Hyeshik Chang

Time is of the essence in biology as in so much else. For example, monitoring disease progression or the timing of developmental defects is important for the processes of drug discovery and therapy trials. Furthermore, an understanding of the basic dynamics of biological phenomena that are often strictly time regulated (e.g. circadian rhythms) is needed to make accurate inferences about the evolution of biological processes. Recent advances in technologies have enabled us to measure timing effects more accurately and in more detail. This has driven related advances in visualization and analysis tools that try to effectively exploit this data. Beyond timeline plots, notable attempts at more involved temporal interpretation have been made in recent years, but awareness of the available resources is still limited within the scientific community. Here, we review some advances in biological visualization of time-driven processes and consider how they aid data analysis and interpretation.

Related Articles

A Biochemical Approach to Identify Direct MicroRNA Targets.

Methods Mol Biol. 2015;1206:29-37

Authors: Subramanian M, Li XL, Hara T, Lal A

Abstract
We have recently developed a biochemical approach to isolate miRNA-bound mRNAs and have used this method to identify the genome-wide mRNAs regulated by the tumor suppressor miRNA miR-34a. This method involves transfection of cells with biotinylated miRNA mimics, streptavidin pulldown, RNA isolation, and qRT-PCR. The protocol in this chapter describes these steps and the issues that should be considered while designing such pulldown experiments.

PMID: 25240884 [PubMed - in process]

Current methods for genomic mapping of 5-hydroxymethylcytosine (5hmC) have been limited by either costly sequencing depth, high DNA input, or lack of single-base resolution. We present an approach called Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP) to map 5hmC sites at single-base resolution by exploiting the use of beta-glucosyltransferase to inhibit enzymatic digestion at the junction where adapters are ligated to a genomic library. Therefore, only library fragments presenting glucosylated 5hmC residues at the junction are sequenced. RRHP can detect sites with low 5hmC abundance, and when combined with RRBS data, 5-methylcytosine and 5-hydroxymethylcytosine can be compared at a specific site.

Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria

Nature 513, 7518 (2014). doi:10.1038/nature13468

Authors: Qingfeng Zhang, T. Nicolai Siegel, Rafael M. Martins, Fei Wang, Jun Cao, Qi Gao, Xiu Cheng, Lubin Jiang, Chung-Chau Hon, Christine Scheidig-Benatar, Hiroshi Sakamoto, Louise Turner, Anja T. R. Jensen, Aurelie Claes, Julien Guizetti, Nicholas A. Malmquist & Artur Scherf

Antigenic variation of the Plasmodium falciparum multicopy var gene family enables parasite evasion of immune destruction by host antibodies. Expression of a particular var subgroup, termed upsA, is linked to the obstruction of blood vessels in the brain and to the pathogenesis of human cerebral malaria. The mechanism determining upsA activation remains unknown. Here we show that an entirely new type of gene silencing mechanism involving an exonuclease-mediated degradation of nascent RNA controls the silencing of genes linked to severe malaria. We identify a novel chromatin-associated exoribonuclease, termed PfRNase II, that controls the silencing of upsAvar genes by marking their transcription start site and intron-promoter regions leading to short-lived cryptic RNA. Parasites carrying a deficient PfRNase II gene produce full-length upsAvar transcripts and intron-derived antisense long non-coding RNA. The presence of stable upsAvar transcripts overcomes monoallelic expression, resulting in the simultaneous expression of both upsA and upsC type PfEMP1 proteins on the surface of individual infected red blood cells. In addition, we observe an inverse relationship between transcript levels of PfRNase II and upsA-type var genes in parasites from severe malaria patients, implying a crucial role of PfRNase II in severe malaria. Our results uncover a previously unknown type of post-transcriptional gene silencing mechanism in malaria parasites with repercussions for other organisms. Additionally, the identification of RNase II as a parasite protein controlling the expression of virulence genes involved in pathogenesis in patients with severe malaria may provide new strategies for reducing malaria mortality.

Publication date: 11 September 2014
Source:Cell, Volume 158, Issue 6
Author(s): David W. Reid , Qiang Chen , Angeline S.-L. Tay , Shirish Shenolikar , Christopher V. Nicchitta
The unfolded protein response (UPR) is a stress response program that reprograms cellular translation and gene expression in response to proteotoxic stress in the endoplasmic reticulum (ER). One of the primary means by which the UPR alleviates this stress is by reducing protein flux into the ER via a general suppression of protein synthesis and ER-specific mRNA degradation. We report here an additional UPR-induced mechanism for the reduction of protein flux into the ER, where mRNAs that encode signal sequences are released from the ER to the cytosol. By removing mRNAs from the site of translocation, this mechanism may serve as a potent means to transiently reduce ER protein folding load and restore proteostasis. These findings identify the dynamic subcellular localization of mRNAs and translation as a selective and rapid regulatory feature of the cellular response to protein folding stress.

Graphical abstract

Teaser

The unfolded protein response induces rapid, selective, and reversible release of secretory- and membrane protein-encoding mRNAs from the endoplasmic reticulum (ER) to release protein folding stress in the ER.

Publication date: 25 September 2014
Source:Cell, Volume 159, Issue 1
Author(s): Schraga Schwartz , Douglas A. Bernstein , Maxwell R. Mumbach , Marko Jovanovic , Rebecca H. Herbst , Brian X. León-Ricardo , Jesse M. Engreitz , Mitchell Guttman , Rahul Satija , Eric S. Lander , Gerald Fink , Aviv Regev
Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo identification of previously reported positions and discover hundreds of unique sites in human and yeast mRNAs and snoRNAs. Perturbing pseudouridine synthases (PUS) uncovers which pseudouridine synthase modifies each site and their target sequence features. mRNA pseudouridinylation depends on both site-specific and snoRNA-guided pseudouridine synthases. Upon heat shock in yeast, Pus7p-mediated pseudouridylation is induced at >200 sites, and PUS7 deletion decreases the levels of otherwise pseudouridylated mRNA, suggesting a role in enhancing transcript stability. rRNA pseudouridine stoichiometries are conserved but reduced in cells from dyskeratosis congenita patients, where the PUS DKC1 is mutated. Our work identifies an enhanced, transcriptome-wide scope for pseudouridine and methods to dissect its underlying mechanisms and function.

Graphical abstract

Teaser

Transcriptome-wide pseudouridine mapping reveals extensive, dynamic pseudouridylation of mRNA and noncoding RNA in yeast and human.

Publication date: 2 October 2014
Source:Molecular Cell, Volume 56, Issue 1
Author(s): Reut Ashwal-Fluss , Markus Meyer , Nagarjuna Reddy Pamudurti , Andranik Ivanov , Osnat Bartok , Mor Hanan , Naveh Evantal , Sebastian Memczak , Nikolaus Rajewsky , Sebastian Kadener
Circular RNAs (circRNAs) are widely expressed noncoding RNAs. However, their biogenesis and possible functions are poorly understood. Here, by studying circRNAs that we identified in neuronal tissues, we provide evidence that animal circRNAs are generated cotranscriptionally and that their production rate is mainly determined by intronic sequences. We demonstrate that circularization and splicing compete against each other. These mechanisms are tissue specific and conserved in animals. Interestingly, we observed that the second exon of the splicing factor muscleblind (MBL/MBNL1) is circularized in flies and humans. This circRNA (circMbl) and its flanking introns contain conserved muscleblind binding sites, which are strongly and specifically bound by MBL. Modulation of MBL levels strongly affects circMbl biosynthesis, and this effect is dependent on the MBL binding sites. Together, our data suggest that circRNAs can function in gene regulation by competing with linear splicing. Furthermore, we identified muscleblind as a factor involved in circRNA biogenesis.

Graphical abstract

Teaser

Ashwal-Fluss et al. provide evidence that circRNA production competes with linear mRNA splicing. They demonstrate that intronic sequences largely determine the production rate of circRNAs and identify a splice factor (muscleblind) that can promote circularization.

Publication date: 25 September 2014
Source:Cell Reports, Volume 8, Issue 6
Author(s): Danijela Koppers-Lalic , Michael Hackenberg , Irene V. Bijnsdorp , Monique A.J. van Eijndhoven , Payman Sadek , Daud Sie , Nicoletta Zini , Jaap M. Middeldorp , Bauke Ylstra , Renee X. de Menezes , Thomas Würdinger , Gerrit A. Meijer , D. Michiel Pegtel
Functional biomolecules, including small noncoding RNAs (ncRNAs), are released and transmitted between mammalian cells via extracellular vesicles (EVs), including endosome-derived exosomes. The small RNA composition in cells differs from exosomes, but underlying mechanisms have not been established. We generated small RNA profiles by RNA sequencing (RNA-seq) from a panel of human B cells and their secreted exosomes. A comprehensive bioinformatics and statistical analysis revealed nonrandomly distributed subsets of microRNA (miRNA) species between B cells and exosomes. Unexpectedly, 3′ end adenylated miRNAs are relatively enriched in cells, whereas 3′ end uridylated isoforms appear overrepresented in exosomes, as validated in naturally occurring EVs isolated from human urine samples. Collectively, our findings suggest that posttranscriptional modifications, notably 3′ end adenylation and uridylation, exert opposing effects that may contribute, at least in part, to direct ncRNA sorting into EVs.

Graphical abstract

Teaser

Small RNA composition in cells differs from that in exosomes, but selection mechanisms are unknown. Koppers-Lalic et al. now demonstrate that nonrandom intra- and extracellular microRNA distribution is directed by 3′ end nucleotide additions.

Publication date: 25 September 2014
Source:Cell, Volume 159, Issue 1
Author(s): Xiao-Ou Zhang , Hai-Bin Wang , Yang Zhang , Xuhua Lu , Ling-Ling Chen , Li Yang
Exon circularization has been identified from many loci in mammals, but the detailed mechanism of its biogenesis has remained elusive. By using genome-wide approaches and circular RNA recapitulation, we demonstrate that exon circularization is dependent on flanking intronic complementary sequences. Such sequences and their distribution exhibit rapid evolutionary changes, showing that exon circularization is evolutionarily dynamic. Strikingly, exon circularization efficiency can be regulated by competition between RNA pairing across flanking introns or within individual introns. Importantly, alternative formation of inverted repeated Alu pairs and the competition between them can lead to alternative circularization, resulting in multiple circular RNA transcripts produced from a single gene. Collectively, exon circularization mediated by complementary sequences in human introns and the potential to generate alternative circularization products extend the complexity of mammalian posttranscriptional regulation.

Graphical abstract

Teaser

The competition of RNA pairing mediated by flanking intronic complementary sequences regulates exon circularization efficiency and alternative circularization.

Publication date: 2 October 2014
Source:Molecular Cell, Volume 56, Issue 1
Author(s): Stephen W. Eichhorn , Huili Guo , Sean E. McGeary , Ricard A. Rodriguez-Mias , Chanseok Shin , Daehyun Baek , Shu-hao Hsu , Kalpana Ghoshal , Judit Villén , David P. Bartel
MicroRNAs (miRNAs) regulate target mRNAs through a combination of translational repression and mRNA destabilization, with mRNA destabilization dominating at steady state in the few contexts examined globally. Here, we extend the global steady-state measurements to additional mammalian contexts and find that regardless of the miRNA, cell type, growth condition, or translational state, mRNA destabilization explains most (66%–>90%) miRNA-mediated repression. We also determine the relative dynamics of translational repression and mRNA destabilization for endogenous mRNAs as a miRNA is induced. Although translational repression occurs rapidly, its effect is relatively weak, such that by the time consequential repression ensues, the effect of mRNA destabilization dominates. These results imply that consequential miRNA-mediated repression is largely irreversible and provide other insights into the nature of miRNA-mediated regulation. They also simplify future studies, dramatically extending the known contexts and time points for which monitoring mRNA changes captures most of the direct miRNA effects.

Graphical abstract

Teaser

miRNAs repress gene expression via mRNA decay and translational repression. Eichhorn et al. characterize the impact and dynamics of mRNA decay and translational repression in numerous contexts, showing that decay is the predominant mode of action whenever there is substantial repression.

Publication date: 25 September 2014
Source:Cell, Volume 159, Issue 1
Author(s): Jesse M. Engreitz , Klara Sirokman , Patrick McDonel , Alexander A. Shishkin , Christine Surka , Pamela Russell , Sharon R. Grossman , Amy Y. Chow , Mitchell Guttman , Eric S. Lander
Intermolecular RNA-RNA interactions are used by many noncoding RNAs (ncRNAs) to achieve their diverse functions. To identify these contacts, we developed a method based on RNA antisense purification to systematically map RNA-RNA interactions (RAP-RNA) and applied it to investigate two ncRNAs implicated in RNA processing: U1 small nuclear RNA, a component of the spliceosome, and Malat1, a large ncRNA that localizes to nuclear speckles. U1 and Malat1 interact with nascent transcripts through distinct targeting mechanisms. Using differential crosslinking, we confirmed that U1 directly hybridizes to 5′ splice sites and 5′ splice site motifs throughout introns and found that Malat1 interacts with pre-mRNAs indirectly through protein intermediates. Interactions with nascent pre-mRNAs cause U1 and Malat1 to localize proximally to chromatin at active genes, demonstrating that ncRNAs can use RNA-RNA interactions to target specific pre-mRNAs and genomic sites. RAP-RNA is sensitive to lower abundance RNAs as well, making it generally applicable for investigating ncRNAs.

Graphical abstract

Teaser

Comprehensive mapping of intermolecular RNA-RNA interactions for U1 snRNA and Malat1 lncRNA reveals mechanisms for targeting noncoding RNAs to chromatin at active gene loci.

The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including the meiotic cell cycle, gamete specification as sperm or oocyte, and gamete development. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. Here, we use RNA-Seq to identify genes expressed in isolated XX gonads, which are approximately 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes [fog-2(q71)], both grown at 22°. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 2748 enriched in spermatogenic gonads, 1732 enriched in oogenic gonads, and the remaining 6274 not enriched in either. These spermatogenic, oogenic, and gender-neutral gene datasets compare well with those of previous studies, but double the number of genes identified. A comparison of the additional genes found in our study with in situ hybridization patterns in the Kohara database suggests that most are expressed in the germline. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-enriched isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology.

Complex higher-order RNA structures play critical roles in all facets of gene expression; however, the through-space interaction networks that define tertiary structures and govern sampling of multiple conformations are poorly understood. Here we describe single-molecule RNA structure analysis in which multiple sites of chemical modification are identified in single RNA...

Nature Reviews Molecular Cell Biology 15, 632 (2014). doi:10.1038/nrm3878

Author: Eytan Zlotorynski

Homologous recombination is a DNA double-strand break (DSB) repair mechanism that usually uses homologous DNA as template. Keskin et al. now report that Saccharomyces cerevisiae uses mRNAs as template for homologous recombination. The authors designed a system to monitor DSB repair through the

Nature Reviews Molecular Cell Biology 15, 632 (2014). doi:10.1038/nrm3880

Author: Eytan Zlotorynski

Following translational stress, mRNAs colocalize with mRNA decay factors in cytoplasmic processing (P) bodies. Tracking fluorescently tagged mRNAs in human cells and using fluorescence in situ hybridization, the authors found that following amino acid starvation, mRNAs that lack poly(A)-tails accumulated in the P bodies;

Nature Protocols 9, 2464 (2014). doi:10.1038/nprot.2014.162

Authors: Frédérique Rozier, Vincent Mirabet, Teva Vernoux & Pradeep Das

In situ mRNA hybridization is one of the most powerful techniques for analyzing patterns of gene expression. However, its usefulness is limited in complex plant tissues by the need to fix, embed and section samples before localizing the desired mRNA. Here we present a

Publication date: October 2014
Source:Trends in Genetics, Volume 30, Issue 10
Author(s): Aurélie Kapusta , Cédric Feschotte
Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.

Complementary Sequence-Mediated Exon Circularization.

Cell. 2014 Sep 17;

Authors: Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL, Yang L

Abstract
Exon circularization has been identified from many loci in mammals, but the detailed mechanism of its biogenesis has remained elusive. By using genome-wide approaches and circular RNA recapitulation, we demonstrate that exon circularization is dependent on flanking intronic complementary sequences. Such sequences and their distribution exhibit rapid evolutionary changes, showing that exon circularization is evolutionarily dynamic. Strikingly, exon circularization efficiency can be regulated by competition between RNA pairing across flanking introns or within individual introns. Importantly, alternative formation of inverted repeated Alu pairs and the competition between them can lead to alternative circularization, resulting in multiple circular RNA transcripts produced from a single gene. Collectively, exon circularization mediated by complementary sequences in human introns and the potential to generate alternative circularization products extend the complexity of mammalian posttranscriptional regulation.

PMID: 25242744 [PubMed - as supplied by publisher]

RNA Binding and Core Complexes Constitute the U-Insertion/Deletion Editosome.

Mol Cell Biol. 2014 Sep 15;

Authors: Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R

Abstract
Enzymes embedded into the RNA editing core complex (RECC) catalyze the U-insertion/deletion editing cascade to generate open reading frames in trypanosomal mitochondrial mRNAs. The sequential reactions of mRNA cleavage, U-addition or removal, and ligation are directed by guide RNAs (gRNAs). We combined proteomic, genetic and functional studies with sequencing of total and complex-bound RNAs to define a protein particle responsible for the recognition of gRNAs and pre-mRNA substrates, editing intermediates and products. This approximately 23-polypeptide tripartite assembly, termed the RNA editing substrate binding complex (RESC), also functions as the interface between mRNA editing, polyadenylation and translation. Furthermore, we found that gRNAs represent only a subset of small mitochondrial RNAs, yet an inexplicably high fraction of them possesses 3' U-tails, which correlates with gRNA's enrichment in the RESC complex. Although both gRNAs and mRNAs are associated with RESC, their metabolic fates are distinct: gRNAs are degraded in an editing-dependent process whereas edited mRNAs undergo 3' adenylation/uridylation prior to translation. Our results demonstrate that the well-characterized editing core complex (RECC) and the RNA binding particle defined in this study (RESC) typify enzymatic and substrate binding macromolecular constituents, respectively, of the ∼40S RNA editing holoenzyme, the editosome.

PMID: 25225332 [PubMed - as supplied by publisher]

Related Articles

Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes.

Cell Rep. 2014 Sep 17;

Authors: Koppers-Lalic D, Hackenberg M, Bijnsdorp IV, van Eijndhoven MA, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, Würdinger T, Meijer GA, Pegtel DM

Abstract
Functional biomolecules, including small noncoding RNAs (ncRNAs), are released and transmitted between mammalian cells via extracellular vesicles (EVs), including endosome-derived exosomes. The small RNA composition in cells differs from exosomes, but underlying mechanisms have not been established. We generated small RNA profiles by RNA sequencing (RNA-seq) from a panel of human B cells and their secreted exosomes. A comprehensive bioinformatics and statistical analysis revealed nonrandomly distributed subsets of microRNA (miRNA) species between B cells and exosomes. Unexpectedly, 3' end adenylated miRNAs are relatively enriched in cells, whereas 3' end uridylated isoforms appear overrepresented in exosomes, as validated in naturally occurring EVs isolated from human urine samples. Collectively, our findings suggest that posttranscriptional modifications, notably 3' end adenylation and uridylation, exert opposing effects that may contribute, at least in part, to direct ncRNA sorting into EVs.

PMID: 25242326 [PubMed - as supplied by publisher]

Evolutionary Conservation and Expression of Human RNA-Binding Proteins and Their Role in Human Genetic Disease.

Adv Exp Med Biol. 2014;825:1-55

Authors: Gerstberger S, Hafner M, Ascano M, Tuschl T

Abstract
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of targets at many sites. The importance of RBPs is underscored by their dysregulation or mutations causing a variety of developmental and neurological diseases. This chapter globally discusses human RBPs and provides a brief introduction to their identification and RNA targets. We review RBPs based on common structural RNA-binding domains, study their evolutionary conservation and expression, and summarize disease associations of different RBP classes.

PMID: 25201102 [PubMed - in process]

Related Articles

circRNA Biogenesis Competes with Pre-mRNA Splicing.

Mol Cell. 2014 Sep 17;

Authors: Ashwal-Fluss R, Meyer M, Pamudurti NR, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S

Abstract
Circular RNAs (circRNAs) are widely expressed noncoding RNAs. However, their biogenesis and possible functions are poorly understood. Here, by studying circRNAs that we identified in neuronal tissues, we provide evidence that animal circRNAs are generated cotranscriptionally and that their production rate is mainly determined by intronic sequences. We demonstrate that circularization and splicing compete against each other. These mechanisms are tissue specific and conserved in animals. Interestingly, we observed that the second exon of the splicing factor muscleblind (MBL/MBNL1) is circularized in flies and humans. This circRNA (circMbl) and its flanking introns contain conserved muscleblind binding sites, which are strongly and specifically bound by MBL. Modulation of MBL levels strongly affects circMbl biosynthesis, and this effect is dependent on the MBL binding sites. Together, our data suggest that circRNAs can function in gene regulation by competing with linear splicing. Furthermore, we identified muscleblind as a factor involved in circRNA biogenesis.

PMID: 25242144 [PubMed - as supplied by publisher]

Nature Reviews Genetics. doi:10.1038/nrg3834

Author: Linda Koch

Nature Reviews Cancer 14, 662 (2014). doi:10.1038/nrc3802

Authors: William D. Foulkes, John R. Priest & Thomas F. Duchaine

Dicer is central to microRNA-mediated silencing and several other RNA interference phenomena that are profoundly embedded in cancer gene networks. Most recently, both germline and somatic mutations in DICER1 have been identified in diverse types of cancer. Although some of the mutations clearly reduce

Nature Protocols 9, 2411 (2014). doi:10.1038/nprot.2014.154

Authors: Brian M Wile, Kiwon Ban, Young-Sup Yoon & Gang Bao

Molecular beacons (MBs) are dual-labeled oligonucleotides that fluoresce only in the presence of complementary mRNA. The use of MBs to target specific mRNAs allows sorting of specific cells from a mixed cell population. In contrast to existing approaches that are limited by available surface markers

Nature Biotechnology 32, 926 (2014). doi:10.1038/nbt.3001

Authors: Charles Wang, Binsheng Gong, Pierre R Bushel, Jean Thierry-Mieg, Danielle Thierry-Mieg, Joshua Xu, Hong Fang, Huixiao Hong, Jie Shen, Zhenqiang Su, Joe Meehan, Xiaojin Li, Lu Yang, Haiqing Li, Paweł P Łabaj, David P Kreil, Dalila Megherbi, Stan Gaj, Florian Caiment, Joost van Delft, Jos Kleinjans, Andreas Scherer, Viswanath Devanarayan, Jian Wang, Yong Yang, Hui-Rong Qian, Lee J Lancashire, Marina Bessarabova, Yuri Nikolsky, Cesare Furlanello, Marco Chierici, Davide Albanese, Giuseppe Jurman, Samantha Riccadonna, Michele Filosi, Roberto Visintainer, Ke K Zhang, Jianying Li, Jui-Hua Hsieh, Daniel L Svoboda, James C Fuscoe, Youping Deng, Leming Shi, Richard S Paules, Scott S Auerbach & Weida Tong

Nature Biotechnology 32, 915 (2014). doi:10.1038/nbt.2972

Authors: Sheng Li, Scott W Tighe, Charles M Nicolet, Deborah Grove, Shawn Levy, William Farmerie, Agnes Viale, Chris Wright, Peter A Schweitzer, Yuan Gao, Dewey Kim, Joe Boland, Belynda Hicks, Ryan Kim, Sagar Chhangawala, Nadereh Jafari, Nalini Raghavachari, Jorge Gandara, Natàlia Garcia-Reyero, Cynthia Hendrickson, David Roberson, Jeffrey Rosenfeld, Todd Smith, Jason G Underwood, May Wang, Paul Zumbo, Don A Baldwin, George S Grills & Christopher E Mason

Nature Biotechnology 32, 888 (2014). doi:10.1038/nbt.3000

Authors: Sheng Li, Paweł P Łabaj, Paul Zumbo, Peter Sykacek, Wei Shi, Leming Shi, John Phan, Po-Yen Wu, May Wang, Charles Wang, Danielle Thierry-Mieg, Jean Thierry-Mieg, David P Kreil & Christopher E Mason

Nature Biotechnology 32, 896 (2014). doi:10.1038/nbt.2931

Authors: Davide Risso, John Ngai, Terence P Speed & Sandrine Dudoit

Nature Biotechnology 32, 882 (2014). doi:10.1038/nbt.3015

Authors: Anton Kratz & Piero Carninci

Large-scale consortium efforts provide a thorough understanding of RNA-seq.