Hyeshik Chang

Nature Reviews Molecular Cell Biology 14, 402 (2013). doi:10.1038/nrm3600

Author: Rachel David

Human embryonic stem cells have been generated through somatic cell nuclear transfer.

Interactions among neighboring cells underpin many physiological processes ranging from early development to immune responses. When these interactions do not function properly, numerous pathologies, including infection and cancer, can result. Molecular imaging technologies, especially optical imaging, are uniquely suited to illuminate complex cellular interactions within the context of living tissues...

by Yuri V. Svitkin, Akiko Yanagiya, Alexey E. Karetnikov, Tommy Alain, Marc R. Fabian, Arkady Khoutorsky, Sandra Perreault, Ivan Topisirovic, Nahum Sonenberg

Translation control often operates via remodeling of messenger ribonucleoprotein particles. The poly(A) binding protein (PABP) simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation. PABP also promotes miRNA-dependent deadenylation and translational repression of target mRNAs. We demonstrate that isoform 2 of the mouse heterogeneous nuclear protein Q (hnRNP-Q2/SYNCRIP) binds poly(A) by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to poly(A) in vitro. Depleting hnRNP-Q2 from translation extracts stimulates cap-dependent and IRES-mediated translation that is dependent on the PABP/poly(A) complex. Adding recombinant hnRNP-Q2 to the extracts inhibited translation in a poly(A) tail-dependent manner. The displacement of PABP from the poly(A) tail by hnRNP-Q2 impaired the association of eIF4E with the 5′ m⁷G cap structure of mRNA, resulting in the inhibition of 48S and 80S ribosome initiation complex formation. In mouse fibroblasts, silencing of hnRNP-Q2 stimulated translation. In addition, hnRNP-Q2 impeded let-7a miRNA-mediated deadenylation and repression of target mRNAs, which require PABP. Thus, by competing with PABP, hnRNP-Q2 plays important roles in the regulation of global translation and miRNA-mediated repression of specific mRNAs.

The genomics of selection in dogs and the parallel evolution between dogs and humans

Nature Communications 4, 1860 (2013). doi:10.1038/ncomms2814

Authors: Guo-dong Wang, Weiwei Zhai, He-chuan Yang, Ruo-xi Fan, Xue Cao, Li Zhong, Lu Wang, Fei Liu, Hong Wu, Lu-guang Cheng, Andrei D. Poyarkov, Nikolai A. Poyarkov JR, Shu-sheng Tang, Wen-ming Zhao, Yun Gao, Xue-mei Lv, David M. Irwin, Peter Savolainen, Chung-I Wu & Ya-ping Zhang

Fruit fly circadian clock function requires protein translation regulated by an RNA-binding protein.

Authors: Chunghun Lim, Ravi Allada

Defining piRNA primary transcripts.

Cell Cycle. 2013 May 10;12(11)

Authors: Li XZ, Roy CK, Moore MJ, Zamore PD

PMID: 23673320 [PubMed - as supplied by publisher]

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The Genetic Makeup of the Drosophila piRNA Pathway.

Mol Cell. 2013 May 9;

Authors: Handler D, Meixner K, Pizka M, Lauss K, Schmied C, Gruber FS, Brennecke J

Abstract
The piRNA (PIWI-interacting RNA) pathway is a small RNA silencing system that acts in animal gonads and protects the genome against the deleterious influence of transposons. A major bottleneck in the field is the lack of comprehensive knowledge of the factors and molecular processes that constitute this pathway. We conducted an RNAi screen in Drosophila and identified ∼50 genes that strongly impact the ovarian somatic piRNA pathway. Many identified genes fall into functional categories that indicate essential roles for mitochondrial metabolism, RNA export, the nuclear pore, transcription elongation, and chromatin regulation in the pathway. Follow-up studies on two factors demonstrate that components acting at distinct hierarchical levels of the pathway were identified. Finally, we define CG2183/Gasz as an essential primary piRNA biogenesis factor in somatic and germline cells. Based on the similarities between insect and vertebrate piRNA pathways, our results have far-reaching implications for the understanding of this conserved genome defense system.

PMID: 23665231 [PubMed - as supplied by publisher]

The shaping and functional consequences of the microRNA landscape in breast cancer

Nature 497, 7449 (2013). doi:10.1038/nature12108

Authors: Heidi Dvinge, Anna Git, Stefan Gräf, Mali Salmon-Divon, Christina Curtis, Andrea Sottoriva, Yongjun Zhao, Martin Hirst, Javier Armisen, Eric A. Miska, Suet-Feung Chin, Elena Provenzano, Gulisa Turashvili, Andrew Green, Ian Ellis, Sam Aparicio & Carlos Caldas

MicroRNAs (miRNAs) show differential expression across breast cancer subtypes, and have both oncogenic and tumour-suppressive roles. Here we report the miRNA expression profiles of 1,302 breast tumours with matching detailed clinical annotation, long-term follow-up and genomic and messenger RNA expression data. This provides a comprehensive overview of the quantity, distribution and variation of the miRNA population and provides information on the extent to which genomic, transcriptional and post-transcriptional events contribute to miRNA expression architecture, suggesting an important role for post-transcriptional regulation. The key clinical parameters and cellular pathways related to the miRNA landscape are characterized, revealing context-dependent interactions, for example with regards to cell adhesion and Wnt signalling. Notably, only prognostic miRNA signatures derived from breast tumours devoid of somatic copy-number aberrations (CNA-devoid) are consistently prognostic across several other subtypes and can be validated in external cohorts. We then use a data-driven approach to seek the effects of miRNAs associated with differential co-expression of mRNAs, and find that miRNAs act as modulators of mRNA–mRNA interactions rather than as on–off molecular switches. We demonstrate such an important modulatory role for miRNAs in the biology of CNA-devoid breast cancers, a common subtype in which the immune response is prominent. These findings represent a new framework for studying the biology of miRNAs in human breast cancer.

Nature Reviews Genetics. doi:10.1038/nrg3510

Author: Louisa Flintoft

Nature Reviews Genetics. doi:10.1038/nrg3507

Author: Mary Muers

Nature Reviews Genetics. doi:10.1038/nrg3506

Author: Mary Muers

Masahito Tachibana, Paula Amato, Michelle Sparman, Nuria Marti Gutierrez, Rebecca Tippner-Hedges, Hong Ma, Eunju Kang, Alimujiang Fulati, Hyo-Sang Lee, Hathaitip Sritanaudomchai, Keith Masterson, Janine Larson, Deborah Eaton, Karen Sadler-Fredd, David Battaglia, David Lee, Diana Wu, Jeffrey Jensen, Phillip Patton, Sumita Gokhale, Richard L. Stouffer, Don Wolf, Shoukhrat Mitalipov. Reprogramming somatic cells into pluripotent embryonic stem cells (ESCs) by somatic cell nuclear transfer (SCNT) has been envisioned as an approach for generating patient-matched nuclear transfer ....

by Philippe Desjardins-Proulx, Ethan P. White, Joel J. Adamson, Karthik Ram, Timothée Poisot, Dominique Gravel

Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing.

Nucleic Acids Res. 2013 May 9;

Authors: Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA

Abstract
During RNA interference and related gene regulatory pathways, the endonuclease Dicer cleaves precursor RNA molecules to produce microRNAs (miRNAs) and short interfering RNAs (siRNAs). Human cells encode a single Dicer enzyme that can associate with two different double-stranded RNA (dsRNA)-binding proteins, protein activator of PKR (PACT) and trans-activation response RNA-binding protein (TRBP). However, the functional redundancy or differentiation of PACT and TRBP in miRNA and siRNA biogenesis is not well understood. Using a reconstituted system, we show here that PACT and TRBP have distinct effects on Dicer-mediated dsRNA processing. In particular, we found that PACT in complex with Dicer inhibits the processing of pre-siRNA substrates when compared with Dicer and a Dicer-TRBP complex. In addition, PACT and TRBP show non-redundant effects on the production of different-sized miRNAs (isomiRs), which in turn alter target-binding specificities. Experiments using chimeric versions of PACT and TRBP suggest that the two N-terminal RNA-binding domains of each protein confer the observed differences in dsRNA substrate recognition and processing behavior of Dicer-dsRNA-binding protein complexes. These results support the conclusion that in humans, Dicer-associated dsRNA-binding proteins are important regulatory factors that contribute both substrate and cleavage specificity during miRNA and siRNA production.

PMID: 23661684 [PubMed - as supplied by publisher]

Casey A. Gifford, Michael J. Ziller, Hongcang Gu, Cole Trapnell, Julie Donaghey, Alexander Tsankov, Alex K. Shalek, David R. Kelley, Alexander A. Shishkin, Robbyn Issner, Xiaolan Zhang, Michael Coyne, Jennifer L. Fostel, Laurie Holmes, Jim Meldrim, Mitchell Guttman, Charles Epstein, Hongkun Park, Oliver Kohlbacher, John Rinn, Andreas Gnirke, Eric S. Lander, Bradley E. Bernstein, Alexander Meissner. Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we perf....

Kathrin Leppek, Johanna Schott, Sonja Reitter, Fabian Poetz, Ming C. Hammond, Georg Stoecklin. Tumor necrosis factor-α (TNF-α) is the most potent proinflammatory cytokine in mammals. The degradation of TNF-α mRNA is critical for restricting TNF-α synthesis and involves a constitutive decay ....

Wei Xie, Matthew D. Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W. Whitaker, Shulan Tian, R. David Hawkins, Danny Leung, Hongbo Yang, Tao Wang, Ah Young Lee, Scott A. Swanson, Jiuchun Zhang, Yun Zhu, Audrey Kim, Joseph R. Nery, Mark A. Urich, Samantha Kuan, Chia-an Yen, Sarit Klugman, Pengzhi Yu, Kran Suknuntha, Nicholas E. Propson, Huaming Chen, Lee E. Edsall, Ulrich Wagner, Yan Li, Zhen Ye, Ashwinikumar Kulkarni, Zhenyu Xuan, Wen-Yu Chung, Neil C. Chi, Jessica E. Antosiewicz-Bourget, Igor Slukvin, Ron Stewart, Michael Q. Zhang, Wei Wang, James A. Thomson, Joseph R. Ecker, Bing Ren. Epigenetic mechanisms have been proposed to play crucial roles in mammalian development, but their precise functions are only partially understood. To investigate epigenetic regulation of embryoni....

Xiong Ji, Yu Zhou, Shatakshi Pandit, Jie Huang, Hairi Li, Charles Y. Lin, Rui Xiao, Christopher B. Burge, Xiang-Dong Fu. RNAP II is frequently paused near gene promoters in mammals, and its transition to productive elongation requires active recruitment of P-TEFb, a cyclin-dependent kinase for RNAP II and other key ....

Nature Biotechnology 31, 453 (2013). doi:10.1038/nbt.2556

Authors: Michiko Kimoto, Rie Yamashige, Ken-ichiro Matsunaga, Shigeyuki Yokoyama & Ichiro Hirao

DNA aptamers produced with natural or modified natural nucleotides often lack the desired binding affinity and specificity to target proteins. Here we describe a method for selecting DNA aptamers containing the four natural nucleotides and an unnatural nucleotide with the hydrophobic base 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds). We incorporated up to three Ds nucleotides in a random sequence library, which is expected to increase the chemical and structural diversity of the DNA molecules. Selection experiments against two human target proteins, vascular endothelial cell growth factor-165 (VEGF-165) and interferon-γ (IFN-γ), yielded DNA aptamers that bind with KD values of 0.65 pM and 0.038 nM, respectively, affinities that are >100-fold improved over those of aptamers containing only natural bases. These results show that incorporation of unnatural bases can yield aptamers with greatly augmented affinities, suggesting the potential of genetic alphabet expansion as a powerful tool for creating highly functional nucleic acids.

Nature Biotechnology 31, 458 (2013). doi:10.1038/nbt.2566

Authors: Vahid Khoddami & Bradley R Cairns

The extent and biological impact of RNA cytosine methylation are poorly understood, in part owing to limitations of current techniques for determining the targets of RNA methyltransferases. Here we describe 5-azacytidine–mediated RNA immunoprecipitation (Aza-IP), a technique that exploits the covalent bond formed between an RNA methyltransferase and the cytidine analog 5-azacytidine to recover RNA targets by immunoprecipitation. Targets are subsequently identified by high-throughput sequencing. When applied in a human cell line to the RNA methyltransferases DNMT2 and NSUN2, Aza-IP enabled >200-fold enrichment of tRNAs that are known targets of the enzymes. In addition, it revealed many tRNA and noncoding RNA targets not previously associated with NSUN2. Notably, we observed a high frequency of C→G transversions at the cytosine residues targeted by both enzymes, allowing identification of the specific methylated cytosine(s) in target RNAs. Given the mechanistic similarity of RNA cytosine methyltransferases, Aza-IP may be generally applicable for target identification.

Benjamin Czech, Jonathan B. Preall, Jon McGinn, Gregory J. Hannon. The Drosophila piRNA pathway provides an RNA-based immune system that defends the germline genome against selfish genetic elements. Two interrelated branches of the piRNA system exist: soma....

Nabanita De, Lisa Young, Pick-Wei Lau, Nicole-Claudia Meisner, David V. Morrissey, Ian J. MacRae. Argonaute proteins use small RNAs to guide the silencing of complementary target RNAs in many eukaryotes. Although small RNA biogenesis pathways are well studied, mechanisms for removal of guide R....

Katsutomo Okamura. In this issue of Molecular Cell, De et al. (2013) report that highly complementary targets promote release of small RNAs from effector Argonaute complexes, thus providing mechanistic insigh....

by Pierre-Étienne Jacques, Justin Jeyakani, Guillaume Bourque

Although emerging evidence suggests that transposable elements (TEs) have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized. Here we show that TEs have contributed to the human genome nearly half of its active elements. Using DNase I hypersensitivity data sets from ENCODE in normal, embryonic, and cancer cells, we found that 44% of open chromatin regions were in TEs and that this proportion reached 63% for primate-specific regions. We also showed that distinct subfamilies of endogenous retroviruses (ERVs) contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily–transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation. We also showed that thousands of ERV–derived sequences were activated in a cell type–specific manner, especially in embryonic and cancer cells, and we demonstrated that this activity was associated with cell type–specific expression of neighboring genes. Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.

Specific microRNAs (miRNAs), including miR-134, localize to neuronal dendrites, where they control synaptic protein synthesis and plasticity. However, the mechanism of miRNA transport is unknown. We found that the neuronal precursor-miRNA-134 (pre-miR-134) accumulates in dendrites of hippocampal neurons and at synapses in vivo. Dendritic localization of pre-miR-134 is mediated by the DEAH-box helicase DHX36, which directly associates with the pre-miR-134 terminal loop. DHX36 function is required for miR-134-dependent inhibition of target gene expression and the control of dendritic spine size. Dendritically localized pre-miR-134 could provide a local source of miR-134 that can be mobilized in an activity-dependent manner during plasticity.

Remodeling of RNA–protein complexes (mRNPs) plays a critical role in mRNA biogenesis and metabolism. However, relatively little is known about the underlying mechanism and regulation of the mRNP remodeling. In this issue of Genes & Development, Zhou and colleagues (pp. 1046–1058) report that a protein remodeling machine, the p97–UBXD8 complex, disassembles mRNPs containing the AU-rich elements (AREs) bound by HuR proteins in a nondegradative, ubiquitin signaling-dependent manner, revealing a novel mechanism to regulate mRNA turnover.

The assembly and disassembly of ribonucleoproteins (RNPs) are dynamic processes that control every step of RNA metabolism, including mRNA stability. However, our knowledge of how RNP remodeling is achieved is largely limited to RNA helicase functions. Here, we report a previously unknown mechanism that implicates the ATPase p97, a protein-remodeling machine, in the dynamic regulation of mRNP disassembly. We found that p97 and its cofactor, UBXD8, destabilize p21, MKP-1, and SIRT1, three established mRNA targets of the RNA-binding protein HuR, by promoting release of HuR from mRNA. Importantly, ubiquitination of HuR with a short K29 chain serves as the signal for release. When cells are subjected to stress conditions, the steady-state levels of HuR ubiquitination change, suggesting a new mechanism through which HuR mediates the stress response. Our studies reveal a new paradigm in RNA biology: nondegradative ubiquitin signaling-dependent disassembly of mRNP promoted by the p97–UBXD8 complex to control mRNA stability.

Nature Structural & Molecular Biology 20, 582 (2013). doi:10.1038/nsmb.2544

Authors: Chunlai Chen, Haibo Zhang, Steven L Broitman, Michael Reiche, Ian Farrell, Barry S Cooperman & Yale E Goldman

Nature Structural & Molecular Biology 20, 541 (2013). doi:10.1038/nsmb.2580

Authors: Riccardo Taulli, Cristian Loretelli & Pier Paolo Pandolfi

RNA is believed to have been the first reservoir of genetic information, but despite its ancient history, RNA continues to fascinate and is only now beginning to be understood in its entire variety and communication modality. New discoveries include the pseudogene RNA network regulating PTEN transcription and translation and the identification of circular RNAs as a new class of competing endogenous RNA molecules that sequester microRNAs to suppress their function.