Ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mRNA translation. Using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beginning of open reading frames in response to stress. Based on the initial studies, the importance of adding or omitting translation inhibitors, such as cycloheximide, was noted as it markedly affected ribosome coverage profiles. For that reason, many recent studies omitted translation inhibitors in the culture medium. Here, we investigate the influence of ranging cycloheximide concentrations on ribosome profiles in Saccharomyces cerevisiae and demonstrate that increasing the drug concentration can overcome some of the artifacts. We subjected cells to various manipulations and show that neither oxidative stress nor heat shock nor amino acid starvation affect translation elongation. Instead, the observations in the initial studies are the result of cycloheximide-inflicted artifacts. Likewise, we find little support for short upstream reading frames to be involved in widespread protein synthesis regulation under stress conditions. Our study highlights the need for better standardization of ribosome profiling methods.
Hyeshik Chang
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Translation inhibitors cause abnormalities in ribosome profiling experiments
3'LIFE: a functional assay to detect miRNA targets in high-throughput
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3'untranslated regions (3'UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3'UTRs, called Luminescent Identification of Functional Elements in 3'UTRs (3'LIFE). We demonstrate the feasibility of 3'LIFE using a data set of 275 human 3'UTRs and two cancer-relevant miRNAs, let-7c and miR-10b, and compare our results to alternative methods to detect miRNA targets throughout the genome. We identify a large number of novel gene targets for these miRNAs, with only 32% of hits being bioinformatically predicted and 27% directed by non-canonical interactions. Functional analysis of target genes reveals consistent roles for each miRNA as either a tumor suppressor (let-7c) or oncogenic miRNA (miR-10b), and preferentially target multiple genes within regulatory networks, suggesting 3'LIFE is a rapid and sensitive method to detect miRNA targets in high-throughput.
The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms
Post-transcriptional gene regulation mechanisms decide on cellular mRNA activities. Essential gatekeepers of post-transcriptional mRNA regulation are broadly conserved mRNA-modifying enzymes, such as cytoplasmic poly(A) polymerases (cytoPAPs). Although these non-canonical nucleotidyltransferases efficiently elongate mRNA poly(A) tails in artificial tethering assays, we still know little about their global impact on poly(A) metabolism and their individual molecular roles in promoting protein production in organisms. Here, we use the animal model Caenorhabditis elegans to investigate the global mechanisms of two germline-enriched cytoPAPs, GLD-2 and GLD-4, by combining polysome profiling with RNA sequencing. Our analyses suggest that GLD-2 activity mediates mRNA stability of many translationally repressed mRNAs. This correlates with a general shortening of long poly(A) tails in gld-2-compromised animals, suggesting that most if not all targets are stabilized via robust GLD-2-mediated polyadenylation. By contrast, only mild polyadenylation defects are found in gld-4-compromised animals and few mRNAs change in abundance. Interestingly, we detect a reduced number of polysomes in gld-4 mutants and GLD-4 protein co-sediments with polysomes, which together suggest that GLD-4 might stimulate or maintain translation directly. Our combined data show that distinct cytoPAPs employ different RNA-regulatory mechanisms to promote gene expression, offering new insights into translational activation of mRNAs.
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers
In the resurging field of RNA modifications, quantification is a bottleneck blocking many exciting avenues. With currently over 150 known nucleoside alterations, detection and quantification methods must encompass multiple modifications for a comprehensive profile. LC–MS/MS approaches offer a perspective for comprehensive parallel quantification of all the various modifications found in total RNA of a given organism. By feeding 13C-glucose as sole carbon source, we have generated a stable isotope-labeled internal standard (SIL-IS) for bacterial RNA, which facilitates relative comparison of all modifications. While conventional SIL-IS approaches require the chemical synthesis of single modifications in weighable quantities, this SIL-IS consists of a nucleoside mixture covering all detectable RNA modifications of Escherichia coli, yet in small and initially unknown quantities. For absolute in addition to relative quantification, those quantities were determined by a combination of external calibration and sample spiking of the biosynthetic SIL-IS. For each nucleoside, we thus obtained a very robust relative response factor, which permits direct conversion of the MS signal to absolute amounts of substance. The application of the validated SIL-IS allowed highly precise quantification with standard deviations <2% during a 12-week period, and a linear dynamic range that was extended by two orders of magnitude.
RNA interference: nuclear Dicer makes the cut.
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Related Articles |
RNA interference: nuclear Dicer makes the cut.
Nat Rev Mol Cell Biol. 2014 Jun;15(6):366-7
Authors: Du Toit A
PMID: 24854784 [PubMed - indexed for MEDLINE]
PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.
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Related Articles |
PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.
Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11467-72
Authors: Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, de Hoon MJ
Abstract
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found that mature miR-21, the most widely researched miRNA because of its importance in human disease, is produced in two prevalent isomiR forms that differ by 1 nt at their 3' end, and moreover that the 3' end of miR-21 is posttranscriptionally adenylated by the noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase in the miR-21 expression level, suggesting that PAPD5-mediated adenylation of miR-21 leads to its degradation. Exoribonuclease knockdown experiments followed by small-RNA sequencing suggested that PARN degrades miR-21 in the 3'-to-5' direction. In accordance with this model, microarray expression profiling demonstrated that PAPD5 knockdown results in a down-regulation of miR-21 target mRNAs. We found that disruption of the miR-21 adenylation and degradation pathway is a general feature in tumors across a wide range of tissues, as evidenced by data from The Cancer Genome Atlas, as well as in the noncancerous proliferative disease psoriasis. We conclude that PAPD5 and PARN mediate degradation of oncogenic miRNA miR-21 through a tailing and trimming process, and that this pathway is disrupted in cancer and other proliferative diseases.
PMID: 25049417 [PubMed - indexed for MEDLINE]
LongTarget: A tool to predict lncRNA DNA-binding motifs binding sites via Hoogsteen base-pairing analysis.
| Related Articles |
LongTarget: A tool to predict lncRNA DNA-binding motifs binding sites via Hoogsteen base-pairing analysis.
Bioinformatics. 2014 Sep 26;
Authors: He S, Zhang H, Liu H, Zhu H
Abstract
MOTIVATION: In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases (DNMTs) and polycomb repressive complexes (PRCs), which both lack sequence-specific DNA-binding motifs, are recruited by long noncoding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNA-binding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program (LongTarget) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide.
PMID: 25262155 [PubMed - as supplied by publisher]
Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.
Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.
Nucleic Acids Res. 2014 Sep 30;
Authors: Gu S, Zhang Y, Jin L, Huang Y, Zhang F, Bassik MC, Kampmann M, Kay MA
Abstract
The use of RNA interference is becoming routine in scientific discovery and treatment of human disease. However, its applications are hampered by unwanted effects, particularly off-targeting through miRNA-like pathways. Recent studies suggest that the efficacy of such off-targeting might be dependent on binding stability. Here, by testing shRNAs and siRNAs of various GC content in different guide strand segments with reporter assays, we establish that weak base pairing in both seed and 3' regions is required to achieve minimal off-targeting while maintaining the intended on-target activity. The reduced off-targeting was confirmed by RNA-Seq analyses from mouse liver RNAs expressing various anti-HCV shRNAs. Finally, our protocol was validated on a large scale by analyzing results of a genome-wide shRNA screen. Compared with previously established work, the new algorithm was more effective in reducing off-targeting without jeopardizing on-target potency. These studies provide new rules that should significantly improve on siRNA/shRNA design.
PMID: 25270879 [PubMed - as supplied by publisher]
mRNA-based therapeutics — developing a new class of drugs
Nature Reviews Drug Discovery 13, 759 (2014). doi:10.1038/nrd4278
Authors: Ugur Sahin, Katalin Karikó & Özlem Türeci
In vitro transcribed (IVT) mRNA has recently come into focus as a potential new drug class to deliver genetic information. Such synthetic mRNA can be engineered to transiently express proteins by structurally resembling natural mRNA. Advances in addressing the inherent challenges of this drug
Rbfox3 controls the biogenesis of a subset of microRNAs
Nature Structural & Molecular Biology 21, 901 (2014). doi:10.1038/nsmb.2892
Authors: Kee K Kim, Yanqin Yang, Jun Zhu, Robert S Adelstein & Sachiyo Kawamoto
The RNA exosome promotes transcription termination of backtracked RNA polymerase II
Nature Structural & Molecular Biology 21, 919 (2014). doi:10.1038/nsmb.2893
Authors: Jean-François Lemay, Marc Larochelle, Samuel Marguerat, Sophie Atkinson, Jürg Bähler & François Bachand
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
Nature Biotechnology 32, 1053 (2014). doi:10.1038/nbt.2967
Authors: Alex A Pollen, Tomasz J Nowakowski, Joe Shuga, Xiaohui Wang, Anne A Leyrat, Jan H Lui, Nianzhen Li, Lukasz Szpankowski, Brian Fowler, Peilin Chen, Naveen Ramalingam, Gang Sun, Myo Thu, Michael Norris, Ronald Lebofsky, Dominique Toppani, Darnell W Kemp, Michael Wong, Barry Clerkson, Brittnee N Jones, Shiquan Wu, Lawrence Knutsson, Beatriz Alvarado, Jing Wang, Lesley S Weaver, Andrew P May, Robert C Jones, Marc A Unger, Arnold R Kriegstein & Jay A A West
Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships but require efficient methods for cell capture and mRNA sequencing. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths, the limitations of shallow sequencing have not been investigated directly. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (∼50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In the developing cortex, we identify diverse cell types, including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.
Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping
Nature Biotechnology 32, 1019 (2014). doi:10.1038/nbt.2959
Authors: Paula J P de Vree, Elzo de Wit, Mehmet Yilmaz, Monique van de Heijning, Petra Klous, Marjon J A M Verstegen, Yi Wan, Hans Teunissen, Peter H L Krijger, Geert Geeven, Paul P Eijk, Daoud Sie, Bauke Ylstra, Lorette O M Hulsman, Marieke F van Dooren, Laura J C M van Zutven, Ans van den Ouweland, Sjef Verbeek, Ko Willems van Dijk, Marion Cornelissen, Atze T Das, Ben Berkhout, Birgit Sikkema-Raddatz, Eva van den Berg, Pieter van der Vlies, Desiree Weening, Johan T den Dunnen, Magdalena Matusiak, Mohamed Lamkanfi, Marjolijn J L Ligtenberg, Petra ter Brugge, Jos Jonkers, John A Foekens, John W Martens, Rob van der Luijt, Hans Kristian Ploos van Amstel, Max van Min, Erik Splinter & Wouter de Laat
How deep is enough in single-cell RNA-seq?
Nature Biotechnology 32, 1005 (2014). doi:10.1038/nbt.3039
Authors: Aaron M Streets & Yanyi Huang
Guidelines for determining sequencing depth facilitate transcriptome profiling of single cells in heterogeneous populations.
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
Source:Cell
Author(s): Luke A. Gilbert , Max A. Horlbeck , Britt Adamson , Jacqueline E. Villalta , Yuwen Chen , Evan H. Whitehead , Carla Guimaraes , Barbara Panning , Hidde L. Ploegh , Michael C. Bassik , Lei S. Qi , Martin Kampmann , Jonathan S. Weissman
While the catalog of mammalian transcripts and their expression levels in different cell types and disease states is rapidly expanding, our understanding of transcript function lags behind. We present a robust technology enabling systematic investigation of the cellular consequences of repressing or inducing individual transcripts. We identify rules for specific targeting of transcriptional repressors (CRISPRi), typically achieving 90%–99% knockdown with minimal off-target effects, and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9. Together they enable modulation of gene expression over a ∼1,000-fold range. Using these rules, we construct genome-scale CRISPRi and CRISPRa libraries, each of which we validate with two pooled screens. Growth-based screens identify essential genes, tumor suppressors, and regulators of differentiation. Screens for sensitivity to a cholera-diphtheria toxin provide broad insights into the mechanisms of pathogen entry, retrotranslocation and toxicity. Our results establish CRISPRi and CRISPRa as powerful tools that provide rich and complementary information for mapping complex pathways.
Graphical abstract
Teaser
Genome-scale-specific targeting of transcriptional repressors (CRISPRi) and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9 have been applied to growth and toxin-resistance screens, establishing CRISPRi and CRISPRa as powerful tools that provide rich and complementary information.Looking at LncRNAs with the Ribozyme Toolkit
Source:Molecular Cell, Volume 56, Issue 1
Author(s): Anna Marie Pyle
A diverse population of large RNA molecules controls every aspect of cellular function, and yet we know very little about their molecular structures. However, robust technologies developed for visualizing ribozymes and riboswitches, together with new approaches for mapping RNA inside cells, provide the foundation for visualizing the structures of long noncoding RNAs, mRNAs, and viral RNAs, thereby facilitating new mechanistic insights.
Dynamic RNA Modifications in Posttranscriptional Regulation
Source:Molecular Cell, Volume 56, Issue 1
Author(s): Xiao Wang , Chuan He
Cellular RNAs can be chemically modified over a hundred different ways. These modifications were once thought to be static, discrete, and utilized to fine-tune RNA structure and function. However, recent studies have revealed that some modifications, like mRNA methylation, can be reversed, and these reversible modifications may play active roles in regulating diverse biological processes. In this perspective, we summarize examples of dynamic RNA modifications that affect biological functions. We further propose that reversible modifications might occur on tRNA, rRNA, and other noncoding RNAs to regulate gene expression analogous to the reversible mRNA methylation.
MicroRNAs Trigger Dissociation of eIF4AI and eIF4AII from Target mRNAs in Humans
Source:Molecular Cell, Volume 56, Issue 1
Author(s): Akira Fukao , Yuichiro Mishima , Naoki Takizawa , Shigenori Oka , Hiroaki Imataka , Jerry Pelletier , Nahum Sonenberg , Christian Thoma , Toshinobu Fujiwara
In animals, key functions of microRNA-induced silencing complex (miRISC) are translational repression and deadenylation followed by mRNA decay. While miRISC represses translation initiation, it is poorly understood how miRISC exerts this function. Here we assessed the effect of miRISC on synergistic recruitment of translation initiation factors to target mRNAs by using direct biochemical assays. We show that miRISC promotes eIF4AI and eIF4AII release from target mRNAs prior to dissociation of eIF4E and eIF4G in a deadenylation-independent manner. Strikingly, miRISC-induced release of eIF4AI and eIF4AII from target mRNAs and miRISC-induced inhibition of cap-dependent translation can both be counteracted by the RNA-binding protein HuD via a direct interaction of HuD with eIF4A. Furthermore, the pharmacological eIF4A inhibitor silvestrol, which locks eIF4A on mRNAs, conferred resistance to miRNA-mediated translational repression. In summary, we propose that both eIF4AI and eIF4AII are functionally important targets in miRISC-mediated translation control.
Graphical abstract
Teaser
MicroRNAs induce translational repression and deadenylation followed by mRNA decay. Fukao et al. show that miRNAs in human cells cause deadenylation-independent dissociation of eIF4AI and eIF4AII from mRNA prior to dissociation of eIF4E and eIF4G.Posttranscriptional Regulation of Gene Expression by Piwi Proteins and piRNAs
Source:Molecular Cell, Volume 56, Issue 1
Author(s): Toshiaki Watanabe , Haifan Lin
Piwi proteins and Piwi-interacting RNAs (piRNAs) are essential for gametogenesis, embryogenesis, and stem cell maintenance in animals. Piwi proteins act on transposon RNAs by cleaving the RNAs and by interacting with factors involved in RNA regulation. Additionally, piRNAs generated from transposons and psuedogenes can be used by Piwi proteins to regulate mRNAs at the posttranscriptional level. Here we discuss piRNA biogenesis, recent findings on posttranscriptional regulation of mRNAs by the piRNA pathway, and the potential importance of this posttranscriptional regulation for a variety of biological processes such as gametogenesis, developmental transitions, and sex determination.
Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo
Source:Cell Reports
Author(s): Thomas Conrad , Annalisa Marsico , Maja Gehre , Ulf Andersson Ørom
In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.
Graphical abstract
Teaser
Conrad et al. describe an approach for the transcriptome-wide assessment of pri-miRNA processing into pre-miRNA. The authors use this to quantify the processing efficiencies of individual miRNAs and show processing to be more important than primary transcript expression itself to determine the level of mature miRNAs within a cell.Widespread intron retention in mammals functionally tunes transcriptomes.
| Related Articles |
Widespread intron retention in mammals functionally tunes transcriptomes.
Genome Res. 2014 Sep 25;
Authors: Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ
Abstract
Alternative splicing (AS) of precursor RNAs is responsible for greatly expanding the regulatory and functional capacity of eukaryotic genomes. Of the different classes of AS, intron retention (IR) is the least well understood. In plants and unicellular eukaryotes, IR is the most common form of AS, whereas in animals, it is thought to represent the least prevalent form. Using high-coverage poly(A)(+) RNA-seq data, we observe that IR is surprisingly frequent in mammals, affecting transcripts from as many as three-quarters of multiexonic genes. A highly correlated set of cis features comprising an "IR code" reliably discriminates retained from constitutively spliced introns. We show that IR acts widely to reduce the levels of transcripts that are less or not required for the physiology of the cell or tissue type in which they are detected. This "transcriptome tuning" function of IR acts through both nonsense-mediated mRNA decay and nuclear sequestration and turnover of IR transcripts. We further show that IR is linked to a cross-talk mechanism involving localized stalling of RNA polymerase II (Pol II) and reduced availability of spliceosomal components. Collectively, the results implicate a global checkpoint-type mechanism whereby reduced recruitment of splicing components coupled to Pol II pausing underlies widespread IR-mediated suppression of inappropriately expressed transcripts.
PMID: 25258385 [PubMed - as supplied by publisher]
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.
Nucleic Acids Res. 2014 Sep 26;
Authors: Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, Haeseler AV, Jantsch MF
Abstract
Adenosine deaminases that act on RNA (ADARs) deaminate adenosines to inosines in double-stranded RNAs including miRNA precursors. A to I editing is widespread and required for normal life. By comparing deep sequencing data of brain miRNAs from wild-type and ADAR2 deficient mouse strains, we detect editing sites and altered miRNA processing at high sensitivity. We detect 48 novel editing events in miRNAs. Some editing events reach frequencies of up to 80%. About half of all editing events depend on ADAR2 while some miRNAs are preferentially edited by ADAR1. Sixty-four percent of all editing events are located within the seed region of mature miRNAs. For the highly edited miR-3099, we experimentally prove retargeting of the edited miRNA to novel 3' UTRs. We show further that an abundant editing event in miR-497 promotes processing by Drosha of the corresponding pri-miRNA. We also detect reproducible changes in the abundance of specific miRNAs in ADAR2-deficient mice that occur independent of adjacent A to I editing events. This indicates that ADAR2 binding but not editing of miRNA precursors may influence their processing. Correlating with changes in miRNA abundance we find misregulation of putative targets of these miRNAs in the presence or absence of ADAR2.
PMID: 25260591 [PubMed - as supplied by publisher]
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
Nature Methods 11, 1064 (2014). doi:10.1038/nmeth.3092
Authors: Katharina Kramer, Timo Sachsenberg, Benedikt M Beckmann, Saadia Qamar, Kum-Loong Boon, Matthias W Hentze, Oliver Kohlbacher & Henning Urlaub
Sequencing: Sampling local sequence with proximity ligation
Nature Methods 11, 991 (2014). doi:10.1038/nmeth.3123
Open-access synthetic spike-in mRNA-seq data for cancer gene fusions
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
Article
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.
Nature Communications doi: 10.1038/ncomms6125
Authors: Sarah A. Munro, Steven P. Lund, P. Scott Pine, Hans Binder, Djork-Arné Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nadereh Jafari, David P. Kreil, Paweł P. Łabaj, Sheng Li, Yang Liao, Simon M. Lin, Joseph Meehan, Christopher E. Mason, Javier Santoyo-Lopez, Robert A. Setterquist, Leming Shi, Wei Shi, Gordon K. Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Weida Tong, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu, Marc Salit
Faculty Searches Get a Facelift
Source:Cell, Volume 159, Issue 1
Author(s): Rachel Bernstein
Hiring committees address the glut of highly qualified applicants for faculty positions by experimenting with new evaluation methods and adapting their expectations for today’s increasingly competitive academic environment.
Biogenesis of Circular RNAs
Source:Cell, Volume 159, Issue 1
Author(s): Quentin Vicens , Eric Westhof
Circular RNAs are generated during splicing through various mechanisms. Ashwal-Fluss et al. demonstrate that exon circularization and linear splicing compete with each other in a tissue-specific fashion, and Zhang et al. show that exon circularization depends on flanking intronic complementary sequences. Both papers show that several types of circular RNA transcripts can be produced from a single gene.