of the importance of growth factor homologs in specific developmental events, aid in establishing the functional interactions between these regulatory molecules, and identify new genes that are important for the biological functions of growth factors. It is likely that some of the newly identified genes will have vertebrate homologs and the analysis of these may be helpful in studies on vertebrate development and tumor biology.     

Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs

Some plant microRNAs have been shown to be de novo generated by inverted duplication from their target genes. Subsequent duplication events potentially generate multigene microRNA families. Within this article we provide supportive evidence for the inverted duplication model of plant microRNA evolution. First, we report that the precursors of four Arabidopsis thaliana microRNA families, miR157, miR158, miR405 and miR447 share nearly identical nucleotide sequences throughout the whole miRNA precursor between the family members. The extent and degree of sequence conservation is suggestive of recent evolutionary duplication events. Furthermore we found that sequence similarities are not restricted to the transcribed part but extend into the promoter regions. Thus the duplication event most probably included the promoter regions as well. Conserved elements in upstream regions of miR163 and its targets were also detected. This implies that the inverted duplication of target genes, at least in certain cases, had included the promoters of the target genes. Sequence conservation within promoters of miRNA families as well as between miRNA and its potential progenitor gene can be exploited for understanding the regulation of microRNA genes.     

Conservation of engrailed-like homeobox sequences during vertebrate evolution

The Drosophila melanogaster developmental gene engrailed (en) is a member of a distinct subfamily of homeobox genes with a wide phylogenetic distribution. Here we report the use of reduced stringency polymerase chain reaction (PCR) to amplify and clone 8 genes related to en from 5 vertebrate species, including representatives of the most ancient vertebrate lineages. Nucleotide and deduced amino acid sequence comparisons between mouse, toad, zebrafish, lamprey and hagfish genes reveal extensive evolutionary conservation, and suggests that 2 en-like genes have been retained in most vertebrate lineages.     

调控DNA损伤修复基因的微小RNA

随着对DNA损伤修复基因研究的深入,其信号转导路径及调控网络也进一步明了,调控DNA损伤修复基因的微小RNA(miRNA)也越来越多地被认识和发现。简要综述了DNA损伤途径中调控主要的损伤修复基因的miRNA,有助于深入阐明DNA损伤修复机制,为开发抗辐射药物和临床上DNA损伤修复异常相关肿瘤的基因治疗提供新的靶点。     

miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature

Background  

MicroRNAs have been discovered as important regulators of gene expression. To identify the target genes of microRNAs, several databases and prediction algorithms have been developed. Only few experimentally confirmed microRNA targets are available in databases. Many of the microRNA targets stored in databases were derived from large-scale experiments that are considered not very reliable. We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories.     

MicroRNA functions in animal development and human disease

Five years into the 'small RNA revolution' it is hard not to share in the excitement about the rapidly unravelling biology of microRNAs. Since the discovery of the first microRNA gene, lin-4, in the nematode Caenorhabditis elegans, many more of these short regulatory RNA genes have been identified in flowering plants, worms, flies, fish, frogs and mammals. Currently, about 2% of the known human genes encode microRNAs. MicroRNAs are essential for development and this review will summarise our current knowledge of animal microRNA function. We will also discuss the emerging links of microRNA biology to stem cell research and human disease, in particular cancer.     

A novel family of ancient vertebrate odorant receptors

Vertebrate odorant receptor (OR) genes have been isolated and characterized in several taxa, including bony fish and mammals. However, the search for more ancient vertebrate OR genes has been unsuccessful to date, indicating that these ancient genes share little sequence identity with previously isolated ORs. The lamprey (Lampetra fluviatilis) olfactory epithelium does not appear to express any of the modern vertebrate ORs previously identified in bony fish and mammals. We have isolated and characterized an ancient family of vertebrate membrane receptors from the olfactory epithelium of the lamprey. Sequence analysis reveals similarities with other Class A (rhodopsin-like) G protein-coupled receptors such as serotonin, dopamine, and histamine receptors, but the expression patterns of members of the new family, as well as certain conserved motifs, strongly suggest that the sequences encode ORs. Sequence similarity within the lamprey OR family is low, and Southern blot analysis suggests reduced-sized subfamilies. This novel vertebrate OR gene family, the most ancient isolated to date, is proposed to be involved in the detection of water-borne molecules in jawless fishes. Lamprey OR genes therefore represent a new level of diversity within the vertebrate OR gene family, but also provide clues as to how vertebrate ORs might have emerged. © 1998 John Wiley & Sons, Inc. J Neurobiol 37: 383–392, 1998     

microRNA及其应用研究进展

microRNA(miRNA)是在多种真核细胞和病毒中发现的一类内源性非编码单链RNA,长约22个核苷酸,在进化上具有高度的保守性。miRNA可以通过碱基互补与靶基因mRNA的特定位点结合,抑制该蛋白合成或诱导该mRNA降解,在生物体生长、发育和疾病发生等过程中发挥着重要的作用。我们简要叙述了miRNA的特点和作用机制,并对miRNA在基因表达调控、胚胎干细胞调控及免疫调节等方面的最新进展进行了综述。