Hyeshik Chang

Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation.

Elife. 2015 Apr 13;4

Authors: Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ

Abstract
Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increases the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. Here, we describe SeqZip, a methodology that uses RNA-templated DNA-DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1 and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1.

PMID: 25866926 [PubMed - as supplied by publisher]

by Megan L. Head, Luke Holman, Rob Lanfear, Andrew T. Kahn, Michael D. Jennions

A focus on novel, confirmatory, and statistically significant results leads to substantial bias in the scientific literature. One type of bias, known as “p-hacking,” occurs when researchers collect or select data or statistical analyses until nonsignificant results become significant. Here, we use text-mining to demonstrate that p-hacking is widespread throughout science. We then illustrate how one can test for p-hacking when performing a meta-analysis and show that, while p-hacking is probably common, its effect seems to be weak relative to the real effect sizes being measured. This result suggests that p-hacking probably does not drastically alter scientific consensuses drawn from meta-analyses.

Related Articles

Uncapped 5' ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags.

FEBS Lett. 2015 Jan 30;589(3):279-84

Authors: Kiss DL, Oman K, Bundschuh R, Schoenberg DR

Abstract
In mammalian transcriptomes approximately 25% of 5' ends determined by Capped Analysis of Gene Expression (CAGE) map to locations within spliced exons. The current study sought to determine if the cytoplasmic capping complex participates in generating these downstream CAGE tags. 5'-RACE was used to amplify the uncapped ends of target transcripts that accumulate when cytoplasmic capping is blocked. Sequencing of these RACE products mapped the positions of uncapped ends either exactly to or just downstream of archived CAGE tags. These findings support a role for cytoplasmic capping in generating the downstream capped ends identified by CAGE.

PMID: 25541487 [PubMed - indexed for MEDLINE]

Background: DNA methylation directs the epigenetic silencing of selected regions of DNA, including the regulation of pseudogenes, and is widespread throughout the genome. Pseudogenes are decayed copies of duplicated genes that have spread throughout the genome by transposition. Pseudogenes are transcriptionally silenced by DNA methylation, but little is known about how pseudogenes are targeted for methylation or how methylation levels are maintained in different tissues. Results: We employed bisulfite next generation sequencing to examine the methylation status of the LIN28 gene and four processed pseudogenes derived from LIN28. The objective was to determine whether LIN28 pseudogenes maintain the same pattern of methylation as the parental gene or acquire a methylation pattern independent of the gene of origin. In this study, we determined that the methylation status of LIN28 pseudogenes does not resemble the pattern evident for the LIN28 gene, but rather these pseudogenes appear to acquire methylation patterns independent of the parental gene. Furthermore, we observed that methylation levels of the examined pseudogenes correlate to the location of insertion within the genome. LIN28 pseudogenes inserted into gene bodies were highly methylated in all tissues examined. In contrast, pseudogenes inserted into genomic regions that are not proximal to genes were differentially methylated in various tissue types. Conclusions: Our analysis of the LIN28 pseudogene family suggests that this model pseudogene does not acquire a pattern tissue-specific methylation signature as the parental gene, but rather is methylated in patterns specific to the local genomic environment into which the pseudogene was inserted.

Deformability in the cleavage site of primary MicroRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8.

Proteins. 2015 Apr 7;

Authors: Quarles KA, Chadalavada D, Showalter SA

Abstract
The prevalence of double-stranded RNA (dsRNA) in eukaryotic cells has only recently been appreciated. Of interest here, RNA silencing begins with dsRNA substrates that are bound by the double-stranded RNA binding domains (dsRBDs) of their processing proteins. Specifically, processing of microRNA (miRNA) in the nucleus minimally requires the enzyme Drosha and its dsRBD-containing cofactor protein, DGCR8. The smallest recombinant construct of DGCR8 that is sufficient for in vitro dsRNA binding, referred to as DGCR8-Core, consists of its two dsRBDs and a C-terminal tail. Because dsRBDs rarely recognize the nucleotide sequence of dsRNA, it is reasonable to hypothesize that DGCR8 function is dependent on recognition of specific structural features in the miRNA precursor. Previously, we demonstrated that non-canonical structural elements that promote RNA flexibility within the stem of miRNA precursors are necessary for efficient in vitro cleavage by reconstituted Microprocessor complexes. Here we combine gel shift assays with in vitro processing assays to demonstrate that neither the N-terminal dsRBD of DGCR8 in isolation, nor the DGCR8-Core construct, are sensitive to the presence of non-canonical structural elements within the stem of miRNA precursors, or to single-stranded segments flanking the stem. Extending DGCR8-Core to include an N-terminal heme-binding region does not change our conclusions. Thus, our data suggest that while the DGCR8-Core region is necessary for dsRNA binding and recruitment to the Microprocessor, it is not sufficient to establish the previously observed connection between RNA flexibility and processing efficiency. This article is protected by copyright. All rights reserved.

PMID: 25851436 [PubMed - as supplied by publisher]

Sample preparation, detection scheme, and normalization approach affect the quantification of protein abundance and modification state by immunoblotting.

The regulation of dendritic branching is critical for sensory reception, cell–cell communication within the nervous system, learning, memory, and behavior. Defects in dendrite morphology are associated with several neurologic disorders; thus, an understanding of the molecular mechanisms that govern dendrite morphogenesis is important. Recent investigations of dendrite morphogenesis have highlighted the importance of gene regulation at the posttranscriptional level. Because RNA-binding proteins mediate many posttranscriptional mechanisms, we decided to investigate the extent to which conserved RNA-binding proteins contribute to dendrite morphogenesis across phyla. Here we identify a core set of RNA-binding proteins that are important for dendrite morphogenesis in the PVD multidendritic sensory neuron in Caenorhabditis elegans. Homologs of each of these genes were previously identified as important in the Drosophila melanogaster dendritic arborization sensory neurons. Our results suggest that RNA processing, mRNA localization, mRNA stability, and translational control are all important mechanisms that contribute to dendrite morphogenesis, and we present a conserved set of RNA-binding proteins that regulate these processes in diverse animal species. Furthermore, homologs of these genes are expressed in the human brain, suggesting that these RNA-binding proteins are candidate regulators of dendrite development in humans.

A precursor microRNA (miRNA) has two arms: miR-5p and miR-3p (miR-5p/-3p). Depending on the tissue or cell types, both arms can become functional. However, little is known about their coregulatory mechanisms during the tumorigenic process. Here, by using the large-scale miRNA expression profiles of five cancer types, we revealed that several of miR-5p/-3p arms were concordantly dysregulated in each cancer. To explore possible coregulatory mechanisms of concordantly dysregulated miR-5p/-3p pairs, we developed a robust computational framework and applied it to lung cancer data. The framework deciphers miR-5p/-3p coregulated protein interaction networks critical to lung cancer development. As a novel part in the method, we uniquely applied the second-order partial correlation to minimize false-positive regulations. Using 279 matched miRNA and mRNA expression profiles extracted from tumor and normal lung tissue samples, we identified 17 aberrantly expressed miR-5p/-3p pairs that potentially modulate the gene expression of 35 protein complexes. Functional analyses revealed that these complexes are associated with cancer-related biological processes, suggesting the oncogenic potential of the reported miR-5p/-3p pairs. Specifically, we revealed that the reduced expression of miR-145-5p/-3p pair potentially contributes to elevated expression of genes in the "FOXM1 transcription factor network" pathway, which may consequently lead to uncontrolled cell proliferation. Subsequently, the regulation of miR-145-5p/-3p in the FOXM1signaling pathway was validated by a cohort of 104 matched miRNA and protein (reverse-phase protein array) expression profiles in lung cancer. In summary, our computational framework provides a novel tool to study miR-5p/-3p coregulatory mechanisms in cancer and other diseases.

Publication date: 30 March 2015
Source:Current Biology, Volume 25, Issue 7
Author(s): Takamasa Hirano , Haruhiko Siomi
Technologies have been developed in animal germ cells that produce artificial piRNAs from transgenes in piRNA clusters to silence target genes by cleaving their transcripts. A new study provides a simple way to generate artificial piRNAs to direct de novo DNA methylation in mice.

Teaser

Technologies have been developed in animal germ cells that produce artificial piRNAs from transgenes in piRNA clusters to silence target genes by cleaving their transcripts. A new study provides a simple way to generate artificial piRNAs to direct de novo DNA methylation in mice.

Related Articles

Polysome fractionation and analysis of mammalian translatomes on a genome-wide scale.

J Vis Exp. 2014;(87)

Authors: Gandin V, Sikström K, Alain T, Morita M, McLaughlan S, Larsson O, Topisirovic I

Abstract
mRNA translation plays a central role in the regulation of gene expression and represents the most energy consuming process in mammalian cells. Accordingly, dysregulation of mRNA translation is considered to play a major role in a variety of pathological states including cancer. Ribosomes also host chaperones, which facilitate folding of nascent polypeptides, thereby modulating function and stability of newly synthesized polypeptides. In addition, emerging data indicate that ribosomes serve as a platform for a repertoire of signaling molecules, which are implicated in a variety of post-translational modifications of newly synthesized polypeptides as they emerge from the ribosome, and/or components of translational machinery. Herein, a well-established method of ribosome fractionation using sucrose density gradient centrifugation is described. In conjunction with the in-house developed "anota" algorithm this method allows direct determination of differential translation of individual mRNAs on a genome-wide scale. Moreover, this versatile protocol can be used for a variety of biochemical studies aiming to dissect the function of ribosome-associated protein complexes, including those that play a central role in folding and degradation of newly synthesized polypeptides.

PMID: 24893926 [PubMed - indexed for MEDLINE]

A new approach for annotation of transposable elements using small RNA mapping.

Nucleic Acids Res. 2015 Mar 26;

Authors: El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA

Abstract
Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants. Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/.

PMID: 25813049 [PubMed - as supplied by publisher]

Related Articles

Dicer partners expand the repertoire of miRNA targets.

Genome Biol. 2012;13(11):179

Authors: Jaskiewicz L, Zavolan M

Abstract
Processing of pre-miRNAs by Dicer is regulated by its dsRNA-binding protein partner, and leads to the generation of alternative miRNA forms with distinct target sets.

PMID: 23194401 [PubMed - indexed for MEDLINE]

Publication date: 9 April 2015
Source:Cell, Volume 161, Issue 2
Author(s): Ci Chu , Qiangfeng Cliff Zhang , Simão Teixeira da Rocha , Ryan A. Flynn , Maheetha Bharadwaj , J. Mauro Calabrese , Terry Magnuson , Edith Heard , Howard Y. Chang
Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA-protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3′ RNA processing machinery. Xist, an essential lncRNA for X chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK, which participates in Xist-mediated gene silencing and histone modifications but not Xist localization, and Drosophila Split ends homolog Spen, which interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.

Graphical abstract

Teaser

Development of a general method for identifying RNA-protein interactions in vivo reveals 81 endogenous proteins that associate with Xist RNA in two waves to control mammalian dosage compensation.

Nature Structural & Molecular Biology 22, 319 (2015). doi:10.1038/nsmb.2982

Authors: Ashish Dhir, Somdutta Dhir, Nick J Proudfoot & Catherine L Jopling

Nature Structural & Molecular Biology 22, 328 (2015). doi:10.1038/nsmb.2979

Authors: Daniel Holoch & Danesh Moazed

Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.

Elife. 2015;4

Authors: Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P

Abstract
mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT.

PMID: 25838129 [PubMed - in process]

Nature Methods 12, 323 (2015). doi:10.1038/nmeth.3313

Authors: Alexander A Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P Bhattacharyya, Robert F Rudy, Milesh M Patel, Nathaniel Novod, Deborah T Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman & Jonathan Livny

Although RNA-seq is a powerful tool, the considerable time and cost associated with library construction has limited its utilization for various applications. RNAtag-Seq, an approach to generate multiple RNA-seq libraries in a single reaction, lowers time and cost per sample, and it produces data on prokaryotic and eukaryotic samples that are comparable to those generated by traditional strand-specific RNA-seq approaches.

Nature Methods 12, 339 (2015). doi:10.1038/nmeth.3321

Authors: Michael B Clark, Tim R Mercer, Giovanni Bussotti, Tommaso Leonardi, Katelin R Haynes, Joanna Crawford, Marion E Brunck, Kim-Anh Lê Cao, Gethin P Thomas, Wendy Y Chen, Ryan J Taft, Lars K Nielsen, Anton J Enright, John S Mattick & Marcel E Dinger

We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.

Nature Methods 12, 284 (2015). doi:10.1038/nmeth.3350

Author: Rita Strack

A new method uses click chemistry to covalently modify any RNA of interest.

Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.

Embryonic patterning in Drosophila melanogaster is initially established through the activity of a number of maternally expressed genes that are expressed during oogenesis. mRNAs from some of these genes accumulate in the posterior pole plasm of the oocyte and early embryo, and localize further into RNA islands, transient ring-like structures that form around the nuclei of future primordial germ cells (pole cells) at stage 3 of embryogenesis. As mRNAs from several genes with known functions in anterior-posterior patterning and/or germ cell specification accumulate in RNA islands, we hypothesized that some other mRNAs that localize in this manner might also function in these developmental processes. To test this, we investigated the developmental functions of 51 genes whose mRNAs accumulate in RNA islands by abrogating their activity in the female germline using RNA interference. This analysis revealed requirements for ttk, pbl, Hip14, eIF5, eIF4G, and CG9977 for progression through early oogenesis. We observed dorsal appendage defects in a proportion of eggs produced by females expressing double-stranded RNA targeting Mkrn1 or jvl, implicating these two genes in dorsal-ventral patterning. In addition, posterior patterning defects and a reduction in pole cell number were seen in the progeny of Mkrn1 females. As the mammalian orthologue of Mkrn1 acts as an E3 ubiquitin ligase, these results suggest an additional link between protein ubiquitination and pole plasm activity.

Related Articles

Unraveling the association between mRNA expressions and mutant phenotypes in a genome-wide assessment of mice.

Proc Natl Acad Sci U S A. 2015 Mar 30;

Authors: Liao BY, Weng MP

Abstract
High-throughput gene expression profiling has revealed substantial leaky and extraneous transcription of eukaryotic genes, challenging the perceptions that transcription is strictly regulated and that changes in transcription have phenotypic consequences. To assess the functional implications of mRNA transcription directly, we analyzed mRNA expression data derived from microarrays, RNA-sequencing, and in situ hybridization, together with phenotype data of mouse mutants as a proxy of gene function at the tissue level. The results indicated that despite the presence of widespread ectopic transcription, mRNA expression and mutant phenotypes of mammalian genes or tissues remain associated. The expression-phenotype association at the gene level was particularly strong for tissue-specific genes, and the association could be underestimated due to data insufficiency and incomprehensive phenotyping of mouse mutants; the strength of expression-phenotype association at the tissue level depended on tissue functions. Mutations on genes expressed at higher levels or expressed at earlier embryonic stages more often result in abnormal phenotypes in the tissues where they are expressed. The mRNA expression profiles that have stronger associations with their phenotype profiles tend to be more evolutionarily conserved, indicating that the evolution of transcriptome and the evolution of phenome are coupled. Therefore, mutations resulting in phenotypic aberrations in expressed tissues are more likely to occur in highly transcribed genes, tissue-specific genes, genes expressed during early embryonic stages, or genes with evolutionarily conserved mRNA expression profiles.

PMID: 25825715 [PubMed - as supplied by publisher]

Deciphering the RNA landscape by RNAome sequencing.

RNA Biol. 2015 Jan 2;12(1):30-42

Authors: Derks KW, Misovic B, van den Hout MC, Kockx CE, Gomez CP, Brouwer RW, Vrieling H, Hoeijmakers JH, van IJcken WF, Pothof J

Abstract
Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods.

PMID: 25826412 [PubMed - as supplied by publisher]

Nature advance online publication 30 March 2015. doi:10.1038/nature14254

Authors: Shintaro Iwasaki, Hiroshi M. Sasaki, Yuriko Sakaguchi, Tsutomu Suzuki, Hisashi Tadakuma & Yukihide Tomari

Linear mRNA amplification approach for RNAseq from limited amount of RNA.

Gene. 2015 Mar 28;

Authors: Ferreira EN, de Campos Molina G, Puga RD, Nagai MA, Campos AH, Guimarães GC, Nunes DN, Pasqualini R, Arapd W, Brentani H, Dias-Neto E, Brentani RR, Carraro DM

Abstract
Whole-transcriptome evaluation by next-generation sequencing (NGS) has been widely applied in the investigation of diverse transcriptional scenarios. In many clinical situations, including needle biopsies samples or laser microdissected cells, limited amounts of RNA are usually available for the assessment of the whole transcriptome. Here, we describe an mRNA amplification protocol based on in vitro T7 transcription for transcriptome evaluation by NGS. Initially, we performed RNAseq from two human mammary epithelial cell lines and evaluated several aspects of the transcriptomes generated by linear amplification of Poly (A)(+) mRNA species, including transcript representation, variability and abundance. Our protocol showed to be efficient with respect to full-length transcript coverage and quantitative expression levels. We then evaluated the applicability of using this protocol in a more realistic research scenario, analyzing tumor tissues samples microdissected by laser capture. In order to increase the quantification power of the libraries only the 3' end of transcripts were sequenced. We found highly reproducible RNAseq data among amplified tumor samples, with a median Spearman's correlation of 80%, strongly suggesting that the amplification step and library protocol preparation leaded to a consistent transcriptional profile. Altogether, we established a robust protocol for assessing the polyadenilated transcriptome derived from limited amounts of total RNA that is applicable to all NGS platforms.

PMID: 25827286 [PubMed - as supplied by publisher]

A subset of messenger RNAs (mRNAs) that contain inverted Alu elements in their 3' untranslated region are inefficiently exported to the cytoplasm and retained in subnuclear bodies called paraspeckles. The arginine methyltransferase CARM1 (coactivator-associated arginine methyltransferase 1) promotes the nuclear export of these mRNAs by methylating the paraspeckle component p54^nrb, which reduces the binding of p54^nrb to the inverted Alu elements, and down-regulating synthesis of another paraspeckle component, the long noncoding RNA NEAT1, which inhibits paraspeckle formation.

by Richard J. Roberts

MicroRNAs (miRNAs) repress the expression of many genes in metazoans by accelerating messenger RNA degradation and inhibiting translation, thereby reducing the level of protein. However, miRNAs only slightly reduce the mean expression of most targeted proteins, leading to speculation about their role in the variability, or noise, of protein expression. We used mathematical modeling and single-cell reporter assays to show that miRNAs, in conjunction with increased transcription, decrease protein expression noise for lowly expressed genes but increase noise for highly expressed genes. Genes that are regulated by multiple miRNAs show more-pronounced noise reduction. We estimate that hundreds of (lowly expressed) genes in mouse embryonic stem cells have reduced noise due to substantial miRNA regulation. Our findings suggest that miRNAs confer precision to protein expression and thus offer plausible explanations for the commonly observed combinatorial targeting of endogenous genes by multiple miRNAs, as well as the preferential targeting of lowly expressed genes. Authors: Jörn M. Schmiedel, Sandy L. Klemm, Yannan Zheng, Apratim Sahay, Nils Blüthgen, Debora S. Marks, Alexander van Oudenaarden

All molecular machines have imperfections, and the biological ones are no exception. One type of flaw is a quantitative one: Although all the cells within an organ are genetically identical, the concentrations of many of their proteins can be “noisy”—that is, vary and fluctuate between all the cells. Biologists decompose such noise into two sources: an intrinsic one, which results from the stochastic nature of the biochemistry operating within cells, and an extrinsic one that manifests global differences between cells, such as the number of protein production facilities (e.g., ribosomes) (1). A major question is whether organisms have evolved means to control noise, especially when imprecisions are detrimental. On page 128 in this issue, Schmiedel et al. (2) report combining mathematical modeling and a synthetic gene approach to establish a complex role for microRNAs (miRNAs) in controlling cellular protein content. Authors: Yonit Hoffman, Yitzhak Pilpel