Hyeshik Chang

Nature Structural & Molecular Biology 20, 1106 (2013). doi:10.1038/nsmb.2646

Authors: Hongliang Zhu, Yuyi Zhou, Claudia Castillo-González, Amber Lu, Chunxiao Ge, Ying-Tao Zhao, Liusheng Duan, Zhaohu Li, Michael J Axtell, Xiu-Jie Wang & Xiuren Zhang

Nature Structural & Molecular Biology 20, 1131 (2013). doi:10.1038/nsmb.2660

Authors: Liying Yan, Mingyu Yang, Hongshan Guo, Lu Yang, Jun Wu, Rong Li, Ping Liu, Ying Lian, Xiaoying Zheng, Jie Yan, Jin Huang, Ming Li, Xinglong Wu, Lu Wen, Kaiqin Lao, Ruiqiang Li, Jie Qiao & Fuchou Tang

Claudia J. Rödel, Anna F. Gilles, Michalis Averof. Noncoding RNAs have recently emerged as important regulators of mRNA translation and turnover [1, 2]. Nevertheless, we largely ignore how their function integrates with protein-mediated translatio....

Genome-wide search for exonic variants affecting translational efficiency.

Nat Commun. 2013 Jul 31;4:2260

Authors: Li Q, Makri A, Lu Y, Marchand L, Grabs R, Rousseau M, Ounissi-Benkalha H, Pelletier J, Robert F, Harmsen E, Hudson TJ, Pastinen T, Polychronakos C, Qu HQ

Abstract
The search for expression quantitative trait loci has traditionally centred entirely on the process of transcription, whereas variants with effects on messenger RNA translation have not been systematically studied. Here we present a high-throughput approach for measuring translational cis-regulation in the human genome. Using ribosomal association as proxy for translational efficiency of polymorphic messenger RNAs, we test the ratio of polysomal/non-polysomal messenger RNA level as a quantitative trait for association with single nucleotide polymorphisms on the same messenger RNA transcript. We identify one important ribosomal distribution effect, from rs1131017 in the 5'-untranslated region of RPS26, that is in high linkage disequilibrium with the 12q13 locus for susceptibility to type 1 diabetes. The effect on translation is confirmed at the protein level by quantitative western blots, both ex vivo and after in vitro translation. Our results are a proof-of-principle that allelic effects on translation can be detected at a transcriptome-wide scale.

PMID: 23900168 [PubMed - in process]

The idea that RNA can be transferred between organisms and function in communication and environmental sensing is discussed.

Authors: Peter Sarkies, Eric A. Miska

Claudia Schneider, David Tollervey.

Article

In Escherichia coli , the highly conserved enzyme endonuclease V has a role in DNA repair. Here the authors show that human endonuclease V is an inosine 3' endoribonuclease and that Tudor Staphylococcal nuclease enhances this activity, suggesting a role for human endonuclease V in RNA metabolism.

Nature Communications doi: 10.1038/ncomms3273

Authors: Yoko Morita, Toshihiro Shibutani, Nozomi Nakanishi, Kazuko Nishikura, Shigenori Iwai, Isao Kuraoka

Article

The control of RNA stability is essential for gene regulation in eukaryotes. Hirayama et al . demonstrate that poly(A)-specific ribonuclease and bacterial-type poly(A) polymerase control mitochondrial mRNA poly(A) status in Arabidopsis , showing that a unique system regulating mitochondrial function operates in plants.

Nature Communications doi: 10.1038/ncomms3247

Authors: Takashi Hirayama, Takakazu Matsuura, Sho Ushiyama, Mari Narusaka, Yukio Kurihara, Michiko Yasuda, Misato Ohtani, Motoaki Seki, Taku Demura, Hideo Nakashita, Yoshihiro Narusaka, Shimpei Hayashi

Nature Reviews Genetics. doi:10.1038/nrg3566

Author: Hannah Stower

Nature Reviews Genetics. doi:10.1038/nrg3561

Author: Louisa Flintoft

Nature Medicine 19, 980 (2013). doi:10.1038/nm.3309

Author: Carolina Pola

Article

The poly(ADP-ribose) polymerase (PARP) family includes 17 proteins in humans, many of which have no known function. Vyas et al. systematically characterize the localization and function of each human PARP and identify PARP14 as a regulator of focal adhesions.

Nature Communications doi: 10.1038/ncomms3240

Authors: Sejal Vyas, Melissa Chesarone-Cataldo, Tanya Todorova, Yun-Han Huang, Paul Chang

The RNA-binding protein repertoire of embryonic stem cells.

Nat Struct Mol Biol. 2013 Aug 4;

Authors: Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, Kim VN

Abstract
RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and yet annotation of RBPs is limited mainly to those with known RNA-binding domains. To systematically identify the RBPs of embryonic stem cells (ESCs), we here employ interactome capture, which combines UV cross-linking of RBP to RNA in living cells, oligo(dT) capture and MS. From mouse ESCs (mESCs), we have defined 555 proteins constituting the mESC mRNA interactome, including 283 proteins not previously annotated as RBPs. Of these, 68 new RBP candidates are highly expressed in ESCs compared to differentiated cells, implicating a role in stem-cell physiology. Two well-known E3 ubiquitin ligases, Trim25 (also called Efp) and Trim71 (also called Lin41), are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways. Our study confirms and expands the atlas of RBPs, providing a useful resource for the study of the RNA-RBP network in stem cells.

PMID: 23912277 [PubMed - as supplied by publisher]

Nature Reviews Genetics. doi:10.1038/nrg3572

Nature Reviews Genetics. doi:10.1038/nrg3569

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

Nature 500, 7461 (2013). doi:10.1038/nature12064

Authors: Andrew Adey, Joshua N. Burton, Jacob O. Kitzman, Joseph B. Hiatt, Alexandra P. Lewis, Beth K. Martin, Ruolan Qiu, Choli Lee & Jay Shendure

The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption—both intentionally and through widespread cross-contamination—and for the past 60 years it has served a role analogous to that of a model organism. The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%). The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.

Molecular biology: Molecular switches in RNA

Nature 500, 7461 (2013). doi:10.1038/500124d

An RNA–protein complex regulates gene expression in an unanticipated way.The cellular machines called spliceosomes reconfigure transcribed RNA into its mature, protein-coding form. The 'minor spliceosome' is less than 1% as abundant as the major spliceosome, but exists in plants, fungi and animals, with precursors

Khek-Chian Tham, Nicolaas Hermans, Herrie H.K. Winterwerp, Michael M. Cox, Claire Wyman, Roland Kanaar, Joyce H.G. Lebbink. Homeologous recombination between divergent DNA sequences is inhibited by DNA mismatch repair. In Escherichia coli, MutS and MutL respond to DNA mismatches within recombination intermediate....

Nature Biotechnology 31, 681 (2013). doi:10.1038/nbt.2661

Authors: Dali Li, Zhongwei Qiu, Yanjiao Shao, Yuting Chen, Yuting Guan, Meizhen Liu, Yongmei Li, Na Gao, Liren Wang, Xiaoling Lu, Yongxiang Zhao & Mingyao Liu

The surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of RNAs, except their astounding diversities. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their abilities to classify the various collections of non-coding RNAs (ncRNAs). To address this, we developed Classification of RNAs by Analysis of Length (CoRAL), a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length and cleavage specificity to distinguish between different ncRNA populations. We evaluated CoRAL using genome-wide small RNA sequencing data sets from four human tissue types and were able to classify six different types of RNAs with ~80% cross-validation accuracy. Analysis by CoRAL revealed that microRNAs, small nucleolar and transposon-derived RNAs are highly discernible and consistent across all human tissue types assessed, whereas long intergenic ncRNAs, small cytoplasmic RNAs and small nuclear RNAs show less consistent patterns. The ability to reliably annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using small RNA sequencing data in less well-characterized organisms.

Splicing of human pre-mRNA is reciprocally coupled to 3' end formation by terminal exon definition, which occurs co-transcriptionally. It is required for the final maturation of most human pre-mRNAs and is therefore important to understand. We have used several strategies to block splicing at specific stages in vivo and studied their effect on 3' end formation. We demonstrate that a terminal splice acceptor site is essential to establish coupling with the poly(A) signal in a chromosomally integrated β-globin gene. This is in part to alleviate the suppression of 3' end formation by U1 small nuclear RNA, which is known to bind pre-mRNA at the earliest stage of spliceosome assembly. Interestingly, blocks to splicing that are subsequent to terminal splice acceptor site function, but before catalysis, have little observable effect on 3' end formation. These data suggest that early stages of spliceosome assembly are sufficient to functionally couple splicing and 3' end formation, but that on-going intron removal is less critical.

by Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, Vincent J. Carey

We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

A single-cell quantitative method reveals changes in the distribution of proteins with single-molecule sensitivity. [Also see Perspective by Rickman and Bickmore]

Authors: Ibrahim I. Cisse, Ignacio Izeddin, Sebastien Z. Causse, Lydia Boudarene, Adrien Senecal, Leila Muresan, Claire Dugast-Darzacq, Bassam Hajj, Maxime Dahan, Xavier Darzacq

A proof-of-principle study reports somatic reprogramming to the pluripotent state using small-molecule compounds.

Authors: Pingping Hou, Yanqin Li, Xu Zhang, Chun Liu, Jingyang Guan, Honggang Li, Ting Zhao, Junqing Ye, Weifeng Yang, Kang Liu, Jian Ge, Jun Xu, Qiang Zhang, Yang Zhao, Hongkui Deng

Peripheral nerve injury induces an lncRNA that reduces the abundance of a potassium channel, thereby increasing neuronal excitability.

Summary: Large numbers of long intergenic non-coding RNA (lincRNA) have been detected through high-throughput sequencing technology. However, currently we still know very little about their functions. Therefore, a lincRNA function annotation database is needed to facilitate the study in this field. In this article, we present Linc2GO, a web resource that aims to provide comprehensive functional annotations for human lincRNA. MicroRNA-mRNA and microRNA-lincRNA interaction data were integrated to generate lincRNA functional annotations based on the ‘competing endogenous RNA hypothesis’. To the best of our knowledge, Linc2GO is the first database that makes use of the ‘competing endogenous RNA hypothesis’ to predict lincRNA functions.

Availability: Freely available at http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index.html

Contact: sunzhr@mail.tsinghua.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Background: The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. Results: We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 238 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. Conclusions: The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.

Related Articles

The core Microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a non-specific RNA-binding protein.

J Biol Chem. 2013 Jul 26;

Authors: Roth BM, Ishimaru D, Hennig M

Abstract
MicroRNA (miRNA) biogenesis follows a conserved succession of processing steps, beginning with the recognition and liberation of a miRNA-containing precursor (pre-miRNA) hairpin from a large primary miRNA transcript (pri-miRNA) by the Microprocessor, which consists of the nuclear RNase III Drosha and the double-stranded RNA-binding domain (dsRBD) protein DGCR8 (DiGeorge syndrome critical region protein 8). Current models suggest that specific recognition is driven by DGCR8 detection of single-stranded (ss) elements of the pri-miRNA stem-loop followed by Drosha recruitment and pri-miRNA cleavage. Since countless RNA transcripts feature ss-dsRNA junctions and DGCR8 can bind hundreds of mRNAs, we explored correlations between RNA-binding properties of DGCR8 and specific pri-miRNA substrate processing. We found that DGCR8 bound single-stranded, double-stranded, and random hairpin transcripts with similar affinity. Further investigation of DGCR8/pri-mir-16 interactions by NMR detected intermediate exchange regimes over a wide range of stoichiometric ratios. Diffusion analysis of DGCR8/pri-mir-16 interactions by pulsed field gradient (PFG) NMR lent further support to dynamic complex formation involving free components in exchange with complexes of varying stoichiometry, though in vitro processing assays showed exclusive cleavage of pri-mir-16 variants bearing ss-flanking regions. Our results indicate that DGCR8 binds RNA nonspecifically. Therefore, a sequential model of DGCR8 recognition followed by Drosha recruitment is unlikely. Known RNA substrate requirements are broad and include 70-nt hairpins with unpaired flanking regions. Thus, specific RNA processing is likely facilitated by preformed DGCR8-Drosha heterodimers that can discriminate between authentic substrates and other hairpins.

PMID: 23893406 [PubMed - as supplied by publisher]

Loss of the decoy function of miR-29 destabilizes A20 transcripts, contributing to oncogenic activation of the transcription factor NF-{kappa}B in sarcomas.