101
|
Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol 2017; 14:865-890. [PMID: 28453393 PMCID: PMC5546720 DOI: 10.1080/15476286.2017.1306171] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/02/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022] Open
Abstract
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.
Collapse
Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Zhiqiao Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alastair Louey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
102
|
Aberrant plasticity of peripheral sensory axons in a painful neuropathy. Sci Rep 2017; 7:3407. [PMID: 28611388 PMCID: PMC5469767 DOI: 10.1038/s41598-017-03390-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/27/2017] [Indexed: 12/21/2022] Open
Abstract
Neuronal cells express considerable plasticity responding to environmental cues, in part, through subcellular mRNA regulation. Here we report on the extensive changes in distribution of mRNAs in the cell body and axon compartments of peripheral sensory neurons and the 3' untranslated region (3'UTR) landscapes after unilateral sciatic nerve entrapment (SNE) injury in rats. Neuronal cells dissociated from SNE-injured and contralateral L4 and L5 dorsal root ganglia were cultured in a compartmentalized system. Axonal and cell body RNA samples were separately subjected to high throughput RNA sequencing (RNA-Seq). The injured axons exhibited enrichment of mRNAs related to protein synthesis and nerve regeneration. Lengthening of 3'UTRs was more prevalent in the injured axons, including the newly discovered alternative cleavage and polyadenylation of NaV1.8 mRNA. Alternative polyadenylation was largely independent from the relative abundance of axonal mRNAs; but they were highly clustered in functional pathways related to RNA granule formation in the injured axons. These RNA-Seq data analyses indicate that peripheral nerve injury may result in highly selective mRNA enrichment in the affected axons with 3'UTR alterations potentially contributing to the mechanism of neuropathic pain.
Collapse
|
103
|
Genome-wide profiling of the 3' ends of polyadenylated RNAs. Methods 2017; 126:86-94. [PMID: 28602807 DOI: 10.1016/j.ymeth.2017.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/29/2017] [Accepted: 06/03/2017] [Indexed: 11/24/2022] Open
Abstract
Alternative polyadenylation (APA) diversifies the 3' termini of a majority of mRNAs in most eukaryotes, and is consequently inferred to have substantial consequences for the utilization of post-transcriptional regulatory mechanisms. Since conventional RNA-sequencing methods do not accurately define mRNA termini, a number of protocols have been developed that permit sequencing of the 3' ends of polyadenylated transcripts (3'-seq). We present here our experimental protocol to generate 3'-seq libraries using a dT-priming approach, including extensive details on considerations that will enable successful library cloning. We pair this with a set of computational tools that allow the user to process the raw sequence data into a filtered set of clusters that represent high-confidence functional polyadenylation sites. The data are single-nucleotide resolution and quantitative, and can be used for downstream analyses of APA.
Collapse
|
104
|
Dehydration stress extends mRNA 3' untranslated regions with noncoding RNA functions in Arabidopsis. Genome Res 2017; 27:1427-1436. [PMID: 28522613 PMCID: PMC5538558 DOI: 10.1101/gr.218669.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/15/2017] [Indexed: 12/12/2022]
Abstract
The 3′ untranslated regions (3′ UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation, and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3′ UTRs, but the involvement of this process in stress response has not yet been clarified. Here, we report that a subset of stress-related genes exhibits 3′ UTR extensions of their mRNAs during dehydration stress. These extended 3′ UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs. Functional studies using T-DNA insertion mutants reveal that they can act as antisense transcripts to repress expression levels of sense genes from the opposite strand or can activate the transcription or lead to read-through transcription of their downstream genes. Further analysis suggests that transcripts with 3′ UTR extensions have weaker poly(A) signals than those without 3′ UTR extensions. Finally, we show that their biogenesis is partially dependent on a trans-acting factor FPA. Taken together, we report that dehydration stress could induce transcript 3′ UTR extensions and elucidate a novel function for these stress-induced 3′ UTR extensions as long noncoding RNAs in the regulation of their neighboring genes.
Collapse
|
105
|
Visualizing the life of mRNA in T cells. Biochem Soc Trans 2017; 45:563-570. [PMID: 28408496 DOI: 10.1042/bst20170003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 12/15/2022]
Abstract
T cells release ample amounts of cytokines during infection. This property is critical to prevent pathogen spreading and persistence. Nevertheless, whereas rapid and ample cytokine production supports the clearance of pathogens, the production must be restricted in time and location to prevent detrimental effects of chronic inflammation and immunopathology. Transcriptional and post-transcriptional processes determine the levels of cytokine production. How these regulatory mechanisms are interconnected, and how they regulate the magnitude of protein production in primary T cells is to date not well studied. Here, we highlight recent advances in the field that boost our understanding of the regulatory processes of cytokine production of T cells, with a focus on transcription, mRNA stability, localization and translation.
Collapse
|
106
|
Dimitrova Y, Gruber AJ, Mittal N, Ghosh S, Dimitriades B, Mathow D, Grandy WA, Christofori G, Zavolan M. TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. Biol Direct 2017; 12:8. [PMID: 28412966 PMCID: PMC5392957 DOI: 10.1186/s13062-017-0180-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/22/2017] [Indexed: 01/28/2023] Open
Abstract
Background The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. Methods From a computational analysis of a variety of high-throughput sequencing data sets we initially inferred that TFAP2A is connected to the core EMT network in both species. We then analysed publicly available human breast cancer data for TFAP2A expression and also studied the expression (by mRNA sequencing), activity (by monitoring the expression of its predicted targets), and binding (by electrophoretic mobility shift assay and chromatin immunoprecipitation) of this factor in a mouse mammary gland EMT model system (NMuMG) cell line. Results We found that upon induction of EMT, the activity of TFAP2A, reflected in the expression level of its predicted targets, is up-regulated in a variety of systems, both murine and human, while TFAP2A’s expression is increased in more “stem-like” cancers. We provide strong evidence for the direct interaction between the TFAP2A TF and the ZEB2 promoter and we demonstrate that this interaction affects ZEB2 expression. Overexpression of TFAP2A from an exogenous construct perturbs EMT, however, in a manner similar to the downregulation of endogenous TFAP2A that takes place during EMT. Conclusions Our study reveals that TFAP2A is a conserved component of the core network that regulates EMT, acting as a repressor of many genes, including ZEB2. Reviewers This article has been reviewed by Dr. Martijn Huynen and Dr. Nicola Aceto. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0180-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yoana Dimitrova
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Andreas J Gruber
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Nitish Mittal
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Souvik Ghosh
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Beatrice Dimitriades
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Daniel Mathow
- Department of Cellular and Molecular Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - William Aaron Grandy
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland
| | - Gerhard Christofori
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
| |
Collapse
|
107
|
The role of alternative polyadenylation in the antiviral innate immune response. Nat Commun 2017; 8:14605. [PMID: 28233779 PMCID: PMC5333124 DOI: 10.1038/ncomms14605] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/17/2017] [Indexed: 01/05/2023] Open
Abstract
Alternative polyadenylation (APA) is an important regulatory mechanism of gene functions in many biological processes. However, the extent of 3' UTR variation and the function of APA during the innate antiviral immune response are unclear. Here, we show genome-wide poly(A) sites switch and average 3' UTR length shortens gradually in response to vesicular stomatitis virus (VSV) infection in macrophages. Genes with APA and mRNA abundance change are enriched in immune-related categories such as the Toll-like receptor, RIG-I-like receptor, JAK-STAT and apoptosis-related signalling pathways. The expression of 3' processing factors is down-regulated upon VSV infection. When the core 3' processing factors are knocked down, viral replication is affected. Thus, our study reports the annotation of genes with APA in antiviral immunity and highlights the roles of 3' processing factors on 3' UTR variation upon viral infection.
Collapse
|
108
|
Galloway A, Turner M. Cell cycle RNA regulons coordinating early lymphocyte development. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28231639 PMCID: PMC5574005 DOI: 10.1002/wrna.1419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 01/19/2023]
Abstract
Lymphocytes undergo dynamic changes in gene expression as they develop from progenitor cells lacking antigen receptors, to mature cells that are prepared to mount immune responses. While transcription factors have established roles in lymphocyte development, they act in concert with post-transcriptional and post-translational regulators to determine the proteome. Furthermore, the post-transcriptional regulation of RNA regulons consisting of mRNAs whose protein products act cooperatively allows RNA binding proteins to exert their effects at multiple points in a pathway. Here, we review recent evidence demonstrating the importance of RNA binding proteins that control the cell cycle in lymphocyte development and discuss the implications for tumorigenesis. WIREs RNA 2017, 8:e1419. doi: 10.1002/wrna.1419 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| |
Collapse
|
109
|
Cai G, Jiang HL. A Modulator-Induced Defect-Formation Strategy to Hierarchically Porous Metal-Organic Frameworks with High Stability. Angew Chem Int Ed Engl 2016; 56:563-567. [DOI: 10.1002/anie.201610914] [Citation(s) in RCA: 358] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Guorui Cai
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| | - Hai-Long Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| |
Collapse
|
110
|
Xiao MS, Zhang B, Li YS, Gao Q, Sun W, Chen W. Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation. Mol Syst Biol 2016; 12:890. [PMID: 27932516 PMCID: PMC5199128 DOI: 10.15252/msb.20167375] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alternative polyadenylation (APA), which is regulated by both cis‐elements and trans‐factors, plays an important role in post‐transcriptional regulation of eukaryotic gene expression. However, comparing to the extensively studied transcription and alternative splicing, the extent of APA divergence during evolution and the relative cis‐ and trans‐contribution remain largely unexplored. To directly address these questions for the first time in mammals, by using deep sequencing‐based methods, we measured APA divergence between C57BL/6J and SPRET/EiJ mouse strains as well as allele‐specific APA pattern in their F1 hybrids. Among the 24,721 polyadenylation sites (pAs) from 7,271 genes expressing multiple pAs, we identified 3,747 pAs showing significant divergence between the two strains. After integrating the allele‐specific data from F1 hybrids, we demonstrated that these events could be predominately attributed to cis‐regulatory effects. Further systematic sequence analysis of the regions in proximity to cis‐divergent pAs revealed that the local RNA secondary structure and a poly(U) tract in the upstream region could negatively modulate the pAs usage.
Collapse
Affiliation(s)
- Mei-Sheng Xiao
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Bin Zhang
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Berlin, Germany.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yi-Sheng Li
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Wei Sun
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Berlin, Germany.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China .,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong, China
| |
Collapse
|
111
|
Cai G, Jiang HL. A Modulator-Induced Defect-Formation Strategy to Hierarchically Porous Metal-Organic Frameworks with High Stability. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610914] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guorui Cai
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| | - Hai-Long Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Suzhou Nano Science and Technology, Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| |
Collapse
|
112
|
Li Z, Zhang J, Luo T, Tan X, Liu C, Sang X, Ma X, Han B, Yang G. High internal ionic liquid phase emulsion stabilized by metal-organic frameworks. SOFT MATTER 2016; 12:8841-8846. [PMID: 27725975 DOI: 10.1039/c6sm01610c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The emulsification of metal-organic frameworks (MOFs) for the two immiscible phases of water and ionic liquid (IL) was investigated for the first time. It was found that Ni-BDC (BDC = 1,4-dicarboxybenzene) can emulsify water and ILs and favor the formation of high internal phase emulsions (HIPEs) under certain experimental conditions. The microstructures of the HIPEs were characterized by confocal laser scanning microscopy using a fluorescent dye Rhodamine B, which proves that the HIPEs are the IL-in-water type. Further results reveal that the HIPE forms during the IL-in-water to water-in-IL emulsion inversion. The possibilities of the HIPE formation by other MOFs (Cu-BDC and Zn-BDC) were explored and the mechanism for HIPE formation was discussed. The MOF-stabilized HIPE was applied to the in situ synthesis of a MOF/polymer composite by HIPE polymerization. The macroporous MOF/polyacrylamide network and MOF/polystyrene microspheres were obtained from the HIPEs, respectively.
Collapse
Affiliation(s)
- Zhihao Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Tian Luo
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
| | - Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
| | - Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xue Ma
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guanying Yang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| |
Collapse
|
113
|
Abstract
Alternative polyadenylation (APA) is an RNA-processing mechanism that generates distinct 3' termini on mRNAs and other RNA polymerase II transcripts. It is widespread across all eukaryotic species and is recognized as a major mechanism of gene regulation. APA exhibits tissue specificity and is important for cell proliferation and differentiation. In this Review, we discuss the roles of APA in diverse cellular processes, including mRNA metabolism, protein diversification and protein localization, and more generally in gene regulation. We also discuss the molecular mechanisms underlying APA, such as variation in the concentration of core processing factors and RNA-binding proteins, as well as transcription-based regulation.
Collapse
|
114
|
Luo T, Zhang J, Tan X, Liu C, Wu T, Li W, Sang X, Han B, Li Z, Mo G, Xing X, Wu Z. Water-in-Supercritical CO2
Microemulsion Stabilized by a Metal Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608695] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tian Luo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Tianbin Wu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Wei Li
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Zhihong Li
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Guang Mo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xueqing Xing
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Zhonghua Wu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| |
Collapse
|
115
|
Luo T, Zhang J, Tan X, Liu C, Wu T, Li W, Sang X, Han B, Li Z, Mo G, Xing X, Wu Z. Water-in-Supercritical CO2
Microemulsion Stabilized by a Metal Complex. Angew Chem Int Ed Engl 2016; 55:13533-13537. [DOI: 10.1002/anie.201608695] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Tian Luo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Tianbin Wu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Wei Li
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Zhihong Li
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Guang Mo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xueqing Xing
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Zhonghua Wu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Department of Chemistry; Capital Normal University; Institute of High Energy Physics; Chinese Academy of Sciences; China
| |
Collapse
|
116
|
Chen CYA, Shyu AB. Emerging Themes in Regulation of Global mRNA Turnover in cis. Trends Biochem Sci 2016; 42:16-27. [PMID: 27647213 DOI: 10.1016/j.tibs.2016.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
Abstract
mRNA is the molecule that conveys genetic information from DNA to the translation apparatus. mRNAs in all organisms display a wide range of stability, and mechanisms have evolved to selectively and differentially regulate individual mRNA stability in response to intracellular and extracellular cues. In recent years, three seemingly distinct aspects of RNA biology-mRNA N6-methyladenosine (m6A) modification, alternative 3' end processing and polyadenylation (APA), and mRNA codon usage-have been linked to mRNA turnover, and all three aspects function to regulate global mRNA stability in cis. Here, we discuss the discovery and molecular dissection of these mechanisms in relation to how they impact the intrinsic decay rate of mRNA in eukaryotes, leading to transcriptome reprogramming.
Collapse
Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| |
Collapse
|
117
|
Hollerer I, Curk T, Haase B, Benes V, Hauer C, Neu-Yilik G, Bhuvanagiri M, Hentze MW, Kulozik AE. The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion. RNA (NEW YORK, N.Y.) 2016; 22:1441-1453. [PMID: 27407180 PMCID: PMC4986898 DOI: 10.1261/rna.055657.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Stress adaptation plays a pivotal role in biological processes and requires tight regulation of gene expression. In this study, we explored the effect of cellular stress on mRNA polyadenylation and investigated the implications of regulated polyadenylation site usage on mammalian gene expression. High-confidence polyadenylation site mapping combined with global pre-mRNA and mRNA expression profiling revealed that stress induces an accumulation of genes with differentially expressed polyadenylated mRNA isoforms in human cells. Specifically, stress provokes a global trend in polyadenylation site usage toward decreased utilization of promoter-proximal poly(A) sites in introns or ORFs and increased utilization of promoter-distal polyadenylation sites in intergenic regions. This extensively affects gene expression beyond regulating mRNA abundance by changing mRNA length and by altering the configuration of open reading frames. Our study highlights the impact of post-transcriptional mechanisms on stress-dependent gene regulation and reveals the differential expression of alternatively polyadenylated transcripts as a common stress-induced mechanism in mammalian cells.
Collapse
Affiliation(s)
- Ina Hollerer
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana 1001, Slovenia
| | - Bettina Haase
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Christian Hauer
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Madhuri Bhuvanagiri
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg 69120, Germany Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg 69120, Germany
| |
Collapse
|
118
|
Liu C, Zhang J, Zheng L, Zhang J, Sang X, Kang X, Zhang B, Luo T, Tan X, Han B. Metal-Organic Framework for Emulsifying Carbon Dioxide and Water. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility (BSRF); Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Jing Zhang
- Beijing Synchrotron Radiation Facility (BSRF); Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Xinchen Kang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Bingxing Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Tian Luo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| |
Collapse
|
119
|
Liu C, Zhang J, Zheng L, Zhang J, Sang X, Kang X, Zhang B, Luo T, Tan X, Han B. Metal-Organic Framework for Emulsifying Carbon Dioxide and Water. Angew Chem Int Ed Engl 2016; 55:11372-6. [DOI: 10.1002/anie.201602150] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/28/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility (BSRF); Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Jing Zhang
- Beijing Synchrotron Radiation Facility (BSRF); Institute of High Energy Physics; Chinese Academy of Sciences; China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Xinchen Kang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Bingxing Zhang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Tian Luo
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Colloid and Interface and Thermodynamics; Institute of Chemistry; Chinese Academy of Sciences; University of Chinese Academy of Sciences; China
| |
Collapse
|
120
|
He S, Chen Y, Zhang Z, Ni B, He W, Wang X. Competitive coordination strategy for the synthesis of hierarchical-pore metal-organic framework nanostructures. Chem Sci 2016; 7:7101-7105. [PMID: 28567265 PMCID: PMC5450591 DOI: 10.1039/c6sc02272c] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/05/2016] [Indexed: 01/26/2023] Open
Abstract
We demonstrate a competitive coordination strategy for the synthesis of H-MOF nanostructures, such as two-dimensional H-MOF nanosheets and H-MOF nanocubes, evolving through an etching process tuned by a competitive ligand.
Metal–organic frameworks (MOFs) usually have micropores smaller than 2 nm, which may restrict their applications in some cases. Hierarchical-pore MOFs (H-MOFs) are a new family of MOF materials, possessing both micro- and mesopores to address this problem. Here we demonstrate a competitive coordination strategy for the synthesis of H-MOF nanostructures, such as two-dimensional (2D) H-MOF nanosheets and H-MOF nanocubes, evolving through an etching process tuned by a competitive ligand. The as-synthesized 2D H-MOF nanosheets can serve as a substrate to in situ immobilize Pd nanoparticles to achieve a surfactant-free Pd catalyst, by means of a simple soaking method of Pd2+ precursors. Combined with the unique structure and gas adsorption capacity of H-MOF-5, the Pd-H-MOF-5 catalyst exhibits superior catalytic performance.
Collapse
Affiliation(s)
- Su He
- Department of Chemistry , Tsinghua University , Beijing , 100084 , China .
| | - Yifeng Chen
- School of Pharmaceutical Science , Tsinghua University , Beijing , 100084 , China
| | - Zhicheng Zhang
- Department of Chemistry , Tsinghua University , Beijing , 100084 , China .
| | - Bing Ni
- Department of Chemistry , Tsinghua University , Beijing , 100084 , China .
| | - Wei He
- School of Pharmaceutical Science , Tsinghua University , Beijing , 100084 , China
| | - Xun Wang
- Department of Chemistry , Tsinghua University , Beijing , 100084 , China .
| |
Collapse
|
121
|
Ahrné E, Glatter T, Viganò C, Schubert CV, Nigg EA, Schmidt A. Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments. J Proteome Res 2016; 15:2537-47. [DOI: 10.1021/acs.jproteome.6b00066] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse
50/70, 4056 Basel, Switzerland
| | - Timo Glatter
- Biozentrum, University of Basel, Klingelbergstrasse
50/70, 4056 Basel, Switzerland
| | - Cristina Viganò
- Biozentrum, University of Basel, Klingelbergstrasse
50/70, 4056 Basel, Switzerland
| | - Conrad von Schubert
- Biozentrum, University of Basel, Klingelbergstrasse
50/70, 4056 Basel, Switzerland
| | - Erich A. Nigg
- Biozentrum, University of Basel, Klingelbergstrasse
50/70, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse
50/70, 4056 Basel, Switzerland
| |
Collapse
|
122
|
Gruber AJ, Schmidt R, Gruber AR, Martin G, Ghosh S, Belmadani M, Keller W, Zavolan M. A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. Genome Res 2016; 26:1145-59. [PMID: 27382025 PMCID: PMC4971764 DOI: 10.1101/gr.202432.115] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3′ untranslated region (3′ UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3′ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3′ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3′ end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3′ end processing in both mouse and human. With 3′ end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3′ UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3′ UTR–dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3′ end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3′ end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle.
Collapse
Affiliation(s)
- Andreas J Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Manuel Belmadani
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Walter Keller
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
123
|
Tan X, Zhang J, Luo T, Sang X, Liu C, Zhang B, Peng L, Li W, Han B. Micellization of long-chain ionic liquids in deep eutectic solvents. SOFT MATTER 2016; 12:5297-5303. [PMID: 27222006 DOI: 10.1039/c6sm00924g] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aggregation behavior of the ionic liquid (IL) 1-alkyl-3-methylimidazolium chloride with different alkyl chain lengths in a deep eutectic solvent (DES, composed of choline chloride and glycerol in a 1 : 2 mole ratio) was studied for the first time. The critical micellar concentration, micellar size and intermolecular interactions in IL/DES solutions were investigated by different techniques including the fluorescence probe technique, small angle X-ray scattering and Fourier transform infrared spectroscopy. The solvophobic effect dominates the micellization of CnmimCl in DES and the intermolecular hydrogen-bond interaction plays a positive role to promote micelle formation. The micellar solutions were utilized for the synthesis of the water-unstable metal-organic framework Cu3(BTC)2 (BTC = 1,3,5-benzenetricarboxylate) at room temperature. X-Ray diffraction, scanning electron microscopy, transmission electron microscopy and nitrogen adsorption-desorption isotherms confirm the formation of crystalline Cu3(BTC)2 nanocrystals with mesoporous structures. The morphologies and porosity properties of Cu3(BTC)2 nanocrystals can be modulated by varying the concentration of CnmimCl.
Collapse
Affiliation(s)
- Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
124
|
Ogorodnikov A, Kargapolova Y, Danckwardt S. Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. Pflugers Arch 2016; 468:993-1012. [PMID: 27220521 PMCID: PMC4893057 DOI: 10.1007/s00424-016-1828-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
The human transcriptome is highly dynamic, with each cell type, tissue, and organ system expressing an ensemble of transcript isoforms that give rise to considerable diversity. Apart from alternative splicing affecting the "body" of the transcripts, extensive transcriptome diversification occurs at the 3' end. Transcripts differing at the 3' end can have profound physiological effects by encoding proteins with distinct functions or regulatory properties or by affecting the mRNA fate via the inclusion or exclusion of regulatory elements (such as miRNA or protein binding sites). Importantly, the dynamic regulation at the 3' end is associated with various (patho)physiological processes, including the immune regulation but also tumorigenesis. Here, we recapitulate the mechanisms of constitutive mRNA 3' end processing and review the current understanding of the dynamically regulated diversity at the transcriptome 3' end. We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.
Collapse
Affiliation(s)
- Anton Ogorodnikov
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Langenbeckstr 1, 55131, Mainz, Germany.
| |
Collapse
|
125
|
Domingues RG, Lago-Baldaia I, Pereira-Castro I, Fachini JM, Oliveira L, Drpic D, Lopes N, Henriques T, Neilson JR, Carmo AM, Moreira A. CD5 expression is regulated during human T-cell activation by alternative polyadenylation, PTBP1, and miR-204. Eur J Immunol 2016; 46:1490-503. [PMID: 27005442 DOI: 10.1002/eji.201545663] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 02/17/2016] [Accepted: 03/16/2016] [Indexed: 01/29/2023]
Abstract
T lymphocytes stimulated through their antigen receptor (TCR) preferentially express mRNA isoforms with shorter 3´ untranslated regions (3´-UTRs) derived from alternative pre-mRNA cleavage and polyadenylation (APA). However, the physiological relevance of APA programs remains poorly understood. CD5 is a T-cell surface glycoprotein that negatively regulates TCR signaling from the onset of T-cell activation. CD5 plays a pivotal role in mediating outcomes of cell survival or apoptosis, and may prevent both autoimmunity and cancer. In human primary T lymphocytes and Jurkat cells we found three distinct mRNA isoforms encoding CD5, each derived from distinct poly(A) signals (PASs). Upon T-cell activation, there is an overall increase in CD5 mRNAs with a specific increase in the relative expression of the shorter isoforms. 3´-UTRs derived from these shorter isoforms confer higher reporter expression in activated T cells relative to the longer isoform. We further show that polypyrimidine tract binding protein (PTB/PTBP1) directly binds to the proximal PAS and PTB siRNA depletion causes a decrease in mRNA derived from this PAS, suggesting an effect on stability or poly(A) site selection to circumvent targeting of the longer CD5 mRNA isoform by miR-204. These mechanisms fine-tune CD5 expression levels and thus ultimately T-cell responses.
Collapse
Affiliation(s)
- Rita G Domingues
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Inês Lago-Baldaia
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Isabel Pereira-Castro
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Joseph M Fachini
- Department of Molecular Physiology and Biophysics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Liliana Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Cell Activation and Gene Expression Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Danica Drpic
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Nair Lopes
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Telmo Henriques
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Alexandre M Carmo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Cell Activation and Gene Expression Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| |
Collapse
|
126
|
Erson-Bensan AE, Can T. Alternative Polyadenylation: Another Foe in Cancer. Mol Cancer Res 2016; 14:507-17. [PMID: 27075335 DOI: 10.1158/1541-7786.mcr-15-0489] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/30/2016] [Indexed: 11/16/2022]
Abstract
Advancements in sequencing and transcriptome analysis methods have led to seminal discoveries that have begun to unravel the complexity of cancer. These studies are paving the way toward the development of improved diagnostics, prognostic predictions, and targeted treatment options. However, it is clear that pieces of the cancer puzzle are still missing. In an effort to have a more comprehensive understanding of the development and progression of cancer, we have come to appreciate the value of the noncoding regions of our genomes, partly due to the discovery of miRNAs and their significance in gene regulation. Interestingly, the miRNA-mRNA interactions are not solely dependent on variations in miRNA levels. Instead, the majority of genes harbor multiple polyadenylation signals on their 3' UTRs (untranslated regions) that can be differentially selected on the basis of the physiologic state of cells, resulting in alternative 3' UTR isoforms. Deregulation of alternative polyadenylation (APA) has increasing interest in cancer research, because APA generates mRNA 3' UTR isoforms with potentially different stabilities, subcellular localizations, translation efficiencies, and functions. This review focuses on the link between APA and cancer and discusses the mechanisms as well as the tools available for investigating APA events in cancer. Overall, detection of deregulated APA-generated isoforms in cancer may implicate some proto-oncogene activation cases of unknown causes and may help the discovery of novel cases; thus, contributing to a better understanding of molecular mechanisms of cancer. Mol Cancer Res; 14(6); 507-17. ©2016 AACR.
Collapse
Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU) (ODTU), Ankara, Turkey.
| | - Tolga Can
- Department of Computer Engineering, Middle East Technical University (METU) (ODTU), Ankara, Turkey
| |
Collapse
|
127
|
Gain-of-function reporters for analysis of mRNA 3′-end formation: Design and optimization. Biotechniques 2016; 60:137-40. [DOI: 10.2144/000114390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/11/2015] [Indexed: 11/23/2022] Open
Abstract
The concept of mRNA 3′-end formation as a static, minimally regulated housekeeping process has undergone a paradigm shift. Many recent studies have shown that accurate and efficient 3′-end formation of mRNA is highly regulated and that dysregulation of this process is a hallmark of several diseases. While there are many global analysis methods for monitoring altered mRNA processing, methods for investigating specific RNA 3′-end processing events in cells have not significantly changed. Here we describe a facile gain-of-function cellular reporter for the analysis of mRNA 3′-end formation as an alternative to approaches that are technically challenging or use radioactivity. We also offer suggestions for optimization of our approach and enhancement of its reproducibility.
Collapse
|
128
|
Zhang B, Zhang J, Liu C, Peng L, Sang X, Han B, Ma X, Luo T, Tan X, Yang G. High-internal-phase emulsions stabilized by metal-organic frameworks and derivation of ultralight metal-organic aerogels. Sci Rep 2016; 6:21401. [PMID: 26892258 PMCID: PMC4759572 DOI: 10.1038/srep21401] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/22/2016] [Indexed: 01/23/2023] Open
Abstract
To design high-internal-phase emulsion (HIPE) systems is of great interest from the viewpoints of both fundamental researches and practical applications. Here we demonstrate for the first time the utilization of metal-organic framework (MOF) for HIPE formation. By stirring the mixture of water, oil and MOF at room temperature, the HIPE stabilized by the assembly of MOF nanocrystals at oil-water interface could be formed. The MOF-stabilized HIPE provides a novel route to produce highly porous metal-organic aerogel (MOA) monolith. After removing the liquids from the MOF-stabilized HIPE, the ultralight MOA with density as low as 0.01 g·cm(-3) was obtained. The HIPE approach for MOA formation has unique advantages and is versatile in producing different kinds of ultralight MOAs with tunable porosities and structures.
Collapse
Affiliation(s)
- Bingxing Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Li Peng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Xue Ma
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Tian Luo
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Xiuniang Tan
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Guanying Yang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| |
Collapse
|
129
|
Mayr C. Evolution and Biological Roles of Alternative 3'UTRs. Trends Cell Biol 2015; 26:227-237. [PMID: 26597575 DOI: 10.1016/j.tcb.2015.10.012] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022]
Abstract
More than half of human genes use alternative cleavage and polyadenylation to generate alternative 3' untranslated region (3'UTR) isoforms. Most efforts have focused on transcriptome-wide mapping of alternative 3'UTRs and on the question of how 3'UTR isoform ratios may be regulated. However, it remains less clear why alternative 3'UTRs have evolved and what biological roles they play. This review summarizes our current knowledge of the functional roles of alternative 3'UTRs, including mRNA localization, mRNA stability, and translational efficiency. Recent work suggests that alternative 3'UTRs may also enable the formation of protein-protein interactions to regulate protein localization or to diversify protein functions. These recent findings open an exciting research direction for the investigation of new biological roles of alternative 3'UTRs.
Collapse
Affiliation(s)
- Christine Mayr
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
130
|
Neve J, Burger K, Li W, Hoque M, Patel R, Tian B, Gullerova M, Furger A. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Res 2015; 26:24-35. [PMID: 26546131 PMCID: PMC4691748 DOI: 10.1101/gr.193995.115] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/04/2015] [Indexed: 11/25/2022]
Abstract
Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3' UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type-specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3' UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice.
Collapse
Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
| | - Kaspar Burger
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom
| | - Wencheng Li
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Mainul Hoque
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, United Kingdom
| | - Andre Furger
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
| |
Collapse
|
131
|
Kim Y, Yang T, Yun G, Ghasemian MB, Koo J, Lee E, Cho SJ, Kim K. Hydrolytic Transformation of Microporous Metal–Organic Frameworks to Hierarchical Micro‐ and Mesoporous MOFs. Angew Chem Int Ed Engl 2015; 54:13273-8. [DOI: 10.1002/anie.201506391] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/20/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Yonghwi Kim
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Tao Yang
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Gyeongwon Yun
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Mohammad Bagher Ghasemian
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Jaehyoung Koo
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
| | - Eunsung Lee
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
| | - Sung June Cho
- Department of Chemical Engineering, Chonnam National University, Gwangju, 500‐757 (Republic of Korea)
| | - Kimoon Kim
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
- Division of Advanced Materials Science, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
| |
Collapse
|
132
|
Kim Y, Yang T, Yun G, Ghasemian MB, Koo J, Lee E, Cho SJ, Kim K. Hydrolytic Transformation of Microporous Metal–Organic Frameworks to Hierarchical Micro‐ and Mesoporous MOFs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506391] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yonghwi Kim
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Tao Yang
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Gyeongwon Yun
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Mohammad Bagher Ghasemian
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
| | - Jaehyoung Koo
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
| | - Eunsung Lee
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
| | - Sung June Cho
- Department of Chemical Engineering, Chonnam National University, Gwangju, 500‐757 (Republic of Korea)
| | - Kimoon Kim
- Center for Self‐assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang, 790‐784 (Republic of Korea) http://csc.ibs.re.kr/
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
- Division of Advanced Materials Science, Pohang University of Science and Technology, Pohang, 790‐784 (Republic of Korea)
| |
Collapse
|
133
|
Ahrné E, Martinez-Segura A, Syed AP, Vina-Vilaseca A, Gruber AJ, Marguerat S, Schmidt A. Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry. Methods 2015; 85:100-107. [PMID: 25952948 DOI: 10.1016/j.ymeth.2015.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/04/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022] Open
Abstract
The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative precision and accuracy as well as proteome coverage in comparison to existing mass spectrometry based strategies.
Collapse
Affiliation(s)
- Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Amalia Martinez-Segura
- Quantitative Gene Expression Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Afzal Pasha Syed
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Arnau Vina-Vilaseca
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Andreas J Gruber
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Samuel Marguerat
- Quantitative Gene Expression Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
| |
Collapse
|
134
|
Kanitz A, Gypas F, Gruber AJ, Gruber AR, Martin G, Zavolan M. Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol 2015. [PMID: 26201343 PMCID: PMC4511015 DOI: 10.1186/s13059-015-0702-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Understanding the regulation of gene expression, including transcription start site usage, alternative splicing, and polyadenylation, requires accurate quantification of expression levels down to the level of individual transcript isoforms. To comparatively evaluate the accuracy of the many methods that have been proposed for estimating transcript isoform abundance from RNA sequencing data, we have used both synthetic data as well as an independent experimental method for quantifying the abundance of transcript ends at the genome-wide level. Results We found that many tools have good accuracy and yield better estimates of gene-level expression compared to commonly used count-based approaches, but they vary widely in memory and runtime requirements. Nucleotide composition and intron/exon structure have comparatively little influence on the accuracy of expression estimates, which correlates most strongly with transcript/gene expression levels. To facilitate the reproduction and further extension of our study, we provide datasets, source code, and an online analysis tool on a companion website, where developers can upload expression estimates obtained with their own tool to compare them to those inferred by the methods assessed here. Conclusions As many methods for quantifying isoform abundance with comparable accuracy are available, a user’s choice will likely be determined by factors such as the memory and runtime requirements, as well as the availability of methods for downstream analyses. Sequencing-based methods to quantify the abundance of specific transcript regions could complement validation schemes based on synthetic data and quantitative PCR in future or ongoing assessments of RNA-seq analysis methods. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0702-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Foivos Gypas
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Andreas J Gruber
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Andreas R Gruber
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Georges Martin
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.
| |
Collapse
|
135
|
Velten L, Anders S, Pekowska A, Järvelin AI, Huber W, Pelechano V, Steinmetz LM. Single-cell polyadenylation site mapping reveals 3' isoform choice variability. Mol Syst Biol 2015; 11:812. [PMID: 26040288 PMCID: PMC4501847 DOI: 10.15252/msb.20156198] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell-to-cell variability in gene expression is important for many processes in biology, including embryonic development and stem cell homeostasis. While heterogeneity of gene expression levels has been extensively studied, less attention has been paid to mRNA polyadenylation isoform choice. 3′ untranslated regions regulate mRNA fate, and their choice is tightly controlled during development, but how 3′ isoform usage varies within genetically and developmentally homogeneous cell populations has not been explored. Here, we perform genome-wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single-cell transcriptomic method, BATSeq. By applying BATBayes, a statistical framework for analyzing single-cell isoform data, we find that while the developmental state of the cell globally determines isoform usage, single cells from the same state differ in the choice of isoforms. Notably this variation exceeds random selection with equal preference in all cells, a finding that was confirmed by RNA FISH data. Variability in 3′ isoform choice has potential implications on functional cell-to-cell heterogeneity as well as utility in resolving cell populations.
Collapse
Affiliation(s)
- Lars Velten
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Simon Anders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Aleksandra Pekowska
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Aino I Järvelin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vicent Pelechano
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
136
|
Zhang B, Zhang J, Liu C, Sang X, Peng L, Ma X, Wu T, Han B, Yang G. Solvent determines the formation and properties of metal–organic frameworks. RSC Adv 2015. [DOI: 10.1039/c5ra02440d] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein we synthesized Cu3(BTC)2 nanocrystals in a series of water/ethanol solvent systems at room temperature. The size and porosity of Cu3(BTC)2 can be easily modulated by controlling the composition of the mixed solvent.
Collapse
Affiliation(s)
- Bingxing Zhang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Jianling Zhang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Chengcheng Liu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Xinxin Sang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Li Peng
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Xue Ma
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Tianbin Wu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| | - Guanying Yang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Colloid and Interface and Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
- China
| |
Collapse
|