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Literature DB >> 27132125

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs.

Eric J Strobel¹, Kyle E Watters¹, David Loughrey¹, Julius B Lucks².

Abstract

RNAs assume sophisticated structures that are active in myriad cellular processes. In this review, we highlight newly identified ribozymes, riboswitches, and small RNAs, some of which control the function of cellular metabolic and gene expression networks. We then examine recent developments in genome-wide RNA structure probing technologies that are yielding new insights into the structural landscape of the transcriptome. Finally, we discuss how these RNA 'structomic' methods can address emerging questions in RNA systems biology, from the mechanisms behind long non-coding RNAs to new bases for human diseases.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
RNA

Year: 2016 PMID： 27132125 PMCID： PMC5098397 DOI： 10.1016/j.copbio.2016.03.019

Source DB: PubMed Journal: Curr Opin Biotechnol ISSN： 0958-1669 Impact factor: 9.740

58 in total

1. A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.

Authors: Yanjie Chao; Jörg Vogel
Journal: Mol Cell Date: 2016-01-21 Impact factor: 17.970

2. Riboswitches. Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA.

Authors: J R Mellin; Mikael Koutero; Daniel Dar; Marie-Anne Nahori; Rotem Sorek; Pascale Cossart
Journal: Science Date: 2014-08-22 Impact factor: 47.728

3. An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism.

Authors: Peter B Kim; James W Nelson; Ronald R Breaker
Journal: Mol Cell Date: 2015-01-22 Impact factor: 17.970

4. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure.

Authors: F Michel; A Jacquier; B Dujon
Journal: Biochimie Date: 1982-10 Impact factor: 4.079

5. In-line alignment and Mg²⁺ coordination at the cleavage site of the env22 twister ribozyme.

Authors: Aiming Ren; Marija Košutić; Kanagalaghatta R Rajashankar; Marina Frener; Tobias Santner; Eric Westhof; Ronald Micura; Dinshaw J Patel
Journal: Nat Commun Date: 2014-11-20 Impact factor: 14.919

6. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

Authors: Zhengqing Ouyang; Michael P Snyder; Howard Y Chang
Journal: Genome Res Date: 2012-10-11 Impact factor: 9.043

7. Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA.

Authors: Masatoshi Miyakoshi; Yanjie Chao; Jörg Vogel
Journal: EMBO J Date: 2015-01-28 Impact factor: 11.598

8. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Authors: Silvi Rouskin; Meghan Zubradt; Stefan Washietl; Manolis Kellis; Jonathan S Weissman
Journal: Nature Date: 2013-12-15 Impact factor: 49.962

9. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.

Authors: Ian M Silverman; Fan Li; Anissa Alexander; Loyal Goff; Cole Trapnell; John L Rinn; Brian D Gregory
Journal: Genome Biol Date: 2014-01-07 Impact factor: 13.583

10. Landscape and variation of RNA secondary structure across the human transcriptome.

Authors: Yue Wan; Kun Qu; Qiangfeng Cliff Zhang; Ryan A Flynn; Ohad Manor; Zhengqing Ouyang; Jiajing Zhang; Robert C Spitale; Michael P Snyder; Eran Segal; Howard Y Chang
Journal: Nature Date: 2014-01-30 Impact factor: 49.962

21 in total

1. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.

Authors: Krishna Choudhary; Fei Deng; Sharon Aviran
Journal: Quant Biol Date: 2017-03-30

2. Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA.

Authors: Alec N Sexton; Peter Y Wang; Michael Rutenberg-Schoenberg; Matthew D Simon
Journal: Biochemistry Date: 2017-08-18 Impact factor: 3.162

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs.

1. A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.

2. Riboswitches. Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA.

3. An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism.

4. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure.

5. In-line alignment and Mg²⁺ coordination at the cleavage site of the env22 twister ribozyme.

6. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

7. Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA.

8. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

9. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.

10. Landscape and variation of RNA secondary structure across the human transcriptome.

1. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.

2. Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA.

3. Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

4. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

5. Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

6. rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow.

7. Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.

8. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

9. Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator.

10. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1.