1
|
Sterniša M, Sabotič J, Janež N, Curk T, Klančnik A. SIMBA Method-Simultaneous Detection of Antimicrobial and Anti-biofilm Activity of New Compounds Using Salmonella Infantis. Bio Protoc 2023; 13:e4783. [PMID: 37575388 PMCID: PMC10415211 DOI: 10.21769/bioprotoc.4783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/06/2023] [Accepted: 06/15/2023] [Indexed: 08/15/2023] Open
Abstract
The development of antimicrobial resistance and the formation of Salmonella biofilms are serious public health problems. For this reason, new natural compounds with antimicrobial and anti-biofilm activity are being sought, and wild fungi represent an untapped potential. Various extraction agents, including organic solvents and aqueous buffers, can be used to obtain bioactive compounds from natural sources. To evaluate their bioactivity, extensive screening studies are required to determine antimicrobial and anti-biofilm activity using methods such as broth microdilution or crystal violet assay, respectively, but none of these methods allow simultaneous evaluation of both activities against bacteria. Cold water extraction from wild fungi offers the advantage of extracting water-soluble compounds. The SIMultaneous detection of antiMicrobial and anti-Biofilm Activity (SIMBA) method combines the testing of both types of activity against bacteria with the evaluation of the 20 h growth curve of the Salmonella Infantis ŽM9 strain determined with absorbance measurements at 600 nm in a 96-well plate. SIMBA method thus shortens the time to determine the bioactivity of extracts, reduces material consumption, and eliminates the need for additional reagents. SIMBA enables rapid selection of bioactive extracts for their fractionation and shortens the time to determine new natural products with antimicrobial and anti-biofilm activity. Graphical overview.
Collapse
Affiliation(s)
- Meta Sterniša
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Nika Janež
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
2
|
Abstract
BACKGROUND Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose a method called Sparse Tropical Matrix Factorization (STMF) for the estimation of missing (unknown) values in sparse data. RESULTS We evaluate the efficiency of the STMF method on both synthetic data and biological data in the form of gene expression measurements downloaded from The Cancer Genome Atlas (TCGA) database. Tests on unique synthetic data showed that STMF approximation achieves a higher correlation than non-negative matrix factorization (NMF), which is unable to recover patterns effectively. On real data, STMF outperforms NMF on six out of nine gene expression datasets. While NMF assumes normal distribution and tends toward the mean value, STMF can better fit to extreme values and distributions. CONCLUSION STMF is the first work that uses tropical semiring on sparse data. We show that in certain cases semirings are useful because they consider the structure, which is different and simpler to understand than it is with standard linear algebra.
Collapse
Affiliation(s)
- Amra Omanović
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Hilal Kazan
- Department of Computer Engineering, Antalya Bilim University, Çıplaklı, Akdeniz Blv. No:290/A, 07190 Antalya, Turkey
| | - Polona Oblak
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| |
Collapse
|
3
|
Pačnik K, Ogrizović M, Diepold M, Eisenberg T, Žganjar M, Žun G, Kužnik B, Gostinčar C, Curk T, Petrovič U, Natter K. Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae. BMC Genomics 2021; 22:110. [PMID: 33563210 PMCID: PMC7871550 DOI: 10.1186/s12864-021-07417-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/31/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The accumulation of intracellular fat depots is a polygenic trait. Therefore, the extent of lipid storage in the individuals of a species covers a broad range and is determined by many genetic factors. Quantitative trait loci analysis can be used to identify those genetic differences between two strains of the same species that are responsible for the differences in a given phenotype. We used this method and complementary approaches to identify genes in the yeast Saccharomyces cerevisiae that are involved in neutral lipid storage. RESULTS We selected two yeast strains, the laboratory strain BY4741 and the wine yeast AWRI1631, with a more than two-fold difference in neutral lipid content. After crossing, sporulation and germination, we used fluorescence activated cell sorting to isolate a subpopulation of cells with the highest neutral lipid content from the pool of segregants. Whole genome sequencing of this subpopulation and of the unsorted pool of segregants implicated several loci that are involved in lipid accumulation. Three of the identified genes, PIG1, PHO23 and RML2, were investigated in more detail. Deletions of these genes and the exchange of the alleles between the two parental strains confirmed that the encoded proteins contribute to neutral lipid storage in S. cerevisiae and that PIG1, PHO23 and RML2 are the major causative genes. Backcrossing of one of the segregants with the parental strains for seven generations revealed additional regions in the genomes of both strains with potential causative genes for the high lipid accumulation phenotype. CONCLUSIONS We identified several genes that contribute to the phenotype of lipid accumulation in an allele-specific manner. Surprisingly, no allelic variations of genes with known functions in lipid metabolism were found, indicating that the level of storage lipid accumulation is determined by many cellular processes that are not directly related to lipid metabolism.
Collapse
Affiliation(s)
- Klavdija Pačnik
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mojca Ogrizović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Matthias Diepold
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Mia Žganjar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Gašper Žun
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Beti Kužnik
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.
| |
Collapse
|
4
|
Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J. A systems view of spliceosomal assembly and branchpoints with iCLIP. Nat Struct Mol Biol 2019; 26:930-940. [PMID: 31570875 PMCID: PMC6859068 DOI: 10.1038/s41594-019-0300-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 08/14/2019] [Indexed: 02/02/2023]
Abstract
Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipitates SmB along with small nuclear ribonucleoprotein particles and auxiliary RNA binding proteins, to map spliceosome engagement with pre-messenger RNAs in human cell lines. This revealed seven peaks of spliceosomal crosslinking around branchpoints (BPs) and splice sites. We identified RNA binding proteins that crosslink to each peak, including known and candidate splicing factors. Moreover, we detected the use of over 40,000 BPs with strong sequence consensus and structural accessibility, which align well to nearby crosslinking peaks. We show how the position and strength of BPs affect the crosslinking patterns of spliceosomal factors, which bind more efficiently upstream of strong or proximally located BPs and downstream of weak or distally located BPs. These insights exemplify spliceosome iCLIP as a broadly applicable method for transcriptomic studies of splicing mechanisms.
Collapse
Affiliation(s)
- Michael Briese
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Institute of Clinical Neurobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Nejc Haberman
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
| | - Christopher R Sibley
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Edinburgh University, Edinburgh, UK
| | - Rupert Faraway
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
| | - Andrea S Elser
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, London, UK
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, London, UK
| | - Zhen Wang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Institute of Molecular Biology GmbH, Mainz, Germany
| | - David Perera
- MRC Cancer Unit at the University of Cambridge, Cambridge, UK
| | - Vihandha O Wickramasinghe
- MRC Cancer Unit at the University of Cambridge, Cambridge, UK
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Luciano Saieva
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | | | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- The Francis Crick Institute, London, UK.
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK.
| |
Collapse
|
5
|
Vodopivec M, Lah L, Narat M, Curk T. Metabolomic profiling of CHO fed-batch growth phases at 10, 100, and 1,000 L. Biotechnol Bioeng 2019; 116:2720-2729. [PMID: 31184374 DOI: 10.1002/bit.27087] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/17/2019] [Accepted: 06/03/2019] [Indexed: 01/08/2023]
Abstract
Established bioprocess monitoring is based on quick and reliable methods, including cell count and viability measurement, extracellular metabolite measurement, and the measurement of physicochemical qualities of the cultivation medium. These methods are sufficient for monitoring of process performance, but rarely give insight into the actual physiological states of the cell culture. However, understanding of the latter is essential for optimization of bioprocess development. Our study used LC-MS metabolomics as a tool for additional resolution of bioprocess monitoring and was designed at three bioreactors scales (10 L, 100 L, and 1,000 L) to gain insight into the basal metabolic states of the Chinese hamster ovary (CHO) cell culture during fed-batch. Metabolites characteristics of the four growth stages (early and late exponential phase, stationary phase, and the phase of decline) were identified by multivariate analysis. Enriched metabolic pathways were then established for each growth phase using the CHO metabolic network model. Biomass generation and nucleotide synthesis were enriched in early exponential phase, followed by increased protein production and imbalanced glutathione metabolism in late exponential phase. Glycolysis became downregulated in stationary phase and amino-acid metabolism increased. Phase of culture decline resulted in rise of oxidized glutathione and fatty acid concentrations. Intracellular metabolic profiles of the CHO fed-batch culture were also shown to be consistent with scale and thus demonstrate metabolomic profiling as an informative method to gain physiological insight into the cell culture states during bioprocess regardless of scale.
Collapse
Affiliation(s)
- Maja Vodopivec
- Bioprocess Development, Technical Development Biologics Mengeš, Novartis Technical Research & Development, Lek Pharmaceuticals d.d, Slovenia
| | - Ljerka Lah
- Bioprocess Development, Technical Development Biologics Mengeš, Novartis Technical Research & Development, Lek Pharmaceuticals d.d, Slovenia
| | - Mojca Narat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Curk
- Bioinformatics Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenija
| |
Collapse
|
6
|
Lee E, Leforestier A, Di Domizio J, Curk T, Abbaspour L, Berezhnoy N, Fazli H, Nordenskiold L, Dobnikar J, Gilliet M, Wong G. 013 NETs generate structured antimicrobial peptide-nucleosome immune complexes with inter-DNA spacings optimal for TLR9 activation. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.03.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
Ehrmann I, Crichton JH, Gazzara MR, James K, Liu Y, Grellscheid SN, Curk T, de Rooij D, Steyn JS, Cockell S, Adams IR, Barash Y, Elliott DJ. An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning. eLife 2019; 8:39304. [PMID: 30674417 PMCID: PMC6345566 DOI: 10.7554/elife.39304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/18/2018] [Indexed: 12/28/2022] Open
Abstract
Male germ cells of all placental mammals express an ancient nuclear RNA binding protein of unknown function called RBMXL2. Here we find that deletion of the retrogene encoding RBMXL2 blocks spermatogenesis. Transcriptome analyses of age-matched deletion mice show that RBMXL2 controls splicing patterns during meiosis. In particular, RBMXL2 represses the selection of aberrant splice sites and the insertion of cryptic and premature terminal exons. Our data suggest a Rbmxl2 retrogene has been conserved across mammals as part of a splicing control mechanism that is fundamentally important to germ cell biology. We propose that this mechanism is essential to meiosis because it buffers the high ambient concentrations of splicing activators, thereby preventing poisoning of key transcripts and disruption to gene expression by aberrant splice site selection. In humans and other mammals, a sperm from a male fuses with an egg cell from a female to produce an embryo that may ultimately grow into a new individual. Sperm and egg cells are made when certain cells in the body divide in a process called meiosis. Many proteins are required for meiosis to happen and these proteins are made using instructions provided by genes, which are made of a molecule called DNA. The DNA within a gene is transcribed to make molecules of ribonucleic acid (or RNA for short). The cell then modifies many of these RNAs in a process called splicing before using them as templates to make proteins. During splicing, segments of RNA known as introns are discarded and other segments termed exons are joined together. Some exons may also be removed from RNAs in different combinations to create different proteins from the same gene. A protein called RBMXL2 is able to bind to RNA molecules and is only made during and after meiosis in humans and most other mammals. RBMXL2 can also bind to other proteins that are known to be involved in controlling splicing of RNAs, but its role in splicing remains unclear. To address this question, Ehrmann et al. studied the gene that encodes the RBMXL2 protein in mice. Removing this gene prevented male mice from being able to make sperm. Further experiments using a technique called RNA sequencing showed that the RBMXL2 protein helps to ensure that splicing happens correctly by preventing bits of exons and introns in mouse genes from being rearranged. These findings suggest that the gene encoding RBMXL2 is part of a splicing control mechanism that is important for making sperm and egg cells. The work of Ehrmann et al. could eventually help some couples understand why they have problems conceiving children. Male infertility is poorly understood, and not knowing its causes can harm the mental health of affected men. Furthermore, these findings may help researchers to understand the role of a closely related protein called RBMY that has also been linked to infertility in men, but is much more difficult to study.
Collapse
Affiliation(s)
- Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - James H Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Katherine James
- Life Sciences, Natural History Museum, London, United Kingdom
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Sushma Nagaraja Grellscheid
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom.,School of Biological and Biomedical Sciences, University of Durham, Durham, United Kingdom
| | - Tomaž Curk
- Laboratory of Bioinformatics, Faculty of Computer and Information Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Dirk de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jannetta S Steyn
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, United States
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| |
Collapse
|
8
|
Curk T, McDonald T, Zazelenchuk D, Weidensaul S, Brinker D, Huy S, Smith N, Miller T, Robillard A, Gauthier G, Lecomte N, Therrien JF. Winter irruptive Snowy Owls (Bubo scandiacus) in North America are not starving. CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Winter irruptions, defined as irregular massive movement of individuals over large distances, have been linked to food supply. Two hypotheses have been put forward: the “lack-of-food” suggests that a shortage of food forces individuals to leave their regular winter range and the “breeding output” suggests that unusually large food supplies during the preceding breeding season allows production of a large number of offspring dispersing in winter. According to the breeding output hypothesis, irruptive Snowy Owls (Bubo scandiacus (Linnaeus, 1758)) in eastern North America should not exhibit a lower body condition than individuals in regular wintering regions and individuals on the breeding grounds. Additionally, body condition of irruptive individuals should be unrelated to irruption intensity. Although body condition of juveniles was generally lower than that of adults and improved during the winter, we measured a fair body condition in both juvenile and adult irruptive Snowy Owls across North America. The results showed that Snowy Owls are not in a starving state during winter and that body condition of all age classes was not related to winter irruption intensity. Those results support the breeding output hypothesis suggesting that winter irruptions seem to be primarily the result of a large number of offspring produced when food availability on the breeding grounds is high.
Collapse
Affiliation(s)
- T. Curk
- Hawk Mountain Sanctuary, Orwigsburg, Pennsylvania, USA
- Max Planck Institute for Ornithology, Radolfzell, Germany
| | | | | | - S. Weidensaul
- Ned Smith Center for Nature and Art, Millersburg, Pennsylvania, USA
| | - D. Brinker
- Maryland Department of Natural Resources, Catonsville, Maryland, USA
| | - S. Huy
- Project Owlnet, Maryland, USA
| | - N. Smith
- Mass Audubon, Lincoln, Massachusetts, USA
| | - T. Miller
- Conservation Science Global, Inc., Cape May, New Jersey, USA
| | - A. Robillard
- Université Laval, Centre d’études nordiques, QC G1V 0A6, Canada
| | - G. Gauthier
- Université Laval, Centre d’études nordiques, QC G1V 0A6, Canada
| | - N. Lecomte
- Canada Research Chair in Polar and Boreal Ecology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - J.-F. Therrien
- Hawk Mountain Sanctuary, Orwigsburg, Pennsylvania, USA
- Canada Research Chair in Polar and Boreal Ecology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| |
Collapse
|
9
|
Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J. High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Rep 2018; 19:1056-1067. [PMID: 28467899 PMCID: PMC5437728 DOI: 10.1016/j.celrep.2017.04.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 11/05/2022] Open
Abstract
Many RNA-binding proteins (RBPs) regulate both alternative exons and poly(A) site selection. To understand their regulatory principles, we developed expressRNA, a web platform encompassing computational tools for integration of iCLIP and RNA motif analyses with RNA-seq and 3′ mRNA sequencing. This reveals at nucleotide resolution the “RNA maps” describing how the RNA binding positions of RBPs relate to their regulatory functions. We use this approach to examine how TDP-43, an RBP involved in several neurodegenerative diseases, binds around its regulated poly(A) sites. Binding close to the poly(A) site generally represses, whereas binding further downstream enhances use of the site, which is similar to TDP-43 binding around regulated exons. Our RNAmotifs2 software also identifies sequence motifs that cluster together with the binding motifs of TDP-43. We conclude that TDP-43 directly regulates diverse types of pre-mRNA processing according to common position-dependent principles. TDP-43 regulates competing poly(A) sites in a highly position-dependent manner expressRNA is a new platform for analysis of alternative polyadenylation and splicing RNAmotifs2 is a cluster motif analysis platform integrated with expressRNA Regulation of pre-mRNA processing might follow common position-dependent principles
Collapse
Affiliation(s)
- Gregor Rot
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Zhen Wang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institut de Biologie de l'ENS (IBENS), 46 rue d'Ulm, Paris 75005, France
| | - Ina Huppertz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Miha Modic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Stem Cell Research, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tina Lenče
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Martina Hallegger
- UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nejc Haberman
- UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, 1001 Ljubljana, Slovenia
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
10
|
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J. Erratum to: Insights into the design and interpretation of iCLIP experiments. Genome Biol 2017; 18:154. [PMID: 28810898 PMCID: PMC5558699 DOI: 10.1186/s13059-017-1294-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Affiliation(s)
- Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ina Huppertz
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.,European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julian König
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Zhen Wang
- Institut de Biologie de l'ENS (IBENS), Paris, France.,CNRS UMR 8197, Paris, Cedex 05, 75230, France
| | - Christian Hauer
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Paris, France.,CNRS UMR 8197, Paris, Cedex 05, 75230, France
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška cesta 25, 1000, Ljubljana, Slovenia
| | - Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK. .,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| |
Collapse
|
11
|
Lee E, Takahashi T, Curk T, Dobnikar J, Gallo R, Wong G. 070 Liquid crystalline ordering of antimicrobial peptide-RNA complexes controls TLR3 activation. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
12
|
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J. Insights into the design and interpretation of iCLIP experiments. Genome Biol 2017; 18:7. [PMID: 28093074 PMCID: PMC5240381 DOI: 10.1186/s13059-016-1130-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 12/08/2016] [Indexed: 01/16/2023] Open
Abstract
Background Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis. This variety of approaches can create challenges for a novice user and can hamper insights from multi-study comparisons. Here, we produce data with multiple variants of CLIP and evaluate the data with various computational methods to better understand their suitability. Results We perform experiments for PTBP1 and eIF4A3 using individual-nucleotide resolution CLIP (iCLIP), employing either UV-C or photoactivatable 4-thiouridine (4SU) combined with UV-A crosslinking and compare the results with published data. As previously noted, the positions of complementary DNA (cDNA)-starts depend on cDNA length in several iCLIP experiments and we now find that this is caused by constrained cDNA-ends, which can result from the sequence and structure constraints of RNA fragmentation. These constraints are overcome when fragmentation by RNase I is efficient and when a broad cDNA size range is obtained. Our study also shows that if RNase does not efficiently cut within the binding sites, the original CLIP method is less capable of identifying the longer binding sites of RBPs. In contrast, we show that a broad size range of cDNAs in iCLIP allows the cDNA-starts to efficiently delineate the complete RNA-binding sites. Conclusions We demonstrate the advantage of iCLIP and related methods that can amplify cDNAs that truncate at crosslink sites and we show that computational analyses based on cDNAs-starts are appropriate for such methods. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1130-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ina Huppertz
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.,European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julian König
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Zhen Wang
- Institut de Biologie de l'ENS (IBENS), 46 rue d'Ulm, Paris, F-75005, France.,CNRS UMR 8197, Paris Cedex 05, 75230, France
| | - Christian Hauer
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), 46 rue d'Ulm, Paris, F-75005, France.,CNRS UMR 8197, Paris Cedex 05, 75230, France
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška cesta 25, 1000, Ljubljana, Slovenia
| | - Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.,Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK. .,The Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| |
Collapse
|
13
|
Mattiazzi Ušaj M, Prelec M, Brložnik M, Primo C, Curk T, Ščančar J, Yenush L, Petrovič U. Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis. Metallomics 2016; 7:1338-51. [PMID: 26067383 DOI: 10.1039/c5mt00095e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The functional link between zinc homeostasis and membrane-related processes, including lipid metabolism regulation, extends from yeast to humans, and has a likely role in the pathogenesis of diabetes. The yeast Izh2 protein has been previously implicated in zinc ion homeostasis and in the regulation of lipid and phosphate metabolism, but its precise molecular function is not known. We performed a chemogenomics experiment to determine the genes conferring resistance or sensitivity to different environmental zinc concentrations. We then determined at normal, depleted and excess zinc concentrations, the genetic interactions of IZH2 at the genome-wide level and measured changes in the transcriptome caused by deletion of IZH2. We found evidence for an important cellular function of the Rim101 pathway in zinc homeostasis in neutral or acidic environments, and observed that phosphatidylinositol is a source of inositol when zinc availability is limited. Comparison of our experimental profiles with published gene expression and genetic interaction profiles revealed pleiotropic functions for Izh2. We propose that Izh2 acts as an integrator of intra- and extracellular signals in providing adequate cellular responses to maintain homeostasis under different external conditions, including - but not limited to - alterations in zinc concentrations.
Collapse
Affiliation(s)
- Mojca Mattiazzi Ušaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Stražar M, Žitnik M, Zupan B, Ule J, Curk T. Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. Bioinformatics 2016; 32:1527-35. [PMID: 26787667 PMCID: PMC4894278 DOI: 10.1093/bioinformatics/btw003] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/01/2016] [Indexed: 12/15/2022] Open
Abstract
Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control of gene expression, including splicing, transport, polyadenylation and RNA stability. To model protein–RNA interactions by considering all available sources of information, it is necessary to integrate the rapidly growing RBP experimental data with the latest genome annotation, gene function, RNA sequence and structure. Such integration is possible by matrix factorization, where current approaches have an undesired tendency to identify only a small number of the strongest patterns with overlapping features. Because protein–RNA interactions are orchestrated by multiple factors, methods that identify discriminative patterns of varying strengths are needed. Results: We have developed an integrative orthogonality-regularized nonnegative matrix factorization (iONMF) to integrate multiple data sources and discover non-overlapping, class-specific RNA binding patterns of varying strengths. The orthogonality constraint halves the effective size of the factor model and outperforms other NMF models in predicting RBP interaction sites on RNA. We have integrated the largest data compendium to date, which includes 31 CLIP experiments on 19 RBPs involved in splicing (such as hnRNPs, U2AF2, ELAVL1, TDP-43 and FUS) and processing of 3’UTR (Ago, IGF2BP). We show that the integration of multiple data sources improves the predictive accuracy of retrieval of RNA binding sites. In our study the key predictive factors of protein–RNA interactions were the position of RNA structure and sequence motifs, RBP co-binding and gene region type. We report on a number of protein-specific patterns, many of which are consistent with experimentally determined properties of RBPs. Availability and implementation: The iONMF implementation and example datasets are available at https://github.com/mstrazar/ionmf. Contact: tomaz.curk@fri.uni-lj.si Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Martin Stražar
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia
| | - Marinka Žitnik
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia
| | - Blaž Zupan
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Tomaž Curk
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, SI 1000, Slovenia
| |
Collapse
|
15
|
Meijnen JP, Randazzo P, Foulquié-Moreno MR, van den Brink J, Vandecruys P, Stojiljkovic M, Dumortier F, Zalar P, Boekhout T, Gunde-Cimerman N, Kokošar J, Štajdohar M, Curk T, Petrovič U, Thevelein JM. Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae. Biotechnol Biofuels 2016; 9:5. [PMID: 26740819 PMCID: PMC4702306 DOI: 10.1186/s13068-015-0421-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/15/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Acetic acid is one of the major inhibitors in lignocellulose hydrolysates used for the production of second-generation bioethanol. Although several genes have been identified in laboratory yeast strains that are required for tolerance to acetic acid, the genetic basis of the high acetic acid tolerance naturally present in some Saccharomyces cerevisiae strains is unknown. Identification of its polygenic basis may allow improvement of acetic acid tolerance in yeast strains used for second-generation bioethanol production by precise genome editing, minimizing the risk of negatively affecting other industrially important properties of the yeast. RESULTS Haploid segregants of a strain with unusually high acetic acid tolerance and a reference industrial strain were used as superior and inferior parent strain, respectively. After crossing of the parent strains, QTL mapping using the SNP variant frequency determined by pooled-segregant whole-genome sequence analysis revealed two major QTLs. All F1 segregants were then submitted to multiple rounds of random inbreeding and the superior F7 segregants were submitted to the same analysis, further refined by sequencing of individual segregants and bioinformatics analysis taking into account the relative acetic acid tolerance of the segregants. This resulted in disappearance in the QTL mapping with the F7 segregants of a major F1 QTL, in which we identified HAA1, a known regulator of high acetic acid tolerance, as a true causative allele. Novel genes determining high acetic acid tolerance, GLO1, DOT5, CUP2, and a previously identified component, VMA7, were identified as causative alleles in the second major F1 QTL and in three newly appearing F7 QTLs, respectively. The superior HAA1 allele contained a unique single point mutation that significantly improved acetic acid tolerance under industrially relevant conditions when inserted into an industrial yeast strain for second-generation bioethanol production. CONCLUSIONS This work reveals the polygenic basis of high acetic acid tolerance in S. cerevisiae in unprecedented detail. It also shows for the first time that a single strain can harbor different sets of causative genes able to establish the same polygenic trait. The superior alleles identified can be used successfully for improvement of acetic acid tolerance in industrial yeast strains.
Collapse
Affiliation(s)
- Jean-Paul Meijnen
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Paola Randazzo
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - María R. Foulquié-Moreno
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | | | - Paul Vandecruys
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Marija Stojiljkovic
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Françoise Dumortier
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Polona Zalar
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Teun Boekhout
- />CBS, Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands
| | - Nina Gunde-Cimerman
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
- />Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Janez Kokošar
- />Genialis d.o.o., Ulica Zore Majcnove 4, 1000 Ljubljana, Slovenia
| | - Miha Štajdohar
- />Genialis d.o.o., Ulica Zore Majcnove 4, 1000 Ljubljana, Slovenia
- />Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Tomaž Curk
- />Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Uroš Petrovič
- />Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, Ljubljana, Slovenia
| | - Johan M. Thevelein
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| |
Collapse
|
16
|
Kavšček M, Stražar M, Curk T, Natter K, Petrovič U. Yeast as a cell factory: current state and perspectives. Microb Cell Fact 2015; 14:94. [PMID: 26122609 PMCID: PMC4486425 DOI: 10.1186/s12934-015-0281-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/11/2015] [Indexed: 02/06/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is one of the oldest and most frequently used microorganisms in biotechnology with successful applications in the production of both bulk and fine chemicals. Yet, yeast researchers are faced with the challenge to further its transition from the old workhorse to a modern cell factory, fulfilling the requirements for next generation bioprocesses. Many of the principles and tools that are applied for this development originate from the field of synthetic biology and the engineered strains will indeed be synthetic organisms. We provide an overview of the most important aspects of this transition and highlight achievements in recent years as well as trends in which yeast currently lags behind. These aspects include: the enhancement of the substrate spectrum of yeast, with the focus on the efficient utilization of renewable feedstocks, the enhancement of the product spectrum through generation of independent circuits for the maintenance of redox balances and biosynthesis of common carbon building blocks, the requirement for accurate pathway control with improved genome editing and through orthogonal promoters, and improvement of the tolerance of yeast for specific stress conditions. The causative genetic elements for the required traits of the future yeast cell factories will be assembled into genetic modules for fast transfer between strains. These developments will benefit from progress in bio-computational methods, which allow for the integration of different kinds of data sets and algorithms, and from rapid advancement in genome editing, which will enable multiplexed targeted integration of whole heterologous pathways. The overall goal will be to provide a collection of modules and circuits that work independently and can be combined at will, depending on the individual conditions, and will result in an optimal synthetic host for a given production process.
Collapse
Affiliation(s)
- Martin Kavšček
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
| | - Martin Stražar
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
| | - Klaus Natter
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
| |
Collapse
|
17
|
Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev 2015; 29:501-12. [PMID: 25737280 PMCID: PMC4358403 DOI: 10.1101/gad.258483.115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/06/2015] [Indexed: 12/14/2022]
Abstract
Cellular morphology is an essential determinant of cellular function in all kingdoms of life, yet little is known about how cell shape is controlled. Here we describe a molecular program that controls the early morphology of neurons through a metazoan-specific zinc finger protein, Unkempt. Depletion of Unkempt in mouse embryos disrupts the shape of migrating neurons, while ectopic expression confers neuronal-like morphology to cells of different nonneuronal lineages. We found that Unkempt is a sequence-specific RNA-binding protein and identified its precise binding sites within coding regions of mRNAs linked to protein metabolism and trafficking. RNA binding is required for Unkempt-induced remodeling of cellular shape and is directly coupled to a reduced production of the encoded proteins. These findings link post-transcriptional regulation of gene expression with cellular shape and have general implications for the development and disease of multicellular organisms.
Collapse
Affiliation(s)
- Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yawei J Yang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA;
| | - Omer Durak
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Elisabeth A Murphy
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Sihem Cheloufi
- Cancer Center, Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Johannes Zuber
- The Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jernej Ule
- Department of Molecular Neuroscience, University College London Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; UCL Genetics Institute, Department of Genetics, Environment, and Evolution, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| |
Collapse
|
18
|
Diaz-Muñoz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Heggermont WA, Heymans S, Gibson GE, Kontoyiannis DL, Ule J, Turner M. The RNA-binding protein HuR is essential for the B cell antibody response. Nat Immunol 2015; 16:415-25. [PMID: 25706746 PMCID: PMC4479220 DOI: 10.1038/ni.3115] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/28/2015] [Indexed: 12/26/2022]
Abstract
Post-transcriptional regulation of mRNA by the RNA-binding protein HuR (encoded by Elavl1) is required in B cells for the germinal center reaction and for the production of class-switched antibodies in response to thymus-independent antigens. Transcriptome-wide examination of RNA isoforms and their abundance and translation in HuR-deficient B cells, together with direct measurements of HuR-RNA interactions, revealed that HuR-dependent splicing of mRNA affected hundreds of transcripts, including that encoding dihydrolipoamide S-succinyltransferase (Dlst), a subunit of the 2-oxoglutarate dehydrogenase (α-KGDH) complex. In the absence of HuR, defective mitochondrial metabolism resulted in large amounts of reactive oxygen species and B cell death. Our study shows how post-transcriptional processes control the balance of energy metabolism required for the proliferation and differentiation of B cells.
Collapse
Affiliation(s)
- Manuel D Diaz-Muñoz
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Sarah E Bell
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Kirsten Fairfax
- 1] Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK. [2] The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Elisa Monzon-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Adam F Cunningham
- MRC Centre for Immune Regulation, Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, UK
| | - Mar Gonzalez-Porta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Victoria I Bunik
- A. N. Belozersky Institute of PhysicoChemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Tomaž Curk
- University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, Slovenia
| | | | - Stephane Heymans
- 1] Center for Molecular and Vascular Biology, KU Leuven, Belgium. [2] Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Gary E Gibson
- Weill Cornell Medical College, Brain and Mind Research Institute, Burke Medical Research Institute, White Plains, New York, USA
| | - Dimitris L Kontoyiannis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Jernej Ule
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, London, UK
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| |
Collapse
|
19
|
Apolonia L, Schulz R, Curk T, Rocha P, Swanson CM, Schaller T, Ule J, Malim MH. Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1. PLoS Pathog 2015; 11:e1004609. [PMID: 25590131 PMCID: PMC4295846 DOI: 10.1371/journal.ppat.1004609] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/07/2014] [Indexed: 11/19/2022] Open
Abstract
The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins are cell-encoded cytidine deaminases, some of which, such as APOBEC3G (A3G) and APOBEC3F (A3F), act as potent human immunodeficiency virus type-1 (HIV-1) restriction factors. These proteins require packaging into HIV-1 particles to exert their antiviral activities, but the molecular mechanism by which this occurs is incompletely understood. The nucleocapsid (NC) region of HIV-1 Gag is required for efficient incorporation of A3G and A3F, and the interaction between A3G and NC has previously been shown to be RNA-dependent. Here, we address this issue in detail by first determining which RNAs are able to bind to A3G and A3F in HV-1 infected cells, as well as in cell-free virions, using the unbiased individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) method. We show that A3G and A3F bind many different types of RNA, including HIV-1 RNA, cellular mRNAs and small non-coding RNAs such as the Y or 7SL RNAs. Interestingly, A3G/F incorporation is unaffected when the levels of packaged HIV-1 genomic RNA (gRNA) and 7SL RNA are reduced, implying that these RNAs are not essential for efficient A3G/F packaging. Confirming earlier work, HIV-1 particles formed with Gag lacking the NC domain (Gag ΔNC) fail to encapsidate A3G/F. Here, we exploit this system by demonstrating that the addition of an assortment of heterologous RNA-binding proteins and domains to Gag ΔNC efficiently restored A3G/F packaging, indicating that A3G and A3F have the ability to engage multiple RNAs to ensure viral encapsidation. We propose that the rather indiscriminate RNA binding characteristics of A3G and A3F promote functionality by enabling recruitment into a wide range of retroviral particles whose packaged RNA genomes comprise divergent sequences.
Collapse
Affiliation(s)
- Luis Apolonia
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Paula Rocha
- Department of Statistical Science, University College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Torsten Schaller
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Jernej Ule
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Michael H. Malim
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| |
Collapse
|
20
|
Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A. Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biol 2014; 11:146-55. [PMID: 24526010 DOI: 10.4161/rna.27991] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a multifunctional RNA-binding protein that is involved in many different processes, such as regulation of transcription, translation, and RNA stability. We have previously characterized hnRNP L as a global regulator of alternative splicing, binding to CA-repeat, and CA-rich RNA elements. Interestingly, hnRNP L can both activate and repress splicing of alternative exons, but the precise mechanism of hnRNP L-mediated splicing regulation remained unclear. To analyze activities of hnRNP L on a genome-wide level, we performed individual-nucleotide resolution crosslinking-immunoprecipitation in combination with deep-sequencing (iCLIP-Seq). Sequence analysis of the iCLIP crosslink sites showed significant enrichment of C/A motifs, which perfectly agrees with the in vitro binding consensus obtained earlier by a SELEX approach, indicating that in vivo hnRNP L binding targets are mainly determined by the RNA-binding activity of the protein. Genome-wide mapping of hnRNP L binding revealed that the protein preferably binds to introns and 3' UTR. Additionally, position-dependent splicing regulation by hnRNP L was demonstrated: The protein represses splicing when bound to intronic regions upstream of alternative exons, and in contrast, activates splicing when bound to the downstream intron. These findings shed light on the longstanding question of differential hnRNP L-mediated splicing regulation. Finally, regarding 3' UTR binding, hnRNP L binding preferentially overlaps with predicted microRNA target sites, indicating global competition between hnRNP L and microRNA binding. Translational regulation by hnRNP L was validated for a subset of predicted target 3'UTRs.
Collapse
Affiliation(s)
- Oliver Rossbach
- Institute of Biochemistry; University of Giessen; Giessen, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry; University of Giessen; Giessen, Germany
| | - Ekaterina Khrameeva
- Kharkevich Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow, Russia; Department of Bioengineering and Bioinformatics; Lomonosov Moscow State University; Moscow, Russia
| | - Silke Schreiner
- Institute of Biochemistry; University of Giessen; Giessen, Germany
| | - Julian König
- Institute of Molecular Biology (IMB); Mainz, Germany; Institute of Neurology; University College London; London, United Kingdom
| | - Tomaž Curk
- Faculty of Computer and Information Science; University of Ljubljana; Ljubljana, Slovenia
| | - Blaž Zupan
- Faculty of Computer and Information Science; University of Ljubljana; Ljubljana, Slovenia
| | - Jernej Ule
- Institute of Neurology; University College London; London, United Kingdom
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow, Russia; Department of Bioengineering and Bioinformatics; Lomonosov Moscow State University; Moscow, Russia
| | | |
Collapse
|
21
|
Wagnon JL, Briese M, Sun W, Mahaffey CL, Curk T, Rot G, Ule J, Frankel WN. CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function. PLoS Genet 2012; 8:e1003067. [PMID: 23209433 PMCID: PMC3510034 DOI: 10.1371/journal.pgen.1003067] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/20/2012] [Indexed: 11/25/2022] Open
Abstract
RNA–binding proteins have emerged as causal agents of complex neurological diseases. Mice deficient for neuronal RNA–binding protein CELF4 have a complex neurological disorder with epilepsy as a prominent feature. Human CELF4 has recently been associated with clinical features similar to those seen in mutant mice. CELF4 is expressed primarily in excitatory neurons, including large pyramidal cells of the cerebral cortex and hippocampus, and it regulates excitatory but not inhibitory neurotransmission. We examined mechanisms underlying neuronal hyperexcitability in Celf4 mutants by identifying CELF4 target mRNAs and assessing their fate in the absence of CELF4 in view of their known functions. CELF4 binds to at least 15%–20% of the transcriptome, with striking specificity for the mRNA 3′ untranslated region. CELF4 mRNA targets encode a variety of proteins, many of which are well established in neuron development and function. While the overall abundance of these mRNA targets is often dysregulated in Celf4 deficient mice, the actual expression changes are modest at the steady-state level. In contrast, by examining the transcriptome of polysome fractions and the mRNA distribution along the neuronal cell body-neuropil axis, we found that CELF4 is critical for maintaining mRNA stability and availability for translation. Among biological processes associated with CELF4 targets that accumulate in neuropil of mutants, regulation of synaptic plasticity and transmission are the most prominent. Together with a related study of the impact of CELF4 loss on sodium channel Nav1.6 function, we suggest that CELF4 deficiency leads to abnormal neuronal function by combining a specific effect on neuronal excitation with a general impairment of synaptic transmission. These results also expand our understanding of the vital roles RNA–binding proteins play in regulating and shaping the activity of neural circuits. Epilepsy is a devastating brain disorder whereby a loss of regulation of electrochemical signals between neurons causes too much excitation and ultimately results in an “electrical storm” known as a seizure. Epilepsy can be heritable, but it is usually genetically complex, resulting from a collaboration of many genes. It is also a frequent feature of other common brain diseases, such as autism spectrum disorder and intellectual disability, likely because these diseases have a similar dysregulation of neuronal communication. To understand more about how the brain regulates electrical activity, we focused on an RNA–binding protein called CELF4, because a) mice that lack CELF4 have a complex form of epilepsy that includes features of other neurological diseases and b) this kind of protein has the potential to be a master regulator. We show that CELF4 binds to a vast array of mRNAs, and without CELF4 these mRNAs accumulate in the wrong places and can produce the wrong amount of protein. Moreover, many of these mRNAs encode key players in electrochemical signaling between neurons. Although the defects in individual mRNAs are modest, like a genetically complex disease, together these alterations collude to cause neurological symptoms including recurrent seizures.
Collapse
Affiliation(s)
- Jacy L. Wagnon
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Michael Briese
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Wenzhi Sun
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Rot
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Wayne N. Frankel
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail:
| |
Collapse
|
22
|
Rogelj B, Easton LE, Bogu GK, Stanton LW, Rot G, Curk T, Zupan B, Sugimoto Y, Modic M, Haberman N, Tollervey J, Fujii R, Takumi T, Shaw CE, Ule J. Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Sci Rep 2012; 2:603. [PMID: 22934129 PMCID: PMC3429604 DOI: 10.1038/srep00603] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/13/2012] [Indexed: 12/12/2022] Open
Abstract
Fused in sarcoma (FUS) and TAR DNA-binding protein 43 (TDP-43) are RNA-binding proteins pathogenetically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), but it is not known if they regulate the same transcripts. We addressed this question using crosslinking and immunoprecipitation (iCLIP) in mouse brain, which showed that FUS binds along the whole length of the nascent RNA with limited sequence specificity to GGU and related motifs. A saw-tooth binding pattern in long genes demonstrated that FUS remains bound to pre-mRNAs until splicing is completed. Analysis of FUS(-/-) brain demonstrated a role for FUS in alternative splicing, with increased crosslinking of FUS in introns around the repressed exons. We did not observe a significant overlap in the RNA binding sites or the exons regulated by FUS and TDP-43. Nevertheless, we found that both proteins regulate genes that function in neuronal development.
Collapse
Affiliation(s)
- Boris Rogelj
- Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, UK
- Now at: Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- These authors contributed equally to this work
| | - Laura E. Easton
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- These authors contributed equally to this work
| | - Gireesh K. Bogu
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore
| | - Lawrence W. Stanton
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, 60 Biopolis Street, S(138672), Singapore
| | - Gregor Rot
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Blaž Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Miha Modic
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Nejc Haberman
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - James Tollervey
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- Now at: The Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Ritsuko Fujii
- Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami, Hiroshima 734-8553, Japan
| | - Toru Takumi
- Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami, Hiroshima 734-8553, Japan
| | - Christopher E. Shaw
- Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, UK
- These authors contributed equally to this work
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- These authors contributed equally to this work
| |
Collapse
|
23
|
Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J. Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol 2012; 13:R67. [PMID: 22863408 PMCID: PMC4053741 DOI: 10.1186/gb-2012-13-8-r67] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/11/2012] [Accepted: 08/03/2012] [Indexed: 11/12/2022] Open
Abstract
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.
Collapse
Affiliation(s)
- Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Shobbir Hussain
- The Wellcome Trust Centre for Stem Cell Research, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Blaž Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Michaela Frye
- The Wellcome Trust Centre for Stem Cell Research, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| |
Collapse
|
24
|
Tollervey JR, Wang Z, Hortobágyi T, Witten JT, Zarnack K, Kayikci M, Clark TA, Schweitzer AC, Rot G, Curk T, Zupan B, Rogelj B, Shaw CE, Ule J. Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res 2011; 21:1572-82. [PMID: 21846794 PMCID: PMC3202275 DOI: 10.1101/gr.122226.111] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 07/05/2011] [Indexed: 01/15/2023]
Abstract
Age is the most important risk factor for neurodegeneration; however, the effects of aging and neurodegeneration on gene expression in the human brain have most often been studied separately. Here, we analyzed changes in transcript levels and alternative splicing in the temporal cortex of individuals of different ages who were cognitively normal, affected by frontotemporal lobar degeneration (FTLD), or affected by Alzheimer's disease (AD). We identified age-related splicing changes in cognitively normal individuals and found that these were present also in 95% of individuals with FTLD or AD, independent of their age. These changes were consistent with increased polypyrimidine tract binding protein (PTB)-dependent splicing activity. We also identified disease-specific splicing changes that were present in individuals with FTLD or AD, but not in cognitively normal individuals. These changes were consistent with the decreased neuro-oncological ventral antigen (NOVA)-dependent splicing regulation, and the decreased nuclear abundance of NOVA proteins. As expected, a dramatic down-regulation of neuronal genes was associated with disease, whereas a modest down-regulation of glial and neuronal genes was associated with aging. Whereas our data indicated that the age-related splicing changes are regulated independently of transcript-level changes, these two regulatory mechanisms affected expression of genes with similar functions, including metabolism and DNA repair. In conclusion, the alternative splicing changes identified in this study provide a new link between aging and neurodegeneration.
Collapse
Affiliation(s)
- James R. Tollervey
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Zhen Wang
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Tibor Hortobágyi
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Joshua T. Witten
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Kathi Zarnack
- EMBL–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Melis Kayikci
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Tyson A. Clark
- Expression Research, Affymetrix, Inc., Santa Clara, California 95051, USA
| | | | - Gregor Rot
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia
| | - Blaž Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia
| | - Boris Rogelj
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Christopher E. Shaw
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
25
|
Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, König J, Hortobágyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE, Ule J. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci 2011; 14:452-8. [PMID: 21358640 PMCID: PMC3108889 DOI: 10.1038/nn.2778] [Citation(s) in RCA: 804] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 02/02/2011] [Indexed: 12/11/2022]
Abstract
TDP-43 is a predominantly nuclear RNA-binding protein that forms inclusion bodies in frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). The mRNA targets of TDP-43 in the human brain and its role in RNA processing are largely unknown. Using individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP), we demonstrated that TDP-43 preferentially binds long clusters of UG-rich sequences in vivo. Analysis of TDP-43 RNA binding in FTLD-TDP brains revealed the greatest increases in binding to MALAT1 and NEAT1 non-coding RNAs. We also showed that TDP-43 binding on pre-mRNAs influences alternative splicing in a similar position-dependent manner to Nova proteins. In addition, we identified unusually long clusters of TDP-43 binding at deep intronic positions downstream of silenced exons. A significant proportion of alternative mRNA isoforms regulated by TDP-43 encode proteins that regulate neuronal development or are implicated in neurological diseases, highlighting the importance of TDP-43 for splicing regulation in the brain.
Collapse
Affiliation(s)
- James R Tollervey
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J. iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biol 2010; 8:e1000530. [PMID: 21048981 PMCID: PMC2964331 DOI: 10.1371/journal.pbio.1000530] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/15/2010] [Indexed: 01/04/2023] Open
Abstract
The regulation of alternative splicing involves interactions between RNA-binding proteins and pre-mRNA positions close to the splice sites. T-cell intracellular antigen 1 (TIA1) and TIA1-like 1 (TIAL1) locally enhance exon inclusion by recruiting U1 snRNP to 5' splice sites. However, effects of TIA proteins on splicing of distal exons have not yet been explored. We used UV-crosslinking and immunoprecipitation (iCLIP) to find that TIA1 and TIAL1 bind at the same positions on human RNAs. Binding downstream of 5' splice sites was used to predict the effects of TIA proteins in enhancing inclusion of proximal exons and silencing inclusion of distal exons. The predictions were validated in an unbiased manner using splice-junction microarrays, RT-PCR, and minigene constructs, which showed that TIA proteins maintain splicing fidelity and regulate alternative splicing by binding exclusively downstream of 5' splice sites. Surprisingly, TIA binding at 5' splice sites silenced distal cassette and variable-length exons without binding in proximity to the regulated alternative 3' splice sites. Using transcriptome-wide high-resolution mapping of TIA-RNA interactions we evaluated the distal splicing effects of TIA proteins. These data are consistent with a model where TIA proteins shorten the time available for definition of an alternative exon by enhancing recognition of the preceding 5' splice site. Thus, our findings indicate that changes in splicing kinetics could mediate the distal regulation of alternative splicing.
Collapse
Affiliation(s)
- Zhen Wang
- Medical Research Council (MRC) – Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
| | - Melis Kayikci
- Medical Research Council (MRC) – Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
| | - Michael Briese
- Medical Research Council (MRC) – Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
| | - Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Nicholas M. Luscombe
- European Molecular Biology Laboratory (EMBL) – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- EMBL, Genome Biology Unit, Heidelberg, Germany
| | - Gregor Rot
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- Medical Research Council (MRC) – Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
| |
Collapse
|
27
|
Zucko J, Skunca N, Curk T, Zupan B, Long PF, Cullum J, Kessin RH, Hranueli D. Polyketide synthase genes and the natural products potential of Dictyostelium discoideum. ACTA ACUST UNITED AC 2007; 23:2543-9. [PMID: 17660200 DOI: 10.1093/bioinformatics/btm381] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION The genome of the social amoeba Dictyostelium discoideum contains an unusually large number of polyketide synthase (PKS) genes. An analysis of the genes is a first step towards understanding the biological roles of their products and exploiting novel products. RESULTS A total of 45 Type I iterative PKS genes were found, 5 of which are probably pseudogenes. Catalytic domains that are homologous with known PKS sequences as well as possible novel domains were identified. The genes often occurred in clusters of 2-5 genes, where members of the cluster had very similar sequences. The D.discoideum PKS genes formed a clade distinct from fungal and bacterial genes. All nine genes examined by RT-PCR were expressed, although at different developmental stages. The promoters of PKS genes were much more divergent than the structural genes, although we have identified motifs that are unique to some PKS gene promoters.
Collapse
Affiliation(s)
- J Zucko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Sacchi L, Bellazzi R, Larizza C, Magni P, Curk T, Petrovic U, Zupan B. Clustering gene expression data with temporal abstractions. Stud Health Technol Inform 2004; 107:798-802. [PMID: 15360922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
This paper describes a new technique for clustering short time series coming from gene expression data. The technique is based on the labelling of the time series through temporal trend abstractions and a consequent clustering of the series on the basis of their labels. Clustering is performed at three different levels of aggregation of the original time series, so that the results are organized and visualized as a three-levels hierarchical tree. Results on simulated and on yeast data are shown. The technique appears robust and efficient and the results obtained are easy to be interpreted.
Collapse
Affiliation(s)
- L Sacchi
- Dipartimento di Informatica e Sistemica, Università di Pavia, Italy.
| | | | | | | | | | | | | |
Collapse
|