Large intergenic RNAs (lincRNA) are involved in numerous cellular processes, including many relevant to normal development and cancer progression. In my doctoral research, we hypothesized that lncRNAs are functionally important to human endothelial biology, more specifically, to the process of human blood vessel formation or angiogenesis. To detect lincRNAs that are functionally important to human angiogenesis, a custom microarray was used to profile long noncoding transcripts in human vascular endothelium in two-dimensional versus three-dimensional pro-angiogenic cultures, with or without VEGF-A165. We identified a VEGF-A-responsive lincRNA near the VEGFR1 gene, which we termed lincRNA-VEGFR1 (LIVE1). Unbiased mRNA microarrays defined a number of potential target genes when LIVE1 was functionally disrupted using RNA interference. Importantly, knockdown and over-expression studies indicated that LIVE1 exerts transcriptional control over VEGFR1 as well as other VEGF receptors and direct angiogenesis in vitro. Furthermore, we found that LIVE1 is highly expressed in glioblastoma, and is enriched in glioma stem cell (GSC) fractions and neoplastic endothelial progenitor populations. In vivo knockdown of LIVE1 in a glioblastoma xenograft model decreased microvascular density, vascular perfusion, pericyte coverage, tumor volume and slowed tumour progression. Our results establish LIVE1 as a key mediator of angiogenesis and demonstrate the potential of lincRNA-based therapeutics.

Large intergenic RNAs (lincRNA) are involved in numerous cellular processes, including many relevant to normal development and cancer progression. In my doctoral research, we hypothesized that lncRNAs are functionally important to human endothelial biology, more specifically, to the process of human blood vessel formation or angiogenesis. To detect lincRNAs that are functionally important to human angiogenesis, a custom microarray was used to profile long noncoding transcripts in human vascular endothelium in two-dimensional versus three-dimensional pro-angiogenic cultures, with or without VEGF-A165. We identified a VEGF-A-responsive lincRNA near the VEGFR1 gene, which we termed lincRNA-VEGFR1 (LIVE1). Unbiased mRNA microarrays defined a number of potential target genes when LIVE1 was functionally disrupted using RNA interference. Importantly, knockdown and over-expression studies indicated that LIVE1 exerts transcriptional control over VEGFR1 as well as other VEGF receptors and direct angiogenesis in vitro. Furthermore, we found that LIVE1 is highly expressed in glioblastoma, and is enriched in glioma stem cell (GSC) fractions and neoplastic endothelial progenitor populations. In vivo knockdown of LIVE1 in a glioblastoma xenograft model decreased microvascular density, vascular perfusion, pericyte coverage, tumor volume and slowed tumour progression. Our results establish LIVE1 as a key mediator of angiogenesis and demonstrate the potential of lincRNA-based therapeutics.

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering similar to 90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analysis workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Here we validate lincRNA catalogs generated with Evolinc-I against previously annotated Arabidopsis and human lincRNA data. Evolinc-I recapitulated earlier findings and uncovered an additional 70 Arabidopsis and 43 human lincRNAs. We demonstrate the usefulness of Evolinc-II by examining the evolutionary histories of a public dataset of 5,361 Arabidopsis lincRNAs. We used Evolinc-II to winnow this dataset to 40 lincRNAs conserved across species in Brassicaceae. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). These latter analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse's Discovery Environment and is free for use by researchers.

Odorantes são detectados por centenas de receptores olfatórios (ORs) que pertencem à superfamília dos receptores acoplados à proteína G. Estes receptores são expressos nos neurônios sensoriais olfatórios localizados na cavidade nasal. Cada neurônio sensorial olfatório expressa um único alelo de gene OR de uma grande família de genes OR. Este padrão característico da expressão de genes OR resulta na formação de um mapa olfatório espacial no bulbo olfatório, que é necessário para a discriminação de odorantes pelo sistema olfatório. Os mecanismos envolvidos nesta regulação ainda não são bem conhecidos. O DNA genômico em neurônios olfatórios é coberto com marcas repressivas de metilação de histonas, indicando que a regulação da estrutura da cromatina deve desempenhar um papel importante na regulação da expressão de genes OR. Trabalhos anteriores demonstraram que RNAs não codificadores (ncRNAs) estão envolvidos na deposição de marcas de histonas em determinados genes. No entanto, os ncRNAs expressos no epitélio olfatório ainda não são conhecidos. Neste trabalho, identificamos e catalogamos o repertório completo de ncRNAs anotados, incluindo os miRNAs, expressos no epitélio olfatório de camundongos recémnascidos e adultos. Muitos destes, apesar de já anotados como ncRNAs, ainda não foram descritos na literatura como expressos no MOE. Identificamos ao todo 1161 miRNAs e 295 lincRNAs expressos no epitélio olfatório, e pudemos verificar como os níveis de expressão destes RNAs variam durante o desenvolvimento. A partir deste repertório, selecionamos lincRNAs que são preferencialmente expressos no epitélio olfatório quando comparados a outros tecidos de camundongo. Dez destes lincRNAs foram selecionados para validação utilizando-se RT-PCR. Cinco lincRNAs foram validados e analisados quanto à sua expressão em diferentes tecidos. Nosso trabalho estabelece uma plataforma de dados que permitirá o estudo do papel desempenhado por ncRNAs no epitélio olfatório. Além disto, os nossos resultados mostram que a abordagem utilizada permite a identificação de novos lincRNAs que apresentam expressão restrita ou preferencial no epitélio olfatório, e que, portanto, devem apresentar uma função relevante para o olfato. / Odorants are detected by hundreds of odorant receptors (ORs) which belong to the superfamily of G protein-coupled receptors. These receptors are expressed in the olfactory sensory neurons of the nose. Each olfactory sensory neuron expresses one single OR gene allele from a large family of OR genes. This characteristic pattern of OR gene expression results in the formation of a spatial olfactory map in the olfactory bulb, which is required for odorant discrimination by the olfactory system. The mechanisms involved in this regulation are unknown. OR genomic DNA in olfactory neurons is covered with repressive histone methylation marks, indicating that the chromatin structure should play an important role in the regulation of OR gene expression. Previous studies suggest that noncoding RNAs (ncRNAs) are involved in the deposition of histone marks in certain genes. However, the ncRNAs expressed in the olfactory epithelium are completely unknown. In this work, we used RNA-seq to identify and catalogue the complete repertoire of ncRNAs, including miRNAs, expressed in the olfactory epithelium from newborn and adult mice. In this way, we were able to identify 1161 miRNAs and 295 lincRNAs and analyze how their levels of expression varies during development. Out of these repertoire, we selected lincRNAs that are preferentially expressed in the olfactory epithelium when compared to other mouse tissues. Ten out of these lincRNAs were selected for validation by using RTPCR, and five of them could be validated and further analyzed. Our work establishes a data platform which will enable the study of the role played by ncRNAs in the olfactory epithelium. In addition, our results show that our approach can be successfully used to identify ncRNAs that are restrictedly or preferentially expressed in the olfactory epithelium, and which therefore must be relevant for olfaction.

Genomweite Bemühungen haben eine große Anzahl langer nichtkodierender RNAs (lncRNAs) identifiziert, obwohl ihre möglichen Funktionen weitgehend rätselhaft bleiben. Hier verwendeten wir ein System zur synchronisierten Blüteninduktion in Arabidopsis, um 4106 blütenbezogene lange intergene RNAs (lincRNAs) zu identifizieren. Blütenbezogene lincRNAs sind typischerweise mit funktionellen Enhancern assoziiert, die bidirektional transkribiert werden und mit verschiedenen funktionellen Genmodulen assoziiert sind, die mit der Entwicklung von Blütenorganen zusammenhängen, die durch Koexpressionsnetzwerkanalyse aufgedeckt wurden. Die Master-regulatorischen Transkriptionsfaktoren (TFs) APETALA1 (AP1) und SEPALLATA3 (SEP3) binden an lincRNA-assoziierte Enhancer. Die Bindung dieser TFs korreliert mit der Zunahme der lincRNA-Transkription und fördert möglicherweise die Zugänglichkeit von Chromatin an Enhancern, gefolgt von der Aktivierung einer Untergruppe von Zielgenen. Darüber hinaus ist die Evolutionsdynamik von lincRNAs in Pflanzen, einschließlich nicht blühender Pflanzen, noch nicht bekannt, und das Expressionsmuster in verschiedenen Pflanzenarten war ziemlich unbekannt. Hier identifizierten wir Tausende von lincRNAs in 26 Pflanzenarten, einschließlich nicht blühender Pflanzen. Ein direkter Vergleich von lincRNAs zeigt, dass die meisten lincRNAs speziesspezifisch sind und das Expressionsmuster von lincRNAs einen hohen Transkriptionsumsatz nahe legt. Darüber hinaus zeigen konservierte lincRNAs eine aktive Regulation durch Transkriptionsfaktoren wie AP1 und SEP3. Konservierte lincRNAs zeigen eine konservierte blütenbezogene Funktionalität sowohl in der Brassicaceae- als auch in der Grasfamilie. Die Evolutionslandschaft von lincRNAs in Pflanzen liefert wichtige Einblicke in die Erhaltung und Funktionalität von lincRNAs. / Genome-wide efforts have identified a large number of long non-coding RNAs (lncRNAs), although their potential functions remain largely enigmatic. Here, we used a system for synchronized floral induction in Arabidopsis to identify 4106 flower-related long intergenic RNAs (lincRNAs). Flower-related lincRNAs are typically associated with functional enhancers which are bi-directionally transcribed and are associated with diverse functional gene modules related to floral organ development revealed by co-expression network analysis. The master regulatory transcription factors (TFs) APETALA1 (AP1) and SEPALLATA3 (SEP3) bind to lincRNA-associated enhancers. The binding of these TFs is correlated with the increase in lincRNA transcription and potentially promotes chromatin accessibility at enhancers, followed by activation of a subset of target genes. Furthermore, the evolutionary dynamics of lincRNAs in plants including non-flowering plants still remain to be elusive and the expression pattern in different plant species was quite unknown. Here, we identified thousands of lincRNAs in 26 plant species including non-flowering plants, and allow us to infer sequence conserved and synteny based homolog lincRNAs, and explore conserved characteristics of lincRNAs during plants evolution. Direct comparison of lincRNAs reveals most lincRNAs are species-specific and the expression pattern of lincRNAs suggests their high evolutionary gain and loss. Moreover, conserved lincRNAs show active regulation by transcriptional factors such as AP1 and SEP3. Conserved lincRNAs demonstrate conserved flower related functionality in both the Brassicaceae and grass family. The evolutionary landscape of lincRNAs in plants provide important insights into the conservation and functionality of lincRNAs.