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| Open AccessSmall RNA zippers lock miRNA molecules and block miRNA function in mammalian cells
MicroRNAs regulate a wide range of biological processes and being able to inhibit their function could allow the development of therapeutic options. Here the authors describe a ‘small RNA zipper’ that sequesters miRNAs by forming a chain of DNA:RNA duplexes.
- Lingyu Meng
- , Cuicui Liu
- & Zuoren Yu
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Article
| Open AccessNon-invasive imaging using reporter genes altering cellular water permeability
Magnetic resonance imaging combined with molecular reporters can visualise cellular functions in intact organisms. Here Mukherjeeet al. present a cellular imaging approach based on intracellular changes in water diffusion using human aquaporin 1 gene as a genetically encoded reporter for MRI.
- Arnab Mukherjee
- , Di Wu
- & Mikhail G. Shapiro
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| Open AccessProduction of individualized V gene databases reveals high levels of immunoglobulin genetic diversity
Current databases of V genes for antibody repertoire have limitations. Here Corcoran et al. develop a computational approach named IgDiscover that can identify germline V gene sequences from expressed antibody repertoires to high specificity and completeness.
- Martin M. Corcoran
- , Ganesh E. Phad
- & Gunilla B. Karlsson Hedestam
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| Open AccessComparative survey of the relative impact of mRNA features on local ribosome profiling read density
Ribosome profiling data can suffer from uneven coverage which hampers estimation of elongation rates. Connor et al.present an enhanced data smoothing method for Ribo-seq data and highlight significant variability in sequence determinants of ribosome density in publicly available data sets.
- Patrick B. F. O’Connor
- , Dmitry E. Andreev
- & Pavel V. Baranov
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| Open AccessIn vivo imaging of clock gene expression in multiple tissues of freely moving mice
The circadian rhythms of peripheral clocks are difficult to study. Here the authors demonstrate a technique to image clock gene expression simultaneously in various tissues of freely moving mice, and use it to show that a long duration light pulse resets the rhythms in the olfactory bulb faster than other tissues.
- Toshiyuki Hamada
- , Kenneth Sutherland
- & Ken-ichi Honma
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| Open AccessNuclear RNA-seq of single neurons reveals molecular signatures of activation
The molecular dynamics associated with neuronal activation patterns in vivo are unclear. Lacar et al. perform single-nuclei RNA-sequencing of hippocampal neurons from mice exposed to a novel environment, and identify large-scale transcriptome changes in individual neurons associated with the experience.
- Benjamin Lacar
- , Sara B. Linker
- & Fred H. Gage
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| Open AccessSingle-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
The spatial organization of the genome within the nucleus impacts many processes. Here the authors combine oligo-based DNA FISH with single-molecule super-resolution microscopy to image single-copy genomic regions and, taking advantage of SNPs, distinguish allelic regions of homologous chromosomes.
- Brian J. Beliveau
- , Alistair N. Boettiger
- & Chao-ting Wu
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| Open AccessMulti-spectral fluorescent reporter influenza viruses (Color-flu) as powerful tools for in vivo studies
Animal models are important to study organismal immune responses to infection with influenza viruses. Here, Fukuyama et al.report a new generation of fluorescently labelled influenza viruses that facilitate the study of viral infections in animal models at cellular level.
- Satoshi Fukuyama
- , Hiroaki Katsura
- & Yoshihiro Kawaoka
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| Open AccessCapture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
Multiple regulatory elements distant from their targets on the linear genome can influence gene expression through chromatin looping. Here, the authors report an improved chromosome conformation capture approach that can be used to identify long-range chromatin interactions in cancer risk loci.
- Roland Jäger
- , Gabriele Migliorini
- & Richard S. Houlston
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High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry
Flow cytometry allows high-throughput analysis of multiple proteins in individual cells, but relies on availability of antibodies. Here Porichis et al.report a sensitive method for multi-parameter flow cytometric and imaging detection of proteins together with mRNA or miRNA at the single-cell level.
- Filippos Porichis
- , Meghan G. Hart
- & Daniel E. Kaufmann
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Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
Differential gene expression experiments yield quantitative insight into biological activity and may be important in disease classification and treatment. Here, the authors analyse external spike-in RNA controls to provide a standard method to assess and compare experiment performance.
- Sarah A. Munro
- , Steven P. Lund
- & Marc Salit
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The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes
The contribution of expressed pseudogenes to cancer pathogenesis is unclear. In this study, Han et al.analyse RNA-seq data from The Cancer Genome Atlas and demonstrate the potential of pseudogenes for investigating cancer mechanisms and discovering prognostic biomarkers.
- Leng Han
- , Yuan Yuan
- & Han Liang
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Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas
Directly comparing patterns of gene expression in matched normal and cancerous tissues provides a powerful tool to identify drivers of tumour progression. Here the authors discover genes that are recruited into mitotic signalling networks in lung adenocarcinoma.
- Il-Jin Kim
- , David Quigley
- & Allan Balmain
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A photoconvertible fluorescent reporter to track chaperone-mediated autophagy
Soluble cytosolic proteins can be degraded in lysosomes by chaperone-mediated autophagy, however, the current method to measure this process requires isolation of lysosomes. Now, a fluorescent reporter is described that can measure this type of autophagy in intact cells.
- Hiroshi Koga
- , Marta Martinez-Vicente
- & Ana Maria Cuervo