Hyeshik Chang

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster.

J Vis Exp. 2014;(90)

Authors: Laneve P, Giangrande A

Abstract
The last decades have witnessed the explosion of scientific interest around gene expression control mechanisms at the RNA level. This branch of molecular biology has been greatly fueled by the discovery of noncoding RNAs as major players in post-transcriptional regulation. Such a revolutionary perspective has been accompanied and triggered by the development of powerful technologies for profiling short RNAs expression, both at the high-throughput level (genome-wide identification) or as single-candidate analysis (steady state accumulation of specific species). Although several state-of-art strategies are currently available for dosing or visualizing such fleeing molecules, Northern Blot assay remains the eligible approach in molecular biology for immediate and accurate evaluation of RNA expression. It represents a first step toward the application of more sophisticated, costly technologies and, in many cases, remains a preferential method to easily gain insights into RNA biology. Here we overview an efficient protocol (Enhanced Northern Blot) for detecting weakly expressed microRNAs (or other small regulatory RNA species) from Drosophila melanogaster whole embryos, manually dissected larval/adult tissues or in vitro cultured cells. A very limited amount of RNA is required and the use of material from flow cytometry-isolated cells can be also envisaged.

PMID: 25177861 [PubMed - as supplied by publisher]

Repeated structural motifs encoded by disease genes impair RNA metabolism and cause cell death. [Also see Perspective by West and Gitler] Authors: Ilmin Kwon, Siheng Xiang, Masato Kato, Leeju Wu, Pano Theodoropoulos, Tao Wang, Jiwoong Kim, Jonghyun Yun, Yang Xie, Steven L. McKnight

Nature advance online publication 03 September 2014. doi:10.1038/nature13682

Authors: Havva Keskin, Ying Shen, Fei Huang, Mikir Patel, Taehwan Yang, Katie Ashley, Alexander V. Mazin & Francesca Storici

Homologous recombination is a molecular process that has multiple important roles in DNA metabolism, both for DNA repair and genetic variation in all forms of life. Generally, homologous recombination involves the exchange of genetic information between two identical or nearly identical DNA molecules; however, homologous recombination can also occur between RNA molecules, as shown for RNA viruses. Previous research showed that synthetic RNA oligonucleotides can act as templates for DNA double-strand break (DSB) repair in yeast and human cells, and artificial long RNA templates injected in ciliate cells can guide genomic rearrangements. Here we report that endogenous transcript RNA mediates homologous recombination with chromosomal DNA in yeast Saccharomyces cerevisiae. We developed a system to detect the events of homologous recombination initiated by transcript RNA following the repair of a chromosomal DSB occurring either in a homologous but remote locus, or in the same transcript-generating locus in reverse-transcription-defective yeast strains. We found that RNA–DNA recombination is blocked by ribonucleases H1 and H2. In the presence of H-type ribonucleases, DSB repair proceeds through a complementary DNA intermediate, whereas in their absence, it proceeds directly through RNA. The proximity of the transcript to its chromosomal DNA partner in the same locus facilitates Rad52-driven homologous recombination during DSB repair. We demonstrate that yeast and human Rad52 proteins efficiently catalyse annealing of RNA to a DSB-like DNA end in vitro. Our results reveal a novel mechanism of homologous recombination and DNA repair in which transcript RNA is used as a template for DSB repair. Thus, considering the abundance of RNA transcripts in cells, RNA may have a marked impact on genomic stability and plasticity.

Publication date: 4 September 2014
Source:Molecular Cell, Volume 55, Issue 5
Author(s): Clémentine Delan-Forino , David Tollervey
Systematic analyses, by UV crosslinking, of the precise binding sites for 23 different proteins across the yeast pre-mRNA population have given insights into the in vivo assembly of, and interactions between, pre-mRNA processing, packaging, and transport complexes.

Publication date: 8 September 2014
Source:Cancer Cell, Volume 26, Issue 3
Author(s): Colm J. Ryan , Christopher J. Lord , Alan Ashworth
A better understanding of genetic interactions in cancer might help identify new therapeutic approaches that exploit the concept of synthetic lethality. Ruppin and colleagues have developed a new computational method, DAISY, that predicts such interactions and potentially facilitates the delineation and validation of comprehensive genetic interaction networks.

Teaser

A better understanding of genetic interactions in cancer might help identify new therapeutic approaches that exploit the concept of synthetic lethality. Ruppin and colleagues have developed a new computational method, DAISY, that predicts such interactions and potentially facilitates the delineation and validation of comprehensive genetic interaction networks.

Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic...

Nature Structural & Molecular Biology 21, 825 (2014). doi:10.1038/nsmb.2862

Authors: Biswajoy Roy-Chaudhuri, Paul N Valdmanis, Yue Zhang, Qing Wang, Qing-Jun Luo & Mark A Kay

Nature Structural & Molecular Biology 21, 743 (2014). doi:10.1038/nsmb.2879

Authors: Daan C Swarts, Kira Makarova, Yanli Wang, Kotaro Nakanishi, René F Ketting, Eugene V Koonin, Dinshaw J Patel & John van der Oost

Article

The human embryonic kidney 293 (HEK293) cell lineage is widely used in cell biology and biotechnology. Here, the authors apply whole genome resequencing methods to characterise genomic variation in six HEK293 cell lines and suggest that this variation could affect experiments using these cell lines.

Nature Communications doi: 10.1038/ncomms5767

Authors: Yao-Cheng Lin, Morgane Boone, Leander Meuris, Irma Lemmens, Nadine Van Roy, Arne Soete, Joke Reumers, Matthieu Moisse, Stéphane Plaisance, Radoje Drmanac, Jason Chen, Frank Speleman, Diether Lambrechts, Yves Van de Peer, Jan Tavernier, Nico Callewaert

Article

Wilms tumour is a common childhood cancer. Here, the authors use whole-exome sequencing in 44 Wilms tumours to characterize their mutational landscape and show that DICER1 and DROSHA mutations can suppress the biogenesis of tumour-suppressing microRNAs.

Nature Communications doi: 10.1038/ncomms5802

Authors: Dinesh Rakheja, Kenneth S. Chen, Yangjian Liu, Abhay A. Shukla, Vanessa Schmid, Tsung-Cheng Chang, Shama Khokhar, Jonathan E. Wickiser, Nitin J. Karandikar, James S. Malter, Joshua T. Mendell, James F. Amatruda

Nature Biotechnology 32, 903 (2014). doi:10.1038/nbt.2957

Authors: Zhenqiang Su, Paweł P Łabaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei Shi, Charles Wang, Gary P Schroth, Robert A Setterquist, John F Thompson, Wendell D Jones, Wenzhong Xiao, Weihong Xu, Roderick V Jensen, Reagan Kelly, Joshua Xu, Ana Conesa, Cesare Furlanello, Hanlin Gao, Huixiao Hong, Nadereh Jafari, Stan Letovsky, Yang Liao, Fei Lu, Edward J Oakeley, Zhiyu Peng, Craig A Praul, Javier Santoyo-Lopez, Andreas Scherer, Tieliu Shi, Gordon K Smyth, Frank Staedtler, Peter Sykacek, Xin-Xing Tan, E Aubrey Thompson, Jo Vandesompele, May D Wang, Jian Wang, Russell D Wolfinger, Jiri Zavadil, Scott S Auerbach, Wenjun Bao, Hans Binder, Thomas Blomquist, Murray H Brilliant, Pierre R Bushel, Weimin Cai, Jennifer G Catalano, Ching-Wei Chang, Tao Chen, Geng Chen, Rong Chen, Marco Chierici, Tzu-Ming Chu, Djork-Arné Clevert, Youping Deng, Adnan Derti, Viswanath Devanarayan, Zirui Dong, Joaquin Dopazo, Tingting Du, Hong Fang, Yongxiang Fang, Mario Fasold, Anita Fernandez, Matthias Fischer, Pedro Furió-Tari, James C Fuscoe, Florian Caimet, Stan Gaj, Jorge Gandara, Huan Gao, Weigong Ge, Yoichi Gondo, Binsheng Gong, Meihua Gong, Zhuolin Gong, Bridgett Green, Chao Guo, Lei Guo, Li-Wu Guo, James Hadfield, Jan Hellemans, Sepp Hochreiter, Meiwen Jia, Min Jian, Charles D Johnson, Suzanne Kay, Jos Kleinjans, Samir Lababidi, Shawn Levy, Quan-Zhen Li, Li Li, Li Li, Peng Li, Yan Li, Haiqing Li, Jianying Li, Shiyong Li, Simon M Lin, Francisco J López, Xin Lu, Heng Luo, Xiwen Ma, Joseph Meehan, Dalila B Megherbi, Nan Mei, Bing Mu, Baitang Ning, Akhilesh Pandey, Javier Pérez-Florido, Roger G Perkins, Ryan Peters, John H Phan, Mehdi Pirooznia, Feng Qian, Tao Qing, Lucille Rainbow, Philippe Rocca-Serra, Laure Sambourg, Susanna-Assunta Sansone, Scott Schwartz, Ruchir Shah, Jie Shen, Todd M Smith, Oliver Stegle, Nancy Stralis-Pavese, Elia Stupka, Yutaka Suzuki, Lee T Szkotnicki, Matthew Tinning, Bimeng Tu, Joost van Delft, Alicia Vela-Boza, Elisa Venturini, Stephen J Walker, Liqing Wan, Wei Wang, Jinhui Wang, Jun Wang, Eric D Wieben, James C Willey, Po-Yen Wu, Jiekun Xuan, Yong Yang, Zhan Ye, Ye Yin, Ying Yu, Yate-Ching Yuan, John Zhang, Ke K Zhang, Wenqian Zhang, Wenwei Zhang, Yanyan Zhang, Chen Zhao, Yuanting Zheng, Yiming Zhou, Paul Zumbo, Weida Tong, David P Kreil, Christopher E Mason & Leming Shi

Aconitase is an iron–sulfur protein and a major enzyme of the TCA cycle that catalyzes the conversion of citrate to isocitrate under iron-rich conditions. In Escherichia coli, aconitase B (AcnB) is a typical moonlighting protein that can switch to its apo form (apo-AcnB) which favors binding its own mRNA 3'UTR and stabilize it when intracellular iron become scarce. The small regulatory RNA (sRNA) RyhB has previously been shown to promote RNase E-dependent degradation of acnB mRNA when it was expressed from an ectopic arabinose-dependent promoter, independently of intracellular iron levels. In marked contrast, we report here that expression of RyhB under low-iron conditions did not result in acnB mRNA degradation even when RyhB was bound to acnB ribosome binding site (RBS). Genetic and biochemical evidence suggested that, under low-iron conditions, apo-AcnB bound to acnB 3'UTR close to a RNase E cleavage site that is essential for RyhB-induced acnB mRNA degradation. Whereas RyhB can block acnB translation initiation, RNase E-dependent degradation of acnB was prevented by apo-AcnB binding close to the cleavage site. This previously uncharacterized regulation suggests an intricate post-transcriptional mechanism that represses protein expression while insuring mRNA stability.

We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2'OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces.

Noncoding RNAs (ncRNAs) and RNA-binding proteins are potent post-transcriptional regulators of gene expression. The ncRNA 7SL is upregulated in cancer cells, but its impact upon the phenotype of cancer cells is unknown. Here, we present evidence that 7SL forms a partial hybrid with the 3'-untranslated region (UTR) of TP53 mRNA, which encodes the tumor suppressor p53. The interaction of 7SL with TP53 mRNA reduced p53 translation, as determined by analyzing p53 expression levels, nascent p53 translation and TP53 mRNA association with polysomes. Silencing 7SL led to increased binding of HuR to TP53 mRNA, an interaction that led to the promotion of p53 translation and increased p53 abundance. We propose that the competition between 7SL and HuR for binding to TP53 3'UTR contributes to determining the magnitude of p53 translation, in turn affecting p53 levels and the growth-suppressive function of p53. Our findings suggest that targeting 7SL may be effective in the treatment of cancers with reduced p53 levels.

Increasing awareness of the importance of protein–RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites.

Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and cancer cell lines independent of their functions. The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length. Both forms are overexpressed in cancer cell lines but display a conserved end distribution. Surprisingly, the long forms are more dependent than the short forms on the expression of the core snoRNP protein NOP58, thought to be essential for C/D snoRNA production. In contrast, a subset of short forms are dependent on the splicing factor RBFOX2. Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP. Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.

Site-directed spin labeling is emerging as an essential tool to investigate the structural and dynamical features of RNA. We propose here an enzymatic method, which allows the insertion of a paramagnetic center at a specific position in an RNA molecule. The technique is based on a segmental approach using a ligation protocol with T4 RNA ligase 2. One transcribed acceptor RNA is ligated to a donor RNA in which a thio-modified nucleotide is introduced at its 5'-end by in vitro transcription with T7 RNA polymerase. The paramagnetic thiol-specific reagent is subsequently attached to the RNA ligation product. This novel strategy is demonstrated by introducing a paramagnetic probe into the 55 nucleotides long RNA corresponding to K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-Box leader RNA. The efficiency of the coupling reaction and the quality of the resulting spin-labeled RNA were assessed by Mass Spectrometry, Electron Paramagnetic Resonance (EPR) and Nuclear Magnetic Resonance (NMR). This method enables various combinations of isotopic segmental labeling and spin labeling schemes, a strategy that will be of particular interest to investigate the structural and dynamical properties of large RNA complexes by NMR and EPR spectroscopies.

Nature Methods 11, 879 (2014). doi:10.1038/nmeth.3091

Authors: Paul Blainey, Martin Krzywinski & Naomi Altman

Quality is often more important than quantity.

Nature Methods 11, 890 (2014). doi:10.1038/nmeth.3089

Author: Allison Doerr

A method to study the domain architecture of long noncoding RNAs provides insights into their biological functions.

Nature Methods 11, (2014). doi:10.1038/nmeth.f.372

Authors: Amy L Beynon, Lindsay J Parkes, Matthew L Turner, Steve Knight, Steve Conlan, Lewis Francis & Ben Stocks

Nature Methods 11, 888 (2014). doi:10.1038/nmeth.3087

Author: Tal Nawy

The protein-RNA specificity code of an RNA-binding protein can be used to target diverse transcripts in the cell for regulation.

by Cristina Tocchini, Jeremy J. Keusch, Sarah B. Miller, Susanne Finger, Heinz Gut, Michael B. Stadler, Rafal Ciosk

The mechanisms controlling cell fate determination and reprogramming are fundamental for development. A profound reprogramming, allowing the production of pluripotent cells in early embryos, takes place during the oocyte-to-embryo transition. To understand how the oocyte reprogramming potential is controlled, we sought Caenorhabditis elegans mutants in which embryonic transcription is initiated precociously in germ cells. This screen identified LIN-41, a TRIM-NHL protein and a component of the somatic heterochronic pathway, as a temporal regulator of pluripotency in the germline. We found that LIN-41 is expressed in the cytoplasm of developing oocytes, which, in lin-41 mutants, acquire pluripotent characteristics of embryonic cells and form teratomas. To understand LIN-41 function in the germline, we conducted structure-function studies. In contrast to other TRIM-NHL proteins, we found that LIN-41 is unlikely to function as an E3 ubiquitin ligase. Similar to other TRIM-NHL proteins, the somatic function of LIN-41 is thought to involve mRNA regulation. Surprisingly, we found that mutations predicted to disrupt the association of LIN-41 with mRNA, which otherwise compromise LIN-41 function in the heterochronic pathway in the soma, have only minor effects in the germline. Similarly, LIN-41-mediated repression of a key somatic mRNA target is dispensable for the germline function. Thus, LIN-41 appears to function in the germline and the soma via different molecular mechanisms. These studies provide the first insight into the mechanism inhibiting the onset of embryonic differentiation in developing oocytes, which is required to ensure a successful transition between generations.

Nature Protocols 9, 2267 (2014). doi:10.1038/nprot.2014.153

Authors: Douglas M Fowler, Jason J Stephany & Stanley Fields

Deep mutational scanning marries selection for protein function to high-throughput DNA sequencing in order to quantify the activity of variants of a protein on a massive scale. First, an appropriate selection system for the protein function of interest is identified and validated. Second, a library

Publication date: 11 September 2014
Source:Cell Reports, Volume 8, Issue 5
Author(s): Cecil Han , Yunhua Liu , Guohui Wan , Hyun Jin Choi , Luqing Zhao , Cristina Ivan , Xiaoming He , Anil K. Sood , Xinna Zhang , Xiongbin Lu
Posttranscriptional maturation is a critical step in microRNA (miRNA) biogenesis that determines mature miRNA levels. In addition to core components (Drosha and DGCR8 [DiGeorge syndrome critical region gene 8]) in the microprocessor, regulatory RNA-binding proteins may confer the specificity for recruiting and processing of individual primary miRNAs (pri-miRNAs). Here, we identify DDX1 as a regulatory protein that promotes the expression of a subset of miRNAs, including five members in the microRNA-200 (miR-200) family and four miRNAs in an eight-miRNA signature of a mesenchymal ovarian cancer subtype. A majority of DDX1-dependent miRNAs are induced after DNA damage. This induction is facilitated by the ataxia telangiectasia mutated (ATM)-mediated phosphorylation of DDX1. Inhibiting DDX1 promotes ovarian tumor growth and metastasis in a syngeneic mouse model. Analysis of The Cancer Genome Atlas (TCGA) reveals that low DDX1 levels are associated with poor clinical outcome in patients with serous ovarian cancer. These findings suggest that DDX1 is a key modulator in miRNA maturation and ovarian tumor suppression.

Graphical abstract

Teaser

Posttranscriptional maturation is a critical step in microRNA (miRNA) biogenesis during which specific recruitment and processing of individual primary miRNAs (pri-miRNAs) might be conferred by regulatory RNA-binding proteins. Han et al. now show that the RNA-binding protein DDX1 promotes the expression of a subset of ovarian-cancer-associated miRNAs. DDX1 levels are positively correlated with clinical outcome in patients with ovarian cancer. Inhibiting DDX1 promotes ovarian tumor progression. The results demonstrate that DDX1 is a key modulator in miRNA maturation and ovarian tumor suppression.

Publication date: 18 September 2014
Source:Molecular Cell, Volume 55, Issue 6
Author(s): Xuhang Liu , Qi Zheng , Nicholas Vrettos , Manolis Maragkakis , Panagiotis Alexiou , Brian D. Gregory , Zissimos Mourelatos
MicroRNAs (miRNAs) are essential for regulation of gene expression. Though numerous miRNAs have been identified by high-throughput sequencing, few precursor miRNAs (pre-miRNAs) are experimentally validated. Here we report a strategy for constructing high-throughput sequencing libraries enriched for full-length pre-miRNAs. We find widespread and extensive uridylation of Argonaute (Ago)-bound pre-miRNAs, which is primarily catalyzed by two terminal uridylyltransferases: TUT7 and TUT4. Uridylation by TUT7/4 not only polishes pre-miRNA 3′ ends, but also facilitates their degradation by the exosome, preventing clogging of Ago with defective species. We show that the exosome exploits distinct substrate preferences of DIS3 and RRP6, its two catalytic subunits, to distinguish productive from defective pre-miRNAs. Furthermore, we identify a positive feedback loop formed by the exosome and TUT7/4 in triggering uridylation and degradation of Ago-bound pre-miRNAs. Our study reveals a pre-miRNA surveillance system that comprises TUT7, TUT4, and the exosome in quality control of miRNA synthesis.

Graphical abstract

Teaser

Liu et al. report a strategy for constructing high-throughput sequencing libraries enriched for pre-miRNAs and find that there is extensive uridylation of Agonaute-bound pre-miRNAs, which they find are generated as part of a pre-miRNA quality control system involving uridylyltransferases and the exosome.

Related Articles

RNA-guided assembly of Rev-RRE nuclear export complexes.

Elife. 2014;3:e03656

Authors: Bai Y, Tambe A, Zhou K, Doudna JA

Abstract
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.DOI: http://dx.doi.org/10.7554/eLife.03656.001.

PMID: 25163983 [PubMed - in process]

Comparative analysis of the transcriptome across distant species.

Nature. 2014 Aug 28;512(7515):445-8

Authors: Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R

Abstract
The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

PMID: 25164755 [PubMed - in process]

Related Articles

Emerging Roles of RNA Modification: m(6)A and U-Tail.

Cell. 2014 Aug 28;158(5):980-987

Authors: Lee M, Kim B, Kim VN

Abstract
Although more than 100 types of RNA modification have been described thus far, most of them were thought to be rare in mRNAs and in regulatory noncoding RNAs. Recent developments have unveiled that at least some of the modifications are considerably abundant and widely conserved. This Minireview summarizes the molecular machineries and biological functions of methylation (N6-methyladenosine, m(6)A) and uridylation (U-tail).

PMID: 25171402 [PubMed - as supplied by publisher]

Related Articles

Data Integration and Reproducibility for High-Throughput Transcriptomics.

Int Rev Neurobiol. 2014;116C:55-71

Authors: Mooney M, McWeeney S

Abstract
The rapid advances in high-throughput transcriptomics allow individual investigators to rapidly and comprehensively interrogate the transcriptome. This phenomenon has placed large volumes of gene expression data in public repositories presenting opportunities for secondary analysis, discovery, and in silico modeling. We focus here on guidelines for best practices for transcriptomics data integration and considerations for reproducibility. In addition, we discuss some considerations for multi-omic and cross-species comparisons.

PMID: 25172471 [PubMed - as supplied by publisher]