Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,577 individuals using genome-wide and custom genotyping arrays. We identify and annotate 157 loci associated with lipid levels at P < 5 × 10(-8), including 62 loci not previously associated with lipid levels in humans. Using dense genotyping in individuals of European, East Asian, South Asian and African ancestry, we narrow association signals in 12 loci. We find that loci associated with blood lipid levels are often associated with cardiovascular and metabolic traits, including coronary artery disease, type 2 diabetes, blood pressure, waist-hip ratio and body mass index. Our results demonstrate the value of using genetic data from individuals of diverse ancestry and provide insights into the biological mechanisms regulating blood lipids to guide future genetic, biological and therapeutic research.

/pdf/discovery-and-refinement-of-loci-associated-with-lipid-17wc78w8iu.pdf

Discovery and refinement of loci associated with lipid levels

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in regulating gene expression. The majority of miRNAs are transcribed from DNA sequences into primary miRNAs and processed into precursor miRNAs, and finally mature miRNAs. In most cases, miRNAs interact with the 3' untranslated region (3' UTR) of target mRNAs to induce mRNA degradation and translational repression. However, interaction of miRNAs with other regions, including the 5' UTR, coding sequence, and gene promoters, have also been reported. Under certain conditions, miRNAs can also activate translation or regulate transcription. The interaction of miRNAs with their target genes is dynamic and dependent on many factors, such as subcellular location of miRNAs, the abundancy of miRNAs and target mRNAs, and the affinity of miRNA-mRNA interactions. miRNAs can be secreted into extracellular fluids and transported to target cells via vesicles, such as exosomes, or by binding to proteins, including Argonautes. Extracellular miRNAs function as chemical messengers to mediate cell-cell communication. In this review, we provide an update on canonical and non-canonical miRNA biogenesis pathways and various mechanisms underlying miRNA-mediated gene regulations. We also summarize the current knowledge of the dynamics of miRNA action and of the secretion, transfer, and uptake of extracellular miRNAs.

/pdf/overview-of-microrna-biogenesis-mechanisms-of-actions-and-2lluskbdwf.pdf

Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation.

Circular RNAs (circRNAs) are covalently closed, endogenous biomolecules in eukaryotes with tissue-specific and cell-specific expression patterns, whose biogenesis is regulated by specific cis-acting elements and trans-acting factors. Some circRNAs are abundant and evolutionarily conserved, and many circRNAs exert important biological functions by acting as microRNA or protein inhibitors ('sponges'), by regulating protein function or by being translated themselves. Furthermore, circRNAs have been implicated in diseases such as diabetes mellitus, neurological disorders, cardiovascular diseases and cancer. Although the circular nature of these transcripts makes their detection, quantification and functional characterization challenging, recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of state-of-the-art approaches for their identification, and novel approaches to functional characterization are emerging.

The biogenesis, biology and characterization of circular RNAs.

Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.

/pdf/gene-regulation-by-long-non-coding-rnas-and-its-biological-25d7y97amp.pdf

Gene regulation by long non-coding RNAs and its biological functions.

Circular RNAs (circRNAs) represent a class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates. Many of these circRNAs are differently expressed between the normal and cancerous tissues. We further characterize one abundant circRNA derived from Exon2 of the HIPK3 gene, termed circHIPK3. The silencing of circHIPK3 but not HIPK3 mRNA significantly inhibits human cell growth. Via a luciferase screening assay, circHIPK3 is observed to sponge to 9 miRNAs with 18 potential binding sites. Specifically, we show that circHIPK3 directly binds to miR-124 and inhibits miR-124 activity. Our results provide evidence that circular RNA produced from precursor mRNA may have a regulatory role in human cells.

/pdf/circular-rna-profiling-reveals-an-abundant-circhipk3-that-1rgu26weno.pdf

Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis

/pdf/circular-rna-is-enriched-and-stable-in-exosomes-a-promising-es3ucfk5wm.pdf

Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis.

Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer.

Cyclin-dependent kinase inhibitor 1A (CDKN1A), also known as p21Cip1/Waf1, is a master downstream effector of tumor suppressors. In this study, we experimentally demonstrate through a high-throughput luciferase reporter screen that p21Cip1/Waf1 can be directly targeted by nearly 28 microRNAs (miRNAs). The results were further confirmed by a series of mutational analyses and luciferase reporter assays. These 28 miRNAs can substantially inhibit p21Cip1/Waf1 expression, predominantly at translational level. Many of these miRNAs were upregulated in cancers and might serve as modulators of oncogenesis. Furthermore, 8 of these 28 p21-regulating miRNAs are located in the chromosome 19 miRNA cluster, the largest miRNA gene cluster in humans, and they can clearly promote cell proliferation and cell-cycle progression in choriocarcinoma cells. In conclusion, our screening strategy provides an alternative approach to uncovering miRNA modulators of an individual mRNA, and it has identified multiple miRNAs that can suppress p21Cip1/Waf1 expression by directly targeting its 3' untranslated region.

/pdf/multiple-micrornas-modulate-p21cip1-waf1-expression-by-2p25yr0elk.pdf

Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region

Exosomes, which are nanosized endocytic vesicles that are secreted by most cells, contain an abundant cargo of different RNA species that can modulate the behavior of recipient cells and may be used as circulating biomarkers for diseases. Here, we develop a web-accessible database (http://www.exoRBase.org), exoRBase, which is a repository of circular RNA (circRNA), long non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA-seq data analyses of human blood exosomes. Experimental validations from the published literature are also included. exoRBase features the integration and visualization of RNA expression profiles based on normalized RNA-seq data spanning both normal individuals and patients with different diseases. exoRBase aims to collect and characterize all long RNA species in human blood exosomes. The first release of exoRBase contains 58 330 circRNAs, 15 501 lncRNAs and 18 333 mRNAs. The annotation, expression level and possible original tissues are provided. exoRBase will aid researchers in identifying molecular signatures in blood exosomes and will trigger new exosomal biomarker discovery and functional implication for human diseases.

Shenglin Huang

Papers

Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis.

Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer.

Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region

exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes.