CompMoby: Comparative MobyDick for detection of cis-regulatory motifs

<p>Abstract</p> <p>Background</p> <p>The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions of genes while sequence elements within the 3' untranslated regions of mRNAs play important roles in post-transcriptional regulation such as mRNA stability and translation efficiency. Identifying cis-regulatory elements, or motifs, in multicellular eukaryotes is more difficult compared to unicellular eukaryotes due to the larger intergenic sequence space and the increased complexity in regulation. Experimental techniques for discovering functional elements are often time consuming and not easily applied on a genome level. Consequently, computational methods are advantageous for genome-wide cis-regulatory motif detection. To decrease the search space in metazoans, many algorithms use cross-species alignment, although studies have demonstrated that a large portion of the binding sites for the same trans-acting factor do not reside in alignable regions. Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans.</p> <p>Results</p> <p>We present CompMoby (Comparative MobyDick), software developed to identify cis-regulatory binding sites at both the transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factors. The CompMoby algorithm was previously shown to identify cis-regulatory binding sites in upstream regions of genes co-regulated in embryonic stem cells. In this paper, we extend the software to identify putative cis-regulatory motifs in 3' UTR sequences and verify our results using experimentally validated data sets in mouse and human. We also detail the implementation of CompMoby into a user-friendly tool that includes a web interface to a streamlined analysis. Our software allows detection of motifs in the following three categories: one, those that are alignable and conserved; two, those that are conserved but not alignable; three, those that are species specific. One of the output files from CompMoby gives the user the option to decide what category of cis-regulatory element to experimentally pursue based on their biological problem. Using experimentally validated biological datasets, we demonstrate that CompMoby is successful in detecting cis-regulatory target sites of known and novel trans-acting factors at the transcriptional and post-transcriptional levels.</p> <p>Conclusion</p> <p>CompMoby is a powerful software tool for systematic <it>de novo </it>discovery of evolutionarily conserved and nonconserved cis-regulatory sequences involved in transcriptional or post-transcriptional regulation in metazoans. This software is freely available to users at <url>http://genome.ucsf.edu/compmoby/</url>.</p

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer

Opposing microRNAs Regulate Mouse Embryonic Stem Cell Self-Renewal

When an embryonic stem cell (ESC) differentiates, it must both silence the ESC self-renewal program as well as activate new tissue-specific programs. In the absence of DGCR8, a protein required for microRNA (miRNA) biogenesis, mouse ESCs are unable to silence the ESC self-renewal program during differentiation. Screening by reintroduction of all known miRNAs one at a time into Dgcr8 -/- ESCs in differentiation-inducing conditions enabled the identification of numerous miRNAs which silence the ESC self-renewal program. Expression levels of many of these miRNAs are induced during ESC differentiation. Of these miRNAs, most are expressed in specific cell types whereas a single family, the let-7 family, is broadly expressed across differentiated cell types. In various assays of ESC self-renewal, let-7 family miRNAs rescue the inability of Dgcr8 -/- ESCs to silence self-renewal. However, let-7 miRNAs failed to silence self-renewal in wild-type ESCs, suggesting that ESC-expressed miRNAs inhibit the capacity of let-7 to silence self-renewal. Indeed, introduction of the embryonic stem cell cycle regulating (ESCC) miRNAs blocked the capacity of let-7 to induce silencing of self-renewal in Dgcr8 -/- ESCs. mRNA profiling and bioinformatic analysis showed that let-7 and ESCC miRNAs function in part through opposite regulation of Myc transcription factors and Lin28. The opposing regulation of these factors contributes to a network, which reinforces the switch from a self-renewing to a differentiated cell state. These results suggested that additional screen positive miRNAs function in similar antagonistic networks with ESCC miRNAs. Indeed, introduction of the ESCC miRNAs prevented the additional screen positive miRNAs from silencing self-renewal in Dgcr8 -/- ESCs. mRNA profiling and bioinformatic analyses suggest that screen positive miRNAs and the ESCC miRNAs oppositely regulate multiple molecular pathways including the G1/S cell cycle transition. Inhibition of the G1/S transition in wild-type ESCs promotes loss of markers of ESC self-renewal. These findings suggest that miRNAs through destabilization of the ESC cell-cycle may promote loss of ESC self-renewal during differentiation. These studies show that different classes of miRNAs positioned in the context of complex biological networks function to either promote or antagonize ESC self-renewal

Opposing microRNA families regulate self-renewal in mouse embryonic stem cells.

When embryonic stem cells (ESCs) differentiate, they must both silence the ESC self-renewal program and activate new tissue-specific programs. In the absence of DGCR8 (Dgcr8(-/-)), a protein required for microRNA (miRNA) biogenesis, mouse ESCs are unable to silence self-renewal. Here we show that the introduction of let-7 miRNAs-a family of miRNAs highly expressed in somatic cells-can suppress self-renewal in Dgcr8(-/-) but not wild-type ESCs. Introduction of ESC cell cycle regulating (ESCC) miRNAs into the Dgcr8(-/-) ESCs blocks the capacity of let-7 to suppress self-renewal. Profiling and bioinformatic analyses show that let-7 inhibits whereas ESCC miRNAs indirectly activate numerous self-renewal genes. Furthermore, inhibition of the let-7 family promotes de-differentiation of somatic cells to induced pluripotent stem cells. Together, these findings show how the ESCC and let-7 miRNAs act through common pathways to alternatively stabilize the self-renewing versus differentiated cell fates

Routine ultrasound screening for abdominal aortic aneurysm among 65- and 75-year-old men in a city of 200,000 inhabitants.

Unruptured abdominal aortic aneurysm (AAA) is seldom recognized. Thus it is difficult to know whether the incidence of AAA in the general population is high enough to warrant routine screening at least in men after a certain age. Ultrasound screening studies to evaluate the incidence of AAA have been carried out in several English-speaking and Scandinavian countries. The purpose of this report is to describe the results of a study carried out in Belgium. All 65- and 75-year-old men living in the city of Liege, Belgium, were given the opportunity to undergo a free ultrasound examination. Only 41% of the target population was examined. AAA defined as abdominal aortic diameter of >30 mm was observed in 28 subjects (incidence: 3.8%). Mean abdominal aortic diameter was 34.7 mm. A diameter >29 mm was observed in 33 subjects (incidence 4.5%). Mean abdominal aortic diameter was 30.4 mm. On the basis of epidemiological data collected, a high-risk population for AAA was identified. Arterial hypertension (p < 0.05), previous coronary artery surgery (p < 0.05), and smoking (p < 0.06) were more common in subjects with than without AAA. The overall cost of screening was $18.175. The cost per AAA diagnosed was$551.00

miR-294/miR-302 Promotes Proliferation, Suppresses G1-S Restriction Point, and Inhibits ESC Differentiation through Separable Mechanisms

The miR-294 and miR-302 microRNAs promote the abbreviated G1 phase of the embryonic stem cell (ESC) cell cycle and suppress differentiation induced by let-7. Here, we evaluated the role of the retinoblastoma (Rb) family proteins in these settings. Under normal growth conditions, miR-294 promoted the rapid G1-S transition independent of the Rb family. In contrast, miR-294 suppressed the further accumulation of cells in G1 in response to nutrient deprivation and cell-cell contact in an Rb-dependent fashion. We uncovered five additional miRNAs (miR-26a, miR-99b, miR-193, miR-199a-5p, and miR-218) that silenced ESC self-renewal in the absence of other miRNAs, all of which were antagonized by miR-294 and miR-302. Four of the six differentiation-inducing miRNAs induced an Rb-dependent G1 accumulation. However, all six still silenced self-renewal in the absence of the Rb proteins. These results show that the miR-294/miR-302 family acts through Rb-dependent and -independent pathways to regulate the G1 restriction point and the silencing of self-renewal, respectively