1
|
Haugen RJ, Barnier C, Elrod ND, Luo H, Jensen MK, Ji P, Smibert CA, Lipshitz HD, Wagner EJ, Freddolino PL, Goldstrohm AC. Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (NEW YORK, N.Y.) 2024; 30:866-890. [PMID: 38627019 PMCID: PMC11182014 DOI: 10.1261/rna.079813.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/04/2024] [Indexed: 05/07/2024]
Abstract
The sequence-specific RNA-binding protein Pumilio (Pum) controls Drosophila development; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we use knockdown and knockout approaches coupled with RNA-seq to measure the impact of Pum on the transcriptome of Drosophila cells in culture. We also use an improved RNA coimmunoprecipitation method to identify Pum-bound mRNAs in Drosophila embryos. Integration of these data sets with the locations of Pum-binding motifs across the transcriptome reveals novel direct Pum target genes involved in neural, muscle, wing, and germ cell development and in cellular proliferation. These genes include components of Wnt, TGF-β, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. We identify the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pum-mediated repression, and observe concordant regulation of Pum:CCR4-NOT target mRNAs. Computational modeling reveals that Pum binding, binding site number, clustering, and sequence context are important determinants of regulation. In contrast, we show that the responses of direct mRNA targets to Pum-mediated repression are not influenced by the content of optimal synonymous codons. Moreover, contrary to a prevailing model, we do not detect a role for CCR4-NOT in the degradation of mRNAs with low codon optimality. Together, the results of this work provide new insights into the Pum regulatory network and mechanisms and the parameters that influence the efficacy of Pum-mediated regulation.
Collapse
Affiliation(s)
- Rebecca J Haugen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Catherine Barnier
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77550, USA
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Madeline K Jensen
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Ping Ji
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Craig A Smibert
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Eric J Wagner
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - P Lydia Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
2
|
Haugen RJ, Barnier C, Elrod ND, Luo H, Jensen MK, Ji P, Smibert CA, Lipshitz HD, Wagner EJ, Lydia Freddolino P, Goldstrohm AC. Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555372. [PMID: 37693497 PMCID: PMC10491259 DOI: 10.1101/2023.08.29.555372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The sequence-specific RNA-binding protein Pumilio controls development of Drosophila; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells. We also used an improved RNA co-immunoprecipitation method to identify Pumilio bound mRNAs in Drosophila embryos. Integration of these datasets with the content of Pumilio binding motifs across the transcriptome revealed novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. Additionally, we identified the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pumilio-mediated repression, and observed concordant regulation of Pumilio:CCR4-NOT target mRNAs. Computational modeling revealed that Pumilio binding, binding site number, density, and sequence context are important determinants of regulation. Moreover, the content of optimal synonymous codons in target mRNAs exhibits a striking functional relationship to Pumilio and CCR4-NOT regulation, indicating that the inherent translation efficiency and stability of the mRNA modulates their response to these trans-acting regulatory factors. Together, the results of this work provide new insights into the Pumilio regulatory network and mechanisms, and the parameters that influence the efficacy of Pumilio-mediated regulation.
Collapse
Affiliation(s)
- Rebecca J. Haugen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Catherine Barnier
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77550, USA
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Madeline K. Jensen
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642
| | - Ping Ji
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642
| | - Craig A. Smibert
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642
| | - P. Lydia Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Aaron C. Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
3
|
Shen Q, Wang YE, Truong M, Mahadevan K, Wu JJ, Zhang H, Li J, Smith HW, Smibert CA, Palazzo AF. RanBP2/Nup358 enhances miRNA activity by sumoylating Argonautes. PLoS Genet 2021; 17:e1009378. [PMID: 33600493 PMCID: PMC7924746 DOI: 10.1371/journal.pgen.1009378] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/02/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Mutations in RanBP2 (also known as Nup358), one of the main components of the cytoplasmic filaments of the nuclear pore complex, contribute to the overproduction of acute necrotizing encephalopathy (ANE1)-associated cytokines. Here we report that RanBP2 represses the translation of the interleukin 6 (IL6) mRNA, which encodes a cytokine that is aberrantly up-regulated in ANE1. Our data indicates that soon after its production, the IL6 messenger ribonucleoprotein (mRNP) recruits Argonautes bound to let-7 microRNA. After this mRNP is exported to the cytosol, RanBP2 sumoylates mRNP-associated Argonautes, thereby stabilizing them and enforcing mRNA silencing. Collectively, these results support a model whereby RanBP2 promotes an mRNP remodelling event that is critical for the miRNA-mediated suppression of clinically relevant mRNAs, such as IL6.
Collapse
Affiliation(s)
- Qingtang Shen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yifan E. Wang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Mathew Truong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kohila Mahadevan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jingze J. Wu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hui Zhang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jiawei Li
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Harrison W. Smith
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Craig A. Smibert
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
4
|
Sha QQ, Zhang J, Fan HY. A story of birth and death: mRNA translation and clearance at the onset of maternal-to-zygotic transition in mammals†. Biol Reprod 2020; 101:579-590. [PMID: 30715134 DOI: 10.1093/biolre/ioz012] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 01/01/2023] Open
Abstract
In mammals, maternal-to-zygotic transition (MZT), or oocyte-to-embryo transition, begins with oocyte meiotic resumption due to the sequential translational activation and destabilization of dormant maternal transcripts stored in the ooplasm. It then continues with the elimination of maternal transcripts during oocyte maturation and fertilization and ends with the full transcriptional activation of the zygotic genome during embryonic development. A hallmark of MZT in mammals is its reliance on translation and the utilization of stored RNAs and proteins, rather than de novo transcription of genes, to sustain meiotic maturation and early development. Impaired maternal mRNA clearance at the onset of MZT prevents zygotic genome activation and causes early arrest of developing embryos. In this review, we discuss recent advances in our knowledge of the mechanisms whereby mRNA translation and degradation are controlled by cytoplasmic polyadenylation and deadenylation which set up the competence of maturing oocyte to accomplish MZT. The emphasis of this review is on the mouse as a model organism for mammals and BTG4 as a licensing factor of MZT under the translational control of the MAPK cascade.
Collapse
Affiliation(s)
- Qian-Qian Sha
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jue Zhang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
5
|
Tang S, Han T, Wang Z, Yue N, Liu Z, Tang S, Yang X, Zhang Z, Zhou Y, Yuan W, Hao H, Sleman S, Pan D, Xuan B, Zhou W, Qian Z. Facile and Modular Pipeline for Protein-Specific Antibody Customization. ACS APPLIED BIO MATERIALS 2020; 3:4380-4387. [DOI: 10.1021/acsabm.0c00385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Shubing Tang
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, 201058 Shanghai, China
| | - Tian Han
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Zewei Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Nan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Zhi Liu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Shuhua Tang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, 300134 Tianjin, China
| | - Xiaoqi Yang
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Zhe Zhang
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Yan Zhou
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Weiming Yuan
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Hongyun Hao
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Sirwan Sleman
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Deng Pan
- Shanghai Public Health Clinical Center, Fudan University, 201058 Shanghai, China
| | - Baoqin Xuan
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Wei Zhou
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Zhikang Qian
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| |
Collapse
|
6
|
Laver JD, Ly J, Winn JK, Karaiskakis A, Lin S, Nie K, Benic G, Jaberi-Lashkari N, Cao WX, Khademi A, Westwood JT, Sidhu SS, Morris Q, Angers S, Smibert CA, Lipshitz HD. The RNA-Binding Protein Rasputin/G3BP Enhances the Stability and Translation of Its Target mRNAs. Cell Rep 2020; 30:3353-3367.e7. [PMID: 32160542 DOI: 10.1016/j.celrep.2020.02.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 01/13/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
G3BP RNA-binding proteins are important components of stress granules (SGs). Here, we analyze the role of the Drosophila G3BP Rasputin (RIN) in unstressed cells, where RIN is not SG associated. Immunoprecipitation followed by microarray analysis identifies over 550 mRNAs that copurify with RIN. The mRNAs found in SGs are long and translationally silent. In contrast, we find that RIN-bound mRNAs, which encode core components of the transcription, splicing, and translation machinery, are short, stable, and highly translated. We show that RIN is associated with polysomes and provide evidence for a direct role for RIN and its human homologs in stabilizing and upregulating the translation of their target mRNAs. We propose that when cells are stressed, the resulting incorporation of RIN/G3BPs into SGs sequesters them away from their short target mRNAs. This would downregulate the expression of these transcripts, even though they are not incorporated into stress granules.
Collapse
Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jimmy Ly
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jamie K Winn
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Kun Nie
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Giulia Benic
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Nima Jaberi-Lashkari
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Alireza Khademi
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - J Timothy Westwood
- Department of Biology, University of Toronto, 3359 Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Vector Institute, 661 University Ave, Toronto, Ontario, Canada, M160 College Street, Toronto, ON M5G 1M1, Canada
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|
7
|
Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY, Lasko P. Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genet 2020; 16:e1008581. [PMID: 31978041 PMCID: PMC7001992 DOI: 10.1371/journal.pgen.1008581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 02/05/2020] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila, maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in a region adjacent to A-rich sequences. Using Drosophila S2R+ cultured cells we show that this binding site overlaps with a Bruno1 (Bru1) responsive element (BREs) that regulates osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR. To ensure accurate development of the Drosophila embryo, proteins and mRNAs are positioned at specific sites within the embryo. Many of these factors are produced and localized during the development of the egg in the mother. One protein essential for this process that has been heavily studied is Oskar (Osk), which is positioned at the posterior pole. During the localization of osk mRNA, its translation is repressed by the RNA-binding protein Bruno1 (Bru1), ensuring that Osk protein is not present outside of the posterior where it is harmful. At the posterior pole, osk mRNA is activated through mechanisms that are not yet understood. In this work, we show that the conserved protein Makorin 1 (Mkrn1) is a novel factor involved in the translational activation of osk. Mkrn1 binds specifically to osk mRNA, overlapping with a binding site of Bru1, thus alleviating the association of Bru1 with osk. Moreover, Mkrn1 is stabilized by poly(A) binding protein (pAbp), a translational activator that binds osk mRNA in close proximity to one Mkrn1 binding site. Our work thus helps to answer a long-standing question in the field, providing insight about the function of Mkrn1 and more generally into embryonic patterning in animals.
Collapse
Affiliation(s)
- Annabelle Dold
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Hong Han
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Niankun Liu
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andrea Hildebrandt
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany.,Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Cornelia Rücklé
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Heike Hänel
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Anke Busch
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Petra Beli
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Jean-Yves Roignant
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
8
|
Gallo E. High-Throughput Generation of In Silico Derived Synthetic Antibodies via One-step Enzymatic DNA Assembly of Fragments. Mol Biotechnol 2020; 62:142-150. [PMID: 31894513 DOI: 10.1007/s12033-019-00232-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phage-display technology offers robust methods for isolating antibody (Ab) molecules with specificity for different target antigens. Recent advancements couple Ab selections with in silico strategies, such as predictive computational models or next-generation sequencing metadata analysis of Ab selections. These advancements result in enhanced Ab clonal diversities with potential for enlarged epitope coverage of the target antigen. A current limitation however, is that de novo Ab sequences must undergo DNA gene synthesis, and subsequent expression as Ab proteins for downstream validations. Due to the high costs and time for commercially generating large sets of DNA genes, we report a high-throughput platform for the synthesis of in silico derived Ab clones. As a proof of concept we demonstrate the simultaneous synthesis of 96 unique Abs with varied lengths and complementary determining region compositions. Each of the 96 Ab clones undergoes a one-step enzymatic assembly of distinct DNA fragments that combine into a circularized Fab expression plasmid. This strategy allows for the rapid and efficient synthesis of 96 DNA constructs in a 3 day window, and exhibits high percentage fidelity-greater than 93%. Accordingly, the synthesis of Ab DNA constructs as Fab expression plasmids allow for rapid execution of downstream Ab protein validations, with potential for implementation into high-throughput Ab protein characterization pipelines. Altogether, the platform presented here proves rapid and also cost-effective, which is important for labs with limited resources, since it utilizes standard laboratory equipment and molecular reagents.
Collapse
Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, Charles Best Institute, University of Toronto, 112 College Street, 112 College Street, Room 70, Toronto, ON, M5G 1L6, Canada.
| |
Collapse
|
9
|
Laflamme C, McKeever PM, Kumar R, Schwartz J, Kolahdouzan M, Chen CX, You Z, Benaliouad F, Gileadi O, McBride HM, Durcan TM, Edwards AM, Healy LM, Robertson J, McPherson PS. Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. eLife 2019; 8:e48363. [PMID: 31612854 PMCID: PMC6794092 DOI: 10.7554/elife.48363] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/26/2019] [Indexed: 01/02/2023] Open
Abstract
Antibodies are a key resource in biomedical research yet there are no community-accepted standards to rigorously characterize their quality. Here we develop a procedure to validate pre-existing antibodies. Human cell lines with high expression of a target, determined through a proteomics database, are modified with CRISPR/Cas9 to knockout (KO) the corresponding gene. Commercial antibodies against the target are purchased and tested by immunoblot comparing parental and KO. Validated antibodies are used to definitively identify the most highly expressing cell lines, new KOs are generated if needed, and the lines are screened by immunoprecipitation and immunofluorescence. Selected antibodies are used for more intensive procedures such as immunohistochemistry. The pipeline is easy to implement and scalable. Application to the major ALS disease gene C9ORF72 identified high-quality antibodies revealing C9ORF72 localization to phagosomes/lysosomes. Antibodies that do not recognize C9ORF72 have been used in highly cited papers, raising concern over previously reported C9ORF72 properties.
Collapse
Affiliation(s)
- Carl Laflamme
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Paul M McKeever
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoCanada
| | - Rahul Kumar
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Julie Schwartz
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Mahshad Kolahdouzan
- Neuroimmunology Unit, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Carol X Chen
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Zhipeng You
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Faiza Benaliouad
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Opher Gileadi
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Heidi M McBride
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Thomas M Durcan
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Aled M Edwards
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
- Structural Genomics Consortium, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Luke M Healy
- Neuroimmunology Unit, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoCanada
| | - Peter S McPherson
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| |
Collapse
|
10
|
Pascoe N, Seetharaman A, Teyra J, Manczyk N, Satori MA, Tjandra D, Makhnevych T, Schwerdtfeger C, Brasher BB, Moffat J, Costanzo M, Boone C, Sicheri F, Sidhu SS. Yeast Two-Hybrid Analysis for Ubiquitin Variant Inhibitors of Human Deubiquitinases. J Mol Biol 2019; 431:1160-1171. [PMID: 30763569 DOI: 10.1016/j.jmb.2019.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 11/20/2022]
Abstract
We applied a yeast-two-hybrid (Y2H) analysis to screen for ubiquitin variant (UbV) inhibitors of a human deubiquitinase (DUB), ubiquitin-specific protease 2 (USP2). The Y2H screen used USP2 as the bait and a prey library consisting of UbVs randomized at four specific positions, which were known to interact with USP2 from phage display analysis. The screen yielded numerous UbVs that bound to USP2 both as a Y2H interaction in vivo and as purified proteins in vitro. The Y2H-derived UbVs inhibited the catalytic activity of USP2 in vitro with nanomolar-range potencies, and they bound and inhibited USP2 in human cells. Mutational and structural analysis showed that potent and selective inhibition could be achieved by just two substitutions in a UbV, which exhibited improved hydrophobic and hydrophilic contacts compared to the wild-type ubiquitin interaction with USP2. Our results establish Y2H as an effective platform for the development of UbV inhibitors of DUBs in vivo, providing an alternative strategy for the analysis of DUBs that are recalcitrant to phage display and other in vitro methods.
Collapse
Affiliation(s)
- Natasha Pascoe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Ashwin Seetharaman
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Joan Teyra
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Maria Augusta Satori
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Donna Tjandra
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Taras Makhnevych
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
11
|
Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods 2018; 15:330-338. [PMID: 29638227 PMCID: PMC6063793 DOI: 10.1038/nmeth.4632] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 01/25/2018] [Indexed: 01/08/2023]
Abstract
A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.
Collapse
Affiliation(s)
- Anand Venkataraman
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kun Yang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Paolo Mita
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zheng Kuang
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Lin Xue
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Devlina Ghosh
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shuang Liu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Sarah Keegan
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Richard Saul
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Hongyan Zhang
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Guang Song
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jessica McDade
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sooyeon Yoo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seva G Khambadkone
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jimmy de Melo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Milanka Stevanovic
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Atul Tandon
- NeoBiotechnologies, Inc., Union City, California, USA
| | - Elliot Campbell
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Stephen Anderson
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jef D Boeke
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Fenyö
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Gordon Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Heng Zhu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
12
|
Rissland OS, Subtelny AO, Wang M, Lugowski A, Nicholson B, Laver JD, Sidhu SS, Smibert CA, Lipshitz HD, Bartel DP. The influence of microRNAs and poly(A) tail length on endogenous mRNA-protein complexes. Genome Biol 2017; 18:211. [PMID: 29089021 PMCID: PMC5664449 DOI: 10.1186/s13059-017-1330-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND All mRNAs are bound in vivo by proteins to form mRNA-protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of the core mRNP components eIF4E, eIF4G, and PABP and of the decay factor DDX6 in human cells. RESULTS Despite the transient nature of repressed intermediates, we detect significant changes in mRNP composition, marked by dissociation of eIF4G and PABP, and by recruitment of DDX6. Furthermore, although poly(A)-tail length has been considered critical in post-transcriptional regulation, differences in steady-state tail length explain little of the variation in either PABP association or mRNP organization more generally. Instead, relative occupancy of core components correlates best with gene expression. CONCLUSIONS These results indicate that posttranscriptional regulatory factors, such as microRNAs, influence the associations of PABP and other core factors, and do so without substantially affecting steady-state tail length.
Collapse
Affiliation(s)
- Olivia S Rissland
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Present address: Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
| | - Alexander O Subtelny
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Miranda Wang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Beth Nicholson
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
13
|
Abstract
With a century-old history of fundamental discoveries, the fruit fly has long been a favored experimental organism for a wide range of scientific inquiries. But Drosophila is not a “legacy” model organism; technical and intellectual innovations continue to revitalize fly research and drive advances in our understanding of conserved mechanisms of animal biology. Here, we provide an overview of this “ecosystem” and discuss how to address emerging challenges to ensure its continued productivity. Drosophila researchers are fortunate to have a sophisticated and ever-growing toolkit for the analysis of gene function. Access to these tools depends upon continued support for both physical and informational resources. Uncertainty regarding stable support for bioinformatic databases is a particular concern, at a time when there is the need to make the vast knowledge of functional biology provided by this model animal accessible to scientists studying other organisms. Communication and advocacy efforts will promote appreciation of the value of the fly in delivering biomedically important insights. Well-tended traditions of large-scale tool development, open sharing of reagents, and community engagement provide a strong basis for coordinated and proactive initiatives to improve the fly research ecosystem. Overall, there has never been a better time to be a fly pusher.
Collapse
|
14
|
Wang M, Ly M, Lugowski A, Laver JD, Lipshitz HD, Smibert CA, Rissland OS. ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition. eLife 2017; 6:27891. [PMID: 28875934 PMCID: PMC5779226 DOI: 10.7554/elife.27891] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/04/2017] [Indexed: 12/27/2022] Open
Abstract
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). We show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a change in the composition of mRNA-protein complexes. We propose that ME31B is a global repressor whose regulatory impact changes based on its biological context.
Collapse
Affiliation(s)
- Miranda Wang
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Ly
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, United States
| |
Collapse
|
15
|
Miersch S, Kuruganti S, Walter MR, Sidhu SS. A panel of synthetic antibodies that selectively recognize and antagonize members of the interferon alpha family. Protein Eng Des Sel 2017; 30:697-704. [PMID: 28981904 PMCID: PMC5914384 DOI: 10.1093/protein/gzx048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/25/2017] [Accepted: 08/09/2017] [Indexed: 11/12/2022] Open
Abstract
The 12 distinct subtypes that comprise the interferon alpha (IFNα) family of cytokines possess anti-viral, anti-proliferative and immunomodulatory activities. They are implicated in the etiology and progression of many diseases, and also used as therapeutic agents for viral and oncologic disorders. However, a deeper understanding of their role in disease is limited by a lack of tools to evaluate single subtypes at the protein level. Antibodies that selectively inhibit single IFNα subtypes could enable interrogation of each protein in biological samples and could be used for characterization and treatment of disease. Using phage-displayed synthetic antibody libraries, we have conducted selections against 12 human IFNα subtypes to explore our ability to obtain fine-specificity antibodies that recognize and antagonize the biological signals induced by a single IFNα subtype. For the first time, we have isolated antibodies that specifically recognize individual IFNα subtypes (IFNα2a/b, IFNα6, IFNα8b and IFNα16) with high affinity that antagonize signaling. Our results show that highly specific antibodies capable of distinguishing between closely related cytokines can be isolated from synthetic libraries and can be used to characterize cytokine abundance and function.
Collapse
Affiliation(s)
- S Miersch
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
| | - S Kuruganti
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M R Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - S S Sidhu
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
| |
Collapse
|
16
|
Jeon J, Arnold R, Singh F, Teyra J, Braun T, Kim PM. PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. BMC Bioinformatics 2016; 17:150. [PMID: 27039071 PMCID: PMC4818438 DOI: 10.1186/s12859-016-1001-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/23/2016] [Indexed: 11/22/2022] Open
Abstract
Background The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool exists to find and optimize structural domains within protein sequences. Results Here, we describe a new tool, PAT (http://www.kimlab.org/software/pat) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. Conclusion PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1001-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jouhyun Jeon
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Roland Arnold
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Fateh Singh
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Joan Teyra
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Tatjana Braun
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, M5S 3E1, ON, Canada.
| |
Collapse
|