1
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Berenson A, Lane R, Soto-Ugaldi LF, Patel M, Ciausu C, Li Z, Chen Y, Shah S, Santoso C, Liu X, Spirohn K, Hao T, Hill DE, Vidal M, Fuxman Bass JI. Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors. Nat Commun 2023; 14:6570. [PMID: 37853017 PMCID: PMC10584920 DOI: 10.1038/s41467-023-42445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for understanding their context-specific functions, existing approaches either rely on DNA binding motif predictions, interrogate one TF at a time, or study individual TFs in parallel. Here, we introduce paired yeast one-hybrid (pY1H) assays to detect cooperativity and antagonism across hundreds of TF-pairs at DNA regions of interest. We provide evidence that a wide variety of TFs are subject to modulation by other TFs in a DNA region-specific manner. We also demonstrate that TF-TF relationships are often affected by alternative isoform usage and identify cooperativity and antagonism between human TFs and viral proteins from human papillomaviruses, Epstein-Barr virus, and other viruses. Altogether, pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.
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Affiliation(s)
- Anna Berenson
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Mahir Patel
- Department of Computer Science, Boston University, Boston, MA, 02215, USA
| | - Cosmin Ciausu
- Department of Computer Science, Boston University, Boston, MA, 02215, USA
| | - Zhaorong Li
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Yilin Chen
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Sakshi Shah
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Xing Liu
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, 02215, USA.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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2
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Fisher WW, Hammonds AS, Weiszmann R, Booth BW, Gevirtzman L, Patton JEJ, Kubo CA, Waterston RH, Celniker SE. A modERN resource: identification of Drosophila transcription factor candidate target genes using RNAi. Genetics 2023; 223:iyad004. [PMID: 36652461 PMCID: PMC10078917 DOI: 10.1093/genetics/iyad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/18/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023] Open
Abstract
Transcription factors (TFs) play a key role in development and in cellular responses to the environment by activating or repressing the transcription of target genes in precise spatial and temporal patterns. In order to develop a catalog of target genes of Drosophila melanogaster TFs, the modERN consortium systematically knocked down the expression of TFs using RNAi in whole embryos followed by RNA-seq. We generated data for 45 TFs which have 18 different DNA-binding domains and are expressed in 15 of the 16 organ systems. The range of inactivation of the targeted TFs by RNAi ranged from log2fold change -3.52 to +0.49. The TFs also showed remarkable heterogeneity in the numbers of candidate target genes identified, with some generating thousands of candidates and others only tens. We present detailed analysis from five experiments, including those for three TFs that have been the focus of previous functional studies (ERR, sens, and zfh2) and two previously uncharacterized TFs (sens-2 and CG32006), as well as short vignettes for selected additional experiments to illustrate the utility of this resource. The RNA-seq datasets are available through the ENCODE DCC (http://encodeproject.org) and the Sequence Read Archive (SRA). TF and target gene expression patterns can be found here: https://insitu.fruitfly.org. These studies provide data that facilitate scientific inquiries into the functions of individual TFs in key developmental, metabolic, defensive, and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks during embryogenesis.
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Affiliation(s)
- William W Fisher
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ann S Hammonds
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard Weiszmann
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin W Booth
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Louis Gevirtzman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jaeda E J Patton
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Connor A Kubo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Robert H Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Susan E Celniker
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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3
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Abstract
The specificity in gene regulation is controlled by interactions between transcription factors (TFs) and genomic DNA regions such as promoters and enhancers. Enhanced yeast one-hybrid (eY1H) assays are among the methods used for high-throughput detection of transcription factor-DNA interactions. Here, we describe the procedure for screening interactions between DNA regions of interest ("DNA-baits") and an array of transcription factors ("TF-preys"), after DNA-bait and TF-prey yeast strains have been generated. Using a high-density array robotic platform, this method can be used to screen interactions between multiple DNA regions and >1000 TFs within a single experiment.
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Affiliation(s)
- Anna Berenson
- Department of Biology, Boston University, Boston, MA, USA
| | - Juan Ignacio Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA.
- Bioinformatics Program, Boston University, Boston, MA, USA.
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4
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Lee U, Stuelsatz P, Karaz S, McKellar DW, Russeil J, Deak M, De Vlaminck I, Lepper C, Deplancke B, Cosgrove BD, Feige JN. A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle. iScience 2022; 25:104589. [PMID: 35789856 PMCID: PMC9250016 DOI: 10.1016/j.isci.2022.104589] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 03/10/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Apelin (Apln) is a myokine that regulates skeletal muscle plasticity and metabolism and declines during aging. Through a yeast one-hybrid transcription factor binding screen, we identified the TEA domain transcription factor 1 (Tead1) as a novel regulator of the Apln promoter. Single-cell analysis of regenerating muscle revealed that the apelin receptor (Aplnr) is enriched in endothelial cells, whereas Tead1 is enriched in myogenic cells. Knock-down of Tead1 stimulates Apln secretion from muscle cells in vitro and myofiber-specific overexpression of Tead1 suppresses Apln secretion in vivo. Apln secretion via Tead1 knock-down in muscle cells stimulates endothelial cell expansion via endothelial Aplnr. In vivo, Apln peptide supplementation enhances endothelial cell expansion while Tead1 muscle overexpression delays endothelial remodeling following muscle injury. Our work describes a novel paracrine crosstalk in which Apln secretion is controlled by Tead1 in myogenic cells and influences endothelial remodeling during muscle repair.
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Affiliation(s)
- Umji Lee
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pascal Stuelsatz
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Sonia Karaz
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - David W. McKellar
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Julie Russeil
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maria Deak
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christoph Lepper
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Jerome N. Feige
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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5
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Zhu H, Zhao SD, Ray A, Zhang Y, Li X. A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing. Nat Commun 2022; 13:1247. [PMID: 35273186 PMCID: PMC8913700 DOI: 10.1038/s41467-022-28915-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 02/12/2022] [Indexed: 12/24/2022] Open
Abstract
During development, neural progenitors are temporally patterned to sequentially generate a variety of neural types. In Drosophila neural progenitors called neuroblasts, temporal patterning is regulated by cascades of Temporal Transcription Factors (TTFs). However, known TTFs were mostly identified through candidate approaches and may not be complete. In addition, many fundamental questions remain concerning the TTF cascade initiation, progression, and termination. In this work, we use single-cell RNA sequencing of Drosophila medulla neuroblasts of all ages to identify a list of previously unknown TTFs, and experimentally characterize their roles in temporal patterning and neuronal specification. Our study reveals a comprehensive temporal gene network that patterns medulla neuroblasts from start to end. Furthermore, the speed of the cascade progression is regulated by Lola transcription factors expressed in all medulla neuroblasts. Our comprehensive study of the medulla neuroblast temporal cascade illustrates mechanisms that may be conserved in the temporal patterning of neural progenitors. During development, neural progenitors generate a variety of neural types sequentially. Here the authors examine gene expression patterns in Drosophila neural progenitors at single-cell level, and identify a gene regulatory network controlling the sequential generation of different neural types.
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Affiliation(s)
- Hailun Zhu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sihai Dave Zhao
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alokananda Ray
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yu Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xin Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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6
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Roth S, Ideses D, Juven-Gershon T, Danielli A. Rapid Biosensing Method for Detecting Protein-DNA Interactions. ACS Sens 2022; 7:60-70. [PMID: 34979074 DOI: 10.1021/acssensors.1c01579] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Identifying and investigating protein-DNA interactions, which play significant roles in many biological processes, is essential for basic and clinical research. Current techniques for identification of protein-DNA interactions are laborious, time-consuming, and suffer from nonspecific binding and limited sensitivity. To overcome these challenges and assess protein-DNA interactions, we use a magnetic modulation biosensing (MMB) system. In MMB, one of the interacting elements (protein or DNA) is immobilized to magnetic beads, and the other is coupled to a fluorescent molecule. Thus, the link between the magnetic bead and the fluorescent molecule is established only when binding occurs, enabling detection of the protein-DNA interaction. Using magnetic forces, the beads are concentrated and manipulated in a periodic motion in and out of a laser beam, producing a detectable oscillating signal. Using MMB, we detected protein-DNA interactions between short GC-rich DNA sequences and both a purified specificity protein 1 (Sp1) and an overexpressed Buttonhead (BTD) protein in a cell lysate. The specificity of the interactions was assessed using mutated DNA sequences and competition experiments. The assays were experimentally compared with commonly used electrophoretic mobility shift assay, which takes approximately 4-72 h. In comparison, the MMB-based assay's turnaround time is ∼2 h, and it provides unambiguous results and quantitative measures of performance. The MMB system uses simple and cheap components, making it an attractive alternative method over current costly and time-consuming techniques for analyzing protein-DNA interactions. Therefore, we anticipate that the MMB-based technique will significantly advance the detection of protein-DNA interactions in biomedical research.
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Affiliation(s)
- Shira Roth
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan 5290002, Israel
| | - Amos Danielli
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Max and Anna Webb Street, Ramat Gan 5290002, Israel
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7
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Tsai NC, Hsu TS, Kuo SC, Kao CT, Hung TH, Lin DG, Yeh CS, Chu CC, Lin JS, Lin HH, Ko CY, Chang TH, Su JC, Lin YCJ. Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex. BMC Biol 2021; 19:214. [PMID: 34560855 PMCID: PMC8461970 DOI: 10.1186/s12915-021-01140-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation. RESULTS We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery. CONCLUSIONS The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.
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Affiliation(s)
- Ni-Chiao Tsai
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shang-Che Kuo
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chung-Ting Kao
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Da-Gin Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Chen Chu
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Chia-Ying Ko
- Department of Life Sciences and Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
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8
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Hagen JFD, Mendes CC, Booth SR, Figueras Jimenez J, Tanaka KM, Franke FA, Baudouin-Gonzalez L, Ridgway AM, Arif S, Nunes MDS, McGregor AP. Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species. Mol Biol Evol 2021; 38:437-448. [PMID: 32931587 PMCID: PMC7826188 DOI: 10.1093/molbev/msaa232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In the last 240,000 years, males of the Drosophila simulans species clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These appendages are used for grasping the female during mating and so their divergence is most likely driven by sexual selection. Mapping studies indicate a highly polygenic and generally additive genetic basis for these morphological differences. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid phenotypic diversification. Here, we used new D. simulans/D. mauritiana introgression lines on chromosome arm 3L to generate higher resolution maps of posterior lobe and clasper differences between these species. We then carried out RNA-seq on the developing genitalia of both species to identify the expressed genes and those that are differentially expressed between the two species. This allowed us to test the function of expressed positional candidates during genital development in D. melanogaster. We identified several new genes involved in the development and possibly the evolution of these genital structures, including the transcription factors Hairy and Grunge. Furthermore, we discovered that during clasper development Hairy negatively regulates tartan (trn), a gene known to contribute to divergence in clasper morphology. Taken together, our results provide new insights into the regulation of genital development and how this has evolved between species.
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Affiliation(s)
- Joanna F D Hagen
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Cláudia C Mendes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Shamma R Booth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Javier Figueras Jimenez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Kentaro M Tanaka
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Franziska A Franke
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Luis Baudouin-Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Amber M Ridgway
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Saad Arif
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
| | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
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9
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Bhatia S, Kumar H, Mahajan M, Yadav S, Saini P, Yadav S, Sahu SK, Sundaram JK, Yadav RK. A cellular expression map of epidermal and subepidermal cell layer-enriched transcription factor genes integrated with the regulatory network in Arabidopsis shoot apical meristem. PLANT DIRECT 2021; 5:e00306. [PMID: 33748654 PMCID: PMC7970154 DOI: 10.1002/pld3.306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/22/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
Transcriptional control of gene expression is an exquisitely regulated process in both animals and plants. Transcription factors (TFs) and the regulatory networks that drive the expression of TF genes in epidermal and subepidermal cell layers in Arabidopsis are unexplored. Here, we identified 65 TF genes enriched in the epidermal and subepidermal cell layers of the shoot apical meristem (SAM). To determine the cell type specificity in different stages of Arabidopsis development, we made YFP based transcriptional fusion constructs by taking a 3-kb upstream noncoding region above the translation start site. Here, we report that for ~52% (22/42) TF genes, we detected transcription activity. TF genes derived from epidermis show uniform expression in early embryo development; however, in the late globular stage, their transcription activity is suppressed in the inner cell layers. Expression patterns linked to subepidermal cell layer identity were apparent in the postembryonic development. Potential upstream regulators that could modulate the activity of epidermal and subepidermal cell layer-enriched TF genes were identified using enhanced yeast-one-hybrid (eY1H) assay and validated. This study describes the activation of TF genes in epidermal and subepidermal cell layers in embryonic and postembryonic development of Arabidopsis shoot apex.
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Affiliation(s)
- Shivani Bhatia
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Harish Kumar
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Monika Mahajan
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Sonal Yadav
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Prince Saini
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Shalini Yadav
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Sangram Keshari Sahu
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Jayesh Kumar Sundaram
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
- Present address:
Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Ram Kishor Yadav
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
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10
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Abstract
Apoptotic processes play an important role in the development and physiology of almost all metazoan clades. In the highly diverse group of insects, apoptotic pathways have been characterized in only a few dipteran and lepidopteran species, which may not be representative of all insect species. Here, we report the first complete annotation of the apoptotic pathway in a hemipteran insect, the pea aphid Acyrthosiphon pisum. We showed that its apoptotic pathway is rewired compared to other insects, with a significant increase in the number of inhibitors of apoptosis (IAPs) and evidence for functional diversification and structural modularity of this protein family. These novelties are widespread in the aphid lineage, suggesting a yet not understood novel aphid-specific function of IAPs. Apoptosis, a conserved form of programmed cell death, shows interspecies differences that may reflect evolutionary diversification and adaptation, a notion that remains largely untested. Among insects, the most speciose animal group, the apoptotic pathway has only been fully characterized in Drosophila melanogaster, and apoptosis-related proteins have been studied in a few other dipteran and lepidopteran species. Here, we studied the apoptotic pathway in the aphid Acyrthosiphon pisum, an insect pest belonging to the Hemiptera, an earlier-diverging and distantly related order. We combined phylogenetic analyses and conserved domain identification to annotate the apoptotic pathway in A. pisum and found low caspase diversity and a large expansion of its inhibitory part, with 28 inhibitors of apoptosis (IAPs). We analyzed the spatiotemporal expression of a selected set of pea aphid IAPs and showed that they are differentially expressed in different life stages and tissues, suggesting functional diversification. Five IAPs are specifically induced in bacteriocytes, the specialized cells housing symbiotic bacteria, during their cell death. We demonstrated the antiapoptotic role of these five IAPs using heterologous expression in a tractable in vivo model, the Drosophila melanogaster developing eye. Interestingly, IAPs with the strongest antiapoptotic potential contain two BIR and two RING domains, a domain association that has not been observed in any other species. We finally analyzed all available aphid genomes and found that they all show large IAP expansion, with new combinations of protein domains, suggestive of evolutionarily novel aphid-specific functions.
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11
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Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML. A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Rep 2020; 27:955-970.e7. [PMID: 30995488 PMCID: PMC6485956 DOI: 10.1016/j.celrep.2019.03.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/04/2019] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation. Combinatorial regulation by transcription factors (TFs) is one mechanism for achieving condition and tissue-specific gene regulation. Shokri et al. mapped TF-TF interactions between most Drosophila TFs, reporting a comprehensive TF-TF network integrated with previously known interactions. They used this network to discern distinct TF-DNA binding modes.
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Affiliation(s)
- Leila Shokri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sachi Inukai
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Antonina Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Kathryn Weinand
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anastasia Vedenko
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen S Gisselbrecht
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Edy Furger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jean-Daniel Feuz
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martha L Bulyk
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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12
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Shrestha S, Sewell JA, Santoso CS, Forchielli E, Carrasco Pro S, Martinez M, Fuxman Bass JI. Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays. Genome Res 2020; 29:1533-1544. [PMID: 31481462 PMCID: PMC6724672 DOI: 10.1101/gr.248823.119] [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: 01/24/2019] [Accepted: 07/23/2019] [Indexed: 12/29/2022]
Abstract
Identifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been technically and computationally challenging. Current experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false-positive and -negative predictions. To address these limitations, we developed an experimental approach based on enhanced yeast one-hybrid assays. The first variation of this approach interrogates the binding of >1000 human TFs to repetitive DNA elements, while the second evaluates TF binding to single nucleotide variants, short insertions and deletions (indels), and novel DNA motifs. Using this approach, we detected the binding of 75 TFs, including several nuclear hormone receptors and ETS factors, to the highly repetitive Alu elements. Further, we identified cancer-associated changes in TF binding, including gain of interactions involving ETS TFs and loss of interactions involving KLF TFs to different mutations in the TERT promoter, and gain of a MYB interaction with an 18-bp indel in the TAL1 superenhancer. Additionally, we identified TFs that bind to three uncharacterized DNA motifs identified in DNase footprinting assays. We anticipate that these enhanced yeast one-hybrid approaches will expand our capabilities to study genetic variation and undercharacterized genomic regions.
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Affiliation(s)
- Shaleen Shrestha
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - Jared Allan Sewell
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | | | - Elena Forchielli
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | | | - Melissa Martinez
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - Juan Ignacio Fuxman Bass
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
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13
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Deng C, Naler LB, Lu C. Microfluidic epigenomic mapping technologies for precision medicine. LAB ON A CHIP 2019; 19:2630-2650. [PMID: 31338502 PMCID: PMC6697104 DOI: 10.1039/c9lc00407f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.
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Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
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14
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Yeh CS, Wang Z, Miao F, Ma H, Kao CT, Hsu TS, Yu JH, Hung ET, Lin CC, Kuan CY, Tsai NC, Zhou C, Qu GZ, Jiang J, Liu G, Wang JP, Li W, Chiang VL, Chang TH, Lin YCJ. A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time. Genome Res 2019; 29:1343-1351. [PMID: 31186303 PMCID: PMC6673709 DOI: 10.1101/gr.245951.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.
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Affiliation(s)
- Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Fang Miao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chung-Ting Kao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jhong-He Yu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Er-Tsi Hung
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Chang Lin
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yu Kuan
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Chiao Tsai
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
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15
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Chen H, Wang JP, Liu H, Li H, Lin YCJ, Shi R, Yang C, Gao J, Zhou C, Li Q, Sederoff RR, Li W, Chiang VL. Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood ( Populus trichocarpa). THE PLANT CELL 2019; 31:602-626. [PMID: 30755461 PMCID: PMC6482634 DOI: 10.1105/tpc.18.00620] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 05/18/2023]
Abstract
Wood remains the world's most abundant and renewable resource for timber and pulp and is an alternative to fossil fuels. Understanding the molecular regulation of wood formation can advance the engineering of wood for more efficient material and energy productions. We integrated a black cottonwood (Populus trichocarpa) wood-forming cell system with quantitative transcriptomics and chromatin binding assays to construct a transcriptional regulatory network (TRN) directed by a key transcription factor (TF), PtrSND1-B1 (secondary wall-associated NAC-domain protein). The network consists of four layers of TF-target gene interactions with quantitative regulatory effects, describing the specificity of how the regulation is transduced through these interactions to activate cell wall genes (effector genes) for wood formation. PtrSND1-B1 directs 57 TF-DNA interactions through 17 TFs transregulating 27 effector genes. Of the 57 interactions, 55 are novel. We tested 42 of these 57 interactions in 30 genotypes of transgenic P. trichocarpa and verified that ∼90% of the tested interactions function in vivo. The TRN reveals common transregulatory targets for distinct TFs, leading to the discovery of nine TF protein complexes (dimers and trimers) implicated in regulating the biosynthesis of specific types of lignin. Our work suggests that wood formation may involve regulatory homeostasis determined by combinations of TF-DNA and TF-TF (protein-protein) regulations.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Huizi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695
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16
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Abstract
Comprehensive mapping of protein-DNA interactions is essential to uncover the mechanisms involved in gene regulation. However, the data generated has been sparse given the number of regulatory elements and transcription factors (TFs) encoded in the genomes of metazoan organisms. Yeast one-hybrid (Y1H) assays provide a powerful "DNA-centered" method, complementary to "TF-centered" methods such as chromatin immunoprecipitation, to identify the TFs that can bind a DNA sequence of interest. Here, we present different technical variations that should be considered when using a Y1H system, including the type of DNA sequence to test, source of TF clones, as well as types of vectors and screening format. Finally, we discuss limitations of the assay and future challenges.
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17
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Li Z, Bonaldi K, Kang SE, Pruneda-Paz JL. High-Throughput Yeast One-Hybrid Screens Using a Cell Surface gLUC Reporter. ACTA ACUST UNITED AC 2019; 4:e20086. [PMID: 30742367 DOI: 10.1002/cppb.20086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gene-centered yeast one-hybrid (Y1H) screens using arrayed genome-wide transcription factor (TF) clone collections provide a simple and effective strategy to identify TF-promoter interactions using a DNA fragment as bait. In an effort to improve the assay we recently developed a Y1H system that uses a cell surface Gaussia luciferase reporter (gLUC59). Compared to other available methods, this luciferase-based strategy requires a shorter processing time, enhances the throughput and improves result analysis of gene-centered Y1H screens. Here, we described the procedure to perform high-throughput screens using this novel strategy, which involves a protocol for mating two haploid yeast strains carrying an arrayed TF clone collection and a promoter::gLUC59 reporter, respectively, and a protocol for analyzing gLUC59 activity in the resulting diploid cells. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zheng Li
- Division of Biological Sciences, University of California San Diego, La Jolla, California
| | - Katia Bonaldi
- Division of Biological Sciences, University of California San Diego, La Jolla, California
| | - S Earl Kang
- Division of Biological Sciences, University of California San Diego, La Jolla, California
- Present address: Department of Plant Biology, University of Georgia, Athens, Georgia
| | - Jose L Pruneda-Paz
- Division of Biological Sciences, University of California San Diego, La Jolla, California
- Center for Circadian Biology, University of California San Diego, La Jolla, California
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18
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Shrestha S, Liu X, Santoso CS, Fuxman Bass JI. Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences. J Vis Exp 2019. [PMID: 30799854 DOI: 10.3791/59192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Identifying the sets of transcription factors (TFs) that regulate each human gene is a daunting task that requires integrating numerous experimental and computational approaches. One such method is the yeast one-hybrid (Y1H) assay, in which interactions between TFs and DNA regions are tested in the milieu of the yeast nucleus using reporter genes. Y1H assays involve two components: a 'DNA-bait' (e.g., promoters, enhancers, silencers, etc.) and a 'TF-prey,' which can be screened for reporter gene activation. Most published protocols for performing Y1H screens are based on transforming TF-prey libraries or arrays into DNA-bait yeast strains. Here, we describe a pipeline, called enhanced Y1H (eY1H) assays, where TF-DNA interactions are interrogated by mating DNA-bait strains with an arrayed collection of TF-prey strains using a high density array (HDA) robotic platform that allows screening in a 1,536 colony format. This allows for a dramatic increase in throughput (60 DNA-bait sequences against >1,000 TFs takes two weeks per researcher) and reproducibility. We illustrate the different types of expected results by testing human promoter sequences against an array of 1,086 human TFs, as well as examples of issues that can arise during screens and how to troubleshoot them.
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Affiliation(s)
| | - Xing Liu
- Department of Biology, Boston University
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19
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Bischof J, Duffraisse M, Furger E, Ajuria L, Giraud G, Vanderperre S, Paul R, Björklund M, Ahr D, Ahmed AW, Spinelli L, Brun C, Basler K, Merabet S. Generation of a versatile BiFC ORFeome library for analyzing protein-protein interactions in live Drosophila. eLife 2018; 7:38853. [PMID: 30247122 PMCID: PMC6177257 DOI: 10.7554/elife.38853] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/18/2018] [Indexed: 11/24/2022] Open
Abstract
Transcription factors achieve specificity by establishing intricate interaction networks that will change depending on the cell context. Capturing these interactions in live condition is however a challenging issue that requires sensitive and non-invasive methods. We present a set of fly lines, called ‘multicolor BiFC library’, which covers most of the Drosophila transcription factors for performing Bimolecular Fluorescence Complementation (BiFC). The multicolor BiFC library can be used to probe two different binary interactions simultaneously and is compatible for large-scale interaction screens. The library can also be coupled with established Drosophila genetic resources to analyze interactions in the developmentally relevant expression domain of each protein partner. We provide proof of principle experiments of these various applications, using Hox proteins in the live Drosophila embryo as a case study. Overall this novel collection of ready-to-use fly lines constitutes an unprecedented genetic toolbox for the identification and analysis of protein-protein interactions in vivo.
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Affiliation(s)
- Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Edy Furger
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | | | | | | | - Mikael Björklund
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
| | | | | | | | - Christine Brun
- INSERM, Aix-Marseille Université, Marseille, France.,TAGC, Centre National de la Recherche Scientifique, Marseille, France
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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20
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Baker LR, Weasner BM, Nagel A, Neuman SD, Bashirullah A, Kumar JP. Eyeless/Pax6 initiates eye formation non-autonomously from the peripodial epithelium. Development 2018; 145:dev.163329. [PMID: 29980566 DOI: 10.1242/dev.163329] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/27/2018] [Indexed: 01/08/2023]
Abstract
The transcription factor Pax6 is considered the master control gene for eye formation because (1) it is present within the genomes and retina/lens of all animals with a visual system; (2) severe retinal defects accompany its loss; (3) Pax6 genes have the ability to substitute for one another across the animal kingdom; and (4) Pax6 genes are capable of inducing ectopic eye/lens in flies and mammals. Many roles of Pax6 were first elucidated in Drosophila through studies of the gene eyeless (ey), which controls both growth of the entire eye-antennal imaginal disc and fate specification of the eye. We show that Ey also plays a surprising role within cells of the peripodial epithelium to control pattern formation. It regulates the expression of decapentaplegic (dpp), which is required for initiation of the morphogenetic furrow in the eye itself. Loss of Ey within the peripodial epithelium leads to the loss of dpp expression within the eye, failure of the furrow to initiate, and abrogation of retinal development. These findings reveal an unexpected mechanism for how Pax6 controls eye development in Drosophila.
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Affiliation(s)
- Luke R Baker
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Bonnie M Weasner
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Athena Nagel
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Sarah D Neuman
- Department of Pharmaceutical Sciences, University of Wisconsin, Madison, WI 53705, USA
| | - Arash Bashirullah
- Department of Pharmaceutical Sciences, University of Wisconsin, Madison, WI 53705, USA
| | - Justin P Kumar
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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21
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True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy. Nat Commun 2018; 9:1605. [PMID: 29686282 PMCID: PMC5913336 DOI: 10.1038/s41467-018-03977-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/16/2018] [Indexed: 01/31/2023] Open
Abstract
The complex patterns of gene expression in metazoans are controlled by selective binding of transcription factors (TFs) to regulatory DNA. To improve the quantitative understanding of this process, we have developed a novel method that uses fluorescence anisotropy measurements in a controlled delivery system to determine TF-DNA binding energies in solution with high sensitivity and throughput. Owing to its large dynamic range, the method, named high performance fluorescence anisotropy (HiP-FA), allows for reliable quantification of both weak and strong binding; binding specificities are calculated on the basis of equilibrium constant measurements for mutational DNA variants. We determine the binding preference landscapes for 26 TFs and measure high absolute affinities, but mostly lower binding specificities than reported by other methods. The revised binding preferences give rise to improved predictions of in vivo TF occupancy and enhancer expression. Our approach provides a powerful new tool for the systems-biological analysis of gene regulation. Methods to measure selective transcription factor-DNA binding often lack sensitivity and are not performed in solution. Here the authors develop a method to perform fluorescence anisotropy measurements of transcription factor-DNA binding energies with high sensitivity and throughput.
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22
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Construction of Arabidopsis Transcription Factor ORFeome Collections and Identification of Protein-DNA Interactions by High-Throughput Yeast One-Hybrid Screens. Methods Mol Biol 2018; 1794:151-182. [PMID: 29855956 DOI: 10.1007/978-1-4939-7871-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Identification of transcription factor (TF)-promoter interactions is key to understanding the basic molecular underpinnings of gene regulation. The complexity of gene regulation, however, is driven by the combined function of several TFs recruited to the promoter region, which often confounds the discovery of transcriptional regulatory mechanisms. Genome sequencing enabled the construction of TF-specific ORFeome clone collections that can be used to study TF function with unprecedented coverage. Among the recently developed methods, gene-centered yeast one-hybrid (Y1H) screens performed with these ORFeome collections provide a simple and reliable strategy to identify TF-promoter interactions. Here, we describe high-throughput cloning protocols used to generate a gold standard TF ORFeome collection for the model organism Arabidopsis thaliana. Furthermore, we outline the protocol to build a daughter clone collection suitable for the Y1H assay and a high-throughput Y1H screening procedure that enables rapid assessment of thousands TF-promoter interactions using a robotic platform. These protocols can be universally adopted to build ORFeome libraries and thus expand the usage of gene-centered Y1H screens or other alternative strategies for discovery and characterization of TF functions.
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23
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Chromatin state changes during neural development revealed by in vivo cell-type specific profiling. Nat Commun 2017; 8:2271. [PMID: 29273756 PMCID: PMC5741632 DOI: 10.1038/s41467-017-02385-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022] Open
Abstract
A key question in developmental biology is how cellular differentiation is controlled during development. While transitions between trithorax-group (TrxG) and polycomb-group (PcG) chromatin states are vital for the differentiation of ES cells to multipotent stem cells, little is known regarding the role of chromatin states during development of the brain. Here we show that large-scale chromatin remodelling occurs during Drosophila neural development. We demonstrate that the majority of genes activated during neuronal differentiation are silent in neural stem cells (NSCs) and occupy black chromatin and a TrxG-repressive state. In neurons, almost all key NSC genes are switched off via HP1-mediated repression. PcG-mediated repression does not play a significant role in regulating these genes, but instead regulates lineage-specific transcription factors that control spatial and temporal patterning in the brain. Combined, our data suggest that forms of chromatin other than canonical PcG/TrxG transitions take over key roles during neural development. While transitions between active and repressive chromatin states are essential for differentiation, little is known regarding their role during development of the brain in Drosophila. Here, the authors investigate the large scale chromatin remodelling taking place during fly neural development.
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King J, Foster J, Davison JM, Rawls JF, Breton G. Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. Zebrafish 2017; 15:202-205. [PMID: 29173090 DOI: 10.1089/zeb.2017.1486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The completion of the zebrafish genome sequence and advances in miniaturization and multiplexing were essential to the creation of techniques such as RNA-seq, ChIP-seq, and high-throughput behavioral and chemical screens. Multiplexing was also instrumental in the recent enhancement of the classic yeast one-hybrid interaction techniques to provide unprecedented discovery capabilities for protein-DNA interactions. Unfortunately its use for zebrafish research is currently hampered by the lack of an open reading frame (ORF) clone collection. As a first step toward a complete collection, we describe a small library of transcriptional regulatory proteins comprising 142 ORFs and its potential applications.
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Affiliation(s)
- Justin King
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - Justin Foster
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - James M Davison
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - John F Rawls
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - Ghislain Breton
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
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Mezan S, Feuz JD, Deplancke B, Kadener S. PDF Signaling Is an Integral Part of the Drosophila Circadian Molecular Oscillator. Cell Rep 2017; 17:708-719. [PMID: 27732848 PMCID: PMC5081397 DOI: 10.1016/j.celrep.2016.09.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/12/2016] [Accepted: 09/15/2016] [Indexed: 12/30/2022] Open
Abstract
Circadian clocks generate 24-hr rhythms in physiology and behavior. Despite numerous studies, it is still uncertain how circadian rhythms emerge from their molecular and neural constituents. Here, we demonstrate a tight connection between the molecular and neuronal circadian networks. Using fluorescent transcriptional reporters in a Drosophila ex vivo brain culture system, we identified a reciprocal negative regulation between the master circadian regulator CLK and expression of pdf, the main circadian neuropeptide. We show that PDF feedback is required for maintaining normal oscillation pattern in CLK-driven transcription. Interestingly, we found that CLK and neuronal firing suppresses pdf transcription, likely through a common pathway involving the transcription factors DHR38 and SR, establishing a direct link between electric activity and the circadian system. In sum, our work provides evidence for the existence of an uncharacterized CLK-PDF feedback loop that tightly wraps together the molecular oscillator with the circadian neuronal network in Drosophila. Monitoring circadian transcription ex vivo using fluorescent reporters CLK activation in the LNvs provokes downregulation in CLK activity in LNds and DNs Reciprocal negative regulation of CLK activity and pdf transcription and signaling PDF signaling is required for the normal oscillation pattern in CLK activity
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Affiliation(s)
- Shaul Mezan
- Biological Chemistry Department, Silberman Institute of Life Sciences, the Hebrew University, Jerusalem 91904, Israel
| | - Jean Daniel Feuz
- Institute of Bioengineering, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, the Hebrew University, Jerusalem 91904, Israel.
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26
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Houtz P, Bonfini A, Liu X, Revah J, Guillou A, Poidevin M, Hens K, Huang HY, Deplancke B, Tsai YC, Buchon N. Hippo, TGF-β, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection. PLoS Genet 2017; 13:e1007091. [PMID: 29108021 PMCID: PMC5690694 DOI: 10.1371/journal.pgen.1007091] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/16/2017] [Accepted: 10/30/2017] [Indexed: 01/31/2023] Open
Abstract
Cytokine signaling is responsible for coordinating conserved epithelial regeneration and immune responses in the digestive tract. In the Drosophila midgut, Upd3 is a major cytokine, which is induced in enterocytes (EC) and enteroblasts (EB) upon oral infection, and initiates intestinal stem cell (ISC) dependent tissue repair. To date, the genetic network directing upd3 transcription remains largely uncharacterized. Here, we have identified the key infection-responsive enhancers of the upd3 gene and show that distinct enhancers respond to various stresses. Furthermore, through functional genetic screening, bioinformatic analyses and yeast one-hybrid screening, we determined that the transcription factors Scalloped (Sd), Mothers against dpp (Mad), and D-Fos are principal regulators of upd3 expression. Our study demonstrates that upd3 transcription in the gut is regulated by the activation of multiple pathways, including the Hippo, TGF-β/Dpp, and Src, as well as p38-dependent MAPK pathways. Thus, these essential pathways, which are known to control ISC proliferation cell-autonomously, are also activated in ECs to promote tissue turnover the regulation of upd3 transcription. Tissue regeneration is a fundamental process that maintains the integrity of the intestinal epithelium when faced with chemical or microbial stresses. In both healthy and diseased conditions, pro-regenerative cytokines function as central coordinators of gut renewal, linking inflammation to stem cell activity. In Drosophila, the upstream events that stimulate the production of the primary cytokine Unpaired 3 (Upd3) in response to indigenous or pathogenic microbes have yet to be elucidated. In this study, we demonstrate that upd3 expression is driven in different cell types by separate microbe-responsive enhancers. In enterocytes (ECs), cytokine induction relies on the Yki/Sd, Mad/Med, and AP-1 transcription factors (TFs). These TF complexes are activated downstream of the Hippo, TGF-β and Src-MAPK pathways, respectively. Inhibiting these pathways in ECs impairs upd3 transcription, which in turn blocks intestinal stem cell proliferation and reduces the survival rate of adult flies following enteric infections. Altogether, our study identifies the major microbe-responsive enhancers of the upd3 gene and sheds light on the complexity of the gene regulatory network required in ECs to regulate tissue homeostasis and stem cell activity in the digestive tract.
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Affiliation(s)
- Philip Houtz
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America
| | - Alessandro Bonfini
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America
| | - Xi Liu
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America
| | - Jonathan Revah
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America
| | - Aurélien Guillou
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America
| | - Mickael Poidevin
- Institut de Biologie Integrative de la Cellule. Avenue de la Terrasse, France
| | - Korneel Hens
- Centre for Neural Circuits and Behavior, The University of Oxford, Tinsley Building, Mansfield Road, Oxford, United Kingdom
| | - Hsin-Yi Huang
- Department of Life Science and Life Science Center, Tunghai University, Taichung, Taiwan, Republic of China
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics (LSBG). School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yu-Chen Tsai
- Department of Life Science and Life Science Center, Tunghai University, Taichung, Taiwan, Republic of China
| | - Nicolas Buchon
- Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America
- * E-mail:
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27
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Bonaldi K, Li Z, Kang SE, Breton G, Pruneda-Paz JL. Novel cell surface luciferase reporter for high-throughput yeast one-hybrid screens. Nucleic Acids Res 2017; 45:e157. [PMID: 28985361 PMCID: PMC5737895 DOI: 10.1093/nar/gkx682] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/25/2017] [Indexed: 01/08/2023] Open
Abstract
Gene-centered yeast one-hybrid (Y1H) screens provide a powerful and effective strategy to identify transcription factor (TF)-promoter interactions. While genome-wide TF ORFeome clone collections are increasingly available, screening protocols have limitations inherent to the properties of the enzymatic reaction used to identify interactions and to the procedure required to perform the assay in a high-throughput format. Here, we present the development and validation of a streamlined strategy for quantitative and fully automated gene-centered Y1H screens using a novel cell surface Gaussia luciferase reporter.
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Affiliation(s)
- Katia Bonaldi
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Zheng Li
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - S Earl Kang
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, TX 77030, USA
| | - Jose L Pruneda-Paz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
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28
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Tissue-specific enhancer repression through molecular integration of cell signaling inputs. PLoS Genet 2017; 13:e1006718. [PMID: 28394894 PMCID: PMC5402979 DOI: 10.1371/journal.pgen.1006718] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 04/24/2017] [Accepted: 03/27/2017] [Indexed: 11/19/2022] Open
Abstract
Drosophila leg morphogenesis occurs under the control of a relatively well-known genetic cascade, which mobilizes both cell signaling pathways and tissue-specific transcription factors. However, their cross-regulatory interactions, deployed to refine leg patterning, remain poorly characterized at the gene expression level. Within the genetically interacting landscape that governs limb development, the bric-à-brac2 (bab2) gene is required for distal leg segmentation. We have previously shown that the Distal-less (Dll) homeodomain and Rotund (Rn) zinc-finger activating transcription factors control limb-specific bab2 expression by binding directly a single critical leg/antennal enhancer (LAE) within the bric-à-brac locus. By genetic and molecular analyses, we show here that the EGFR-responsive C15 homeodomain and the Notch-regulated Bowl zinc-finger transcription factors also interact directly with the LAE enhancer as a repressive duo. The appendage patterning gene bab2 is the first identified direct target of the Bowl repressor, an Odd-skipped/Osr family member. Moreover, we show that C15 acts on LAE activity independently of its regular partner, the Aristaless homeoprotein. Instead, we find that C15 interacts physically with the Dll activator through contacts between their homeodomain and binds competitively with Dll to adjacent cognate sites on LAE, adding potential new layers of regulation by C15. Lastly, we show that C15 and Bowl activities regulate also rn expression. Our findings shed light on how the concerted action of two transcriptional repressors, in response to cell signaling inputs, shapes and refines gene expression along the limb proximo-distal axis in a timely manner. Limb morphogenesis is controlled by a well-known genetic cascade, mobilizing both cell signaling and tissue-specific transcription factors (TFs). However, how their concerted action refines gene expression remains to be deciphered. It is thus crucial to understand how cell signaling inputs are integrated by transcriptional “enhancers”. The Drosophila leg provides a good paradigm to dissect the molecular mechanisms underlying gene regulation. Here, we used the bric-a-brac2 (bab2) gene as a model to study the integrated regulation of patterning genes implicated in tarsal segmentation. bab2 expression in the leg primordium is dynamic and complex, going from initial broad distal expression to precisely positioned tarsal rings. By genetic and molecular analyses, we show here that the cell signaling-responding TFs C15 and Bowl interact directly with the limb-specific bab2 enhancer as a repressive duo. Moreover, C15 acts independently of its partner Aristaless through physical interaction with the Dll activator. We propose that Dll induces early circular bab2 expression pattern, then EGFR signaling-induced C15 in the distalmost cells competes with Dll for LAE binding and resolves bab2 pattern as a ring. Taken together our data shed light on how the concerted action of a quartet of transcription factors reshapes gene expression during limb proximo-distal axis development.
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29
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Mendoza-García P, Hugosson F, Fallah M, Higgins ML, Iwasaki Y, Pfeifer K, Wolfstetter G, Varshney G, Popichenko D, Gergen JP, Hens K, Deplancke B, Palmer RH. The Zic family homologue Odd-paired regulates Alk expression in Drosophila. PLoS Genet 2017; 13:e1006617. [PMID: 28369060 PMCID: PMC5393633 DOI: 10.1371/journal.pgen.1006617] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 04/17/2017] [Accepted: 02/07/2017] [Indexed: 01/30/2023] Open
Abstract
The Anaplastic Lymphoma Kinase (Alk) receptor tyrosine kinase (RTK) plays a critical role in the specification of founder cells (FCs) in the Drosophila visceral mesoderm (VM) during embryogenesis. Reporter gene and CRISPR/Cas9 deletion analysis reveals enhancer regions in and upstream of the Alk locus that influence tissue-specific expression in the amnioserosa (AS), the VM and the epidermis. By performing high throughput yeast one-hybrid screens (Y1H) with a library of Drosophila transcription factors (TFs) we identify Odd-paired (Opa), the Drosophila homologue of the vertebrate Zic family of TFs, as a novel regulator of embryonic Alk expression. Further characterization identifies evolutionarily conserved Opa-binding cis-regulatory motifs in one of the Alk associated enhancer elements. Employing Alk reporter lines as well as CRISPR/Cas9-mediated removal of regulatory elements in the Alk locus, we show modulation of Alk expression by Opa in the embryonic AS, epidermis and VM. In addition, we identify enhancer elements that integrate input from additional TFs, such as Binou (Bin) and Bagpipe (Bap), to regulate VM expression of Alk in a combinatorial manner. Taken together, our data show that the Opa zinc finger TF is a novel regulator of embryonic Alk expression. The Alk receptor tyrosine kinase is employed repeatedly during Drosophila development to drive signaling events in a variety of tissues. The spatial and temporal expression pattern of the Alk gene is tightly regulated. Identifying factors that influence the expression of Alk is important to better understand how Alk signaling is controlled. In this paper we characterize cis-regulatory sequences in the Alk locus and the transcription factors that bind them to govern Alk expression in the Drosophila embryo. Using a robotic protein-DNA interaction assay, we identified the Zic family transcription factor Odd-paired as a factor that binds to regulatory elements in the Alk locus. Binding of Odd-paired to Alkcis-regulatory elements varies spatially, revealing a requirement for additional transcription factors such as the NK3 and FoxF orthologues Bagpipe and Biniou in a subset of Alk-expressing tissues. Our findings provide new insight into the dynamics underlying temporal and spatial regulation of the Alk receptor during embryogenesis.
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Affiliation(s)
- Patricia Mendoza-García
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fredrik Hugosson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mahsa Fallah
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Michael L. Higgins
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Yasuno Iwasaki
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Kathrin Pfeifer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Georg Wolfstetter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gaurav Varshney
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | - J. Peter Gergen
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Korneel Hens
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Lausanne, Switzerland
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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30
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Meireles-Filho AC, Deplancke B. Gene regulatory mechanisms underlying the intestinal innate immune response. Curr Opin Genet Dev 2016; 43:46-52. [PMID: 28011293 DOI: 10.1016/j.gde.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 12/24/2022]
Abstract
In the mammalian gastrointestinal tract, distinct types of cells, including epithelial cells and macrophages, collaborate to eliminate ingested pathogens while striving to preserve the commensal microbiota. The underlying innate immune response is driven by significant gene expression changes in each cell, and recent work has provided novel insights into the gene regulatory mechanisms that mediate such transcriptional changes. These mechanisms differ from those underlying the canonical cellular differentiation model in which a sequential deposition of DNA methylation and histone modification marks progressively restricts the chromatin landscape. Instead, inflammatory macrophages and intestinal epithelial cells appear to largely rely on transcription factors that explore an accessible chromatin landscape to generate dynamic stimulus-specific and spatial-specific physiological responses.
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Affiliation(s)
- Antonio Ca Meireles-Filho
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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31
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Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Gene-Centered Yeast One-Hybrid Assays. Cold Spring Harb Protoc 2016; 2016:2016/12/pdb.top077669. [PMID: 27934693 PMCID: PMC5443116 DOI: 10.1101/pdb.top077669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful "gene-centered" method to identify the TFs that can bind a DNA sequence of interest. In this introduction, we describe the basic principles of the Y1H assay and its advantages and disadvantages and briefly discuss how it is complementary to "TF-centered" methods that identify protein-DNA interactions for a known protein of interest.
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Affiliation(s)
- Juan I. Fuxman Bass
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - John S. Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Albertha J.M. Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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32
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Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. Mol Syst Biol 2016; 12:884. [PMID: 27777270 PMCID: PMC5081483 DOI: 10.15252/msb.20167131] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein–DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene‐centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two‐thirds of which are novel, as well as integrate gene expression, protein–protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Lucie Kozlowski
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - John S Reece-Hoyes
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amy D Holdorf
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Akihiro Mori
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Albertha Jm Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens. G3-GENES GENOMES GENETICS 2016; 6:3419-3430. [PMID: 27527791 PMCID: PMC5068961 DOI: 10.1534/g3.116.032607] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The regulation of gene expression controls development, and changes in this regulation often contribute to phenotypic evolution. Drosophila pigmentation is a model system for studying evolutionary changes in gene regulation, with differences in expression of pigmentation genes such as yellow that correlate with divergent pigment patterns among species shown to be caused by changes in cis- and trans-regulation. Currently, much more is known about the cis-regulatory component of divergent yellow expression than the trans-regulatory component, in part because very few trans-acting regulators of yellow expression have been identified. This study aims to improve our understanding of the trans-acting control of yellow expression by combining yeast-one-hybrid and RNAi screens for transcription factors binding to yellow cis-regulatory sequences and affecting abdominal pigmentation in adults, respectively. Of the 670 transcription factors included in the yeast-one-hybrid screen, 45 showed evidence of binding to one or more sequence fragments tested from the 5′ intergenic and intronic yellow sequences from D. melanogaster, D. pseudoobscura, and D. willistoni, suggesting that they might be direct regulators of yellow expression. Of the 670 transcription factors included in the yeast-one-hybrid screen, plus another TF previously shown to be genetically upstream of yellow, 125 were also tested using RNAi, and 32 showed altered abdominal pigmentation. Nine transcription factors were identified in both screens, including four nuclear receptors related to ecdysone signaling (Hr78, Hr38, Hr46, and Eip78C). This finding suggests that yellow expression might be directly controlled by nuclear receptors influenced by ecdysone during early pupal development when adult pigmentation is forming.
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Chen D, Orenstein Y, Golodnitsky R, Pellach M, Avrahami D, Wachtel C, Ovadia-Shochat A, Shir-Shapira H, Kedmi A, Juven-Gershon T, Shamir R, Gerber D. SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics. Sci Rep 2016; 6:33351. [PMID: 27628341 PMCID: PMC5024299 DOI: 10.1038/srep33351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 08/19/2016] [Indexed: 01/19/2023] Open
Abstract
Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.
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Affiliation(s)
- Dana Chen
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Yaron Orenstein
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Rada Golodnitsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Michal Pellach
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Dorit Avrahami
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Chaim Wachtel
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Avital Ovadia-Shochat
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Hila Shir-Shapira
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Adi Kedmi
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Tamar Juven-Gershon
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Doron Gerber
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, 5290002, Israel
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Breton G, Kay SA, Pruneda-Paz JL. Identification of Arabidopsis Transcriptional Regulators by Yeast One-Hybrid Screens Using a Transcription Factor ORFeome. Methods Mol Biol 2016; 1398:107-18. [PMID: 26867619 DOI: 10.1007/978-1-4939-3356-3_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Genetic and molecular approaches revealed that the circadian clock network structure is comprised of several interlocked positive and negative transcriptional feedback loops. The network evolved to sense and integrate inputs from environmental cues to adjust daily rhythms in physiological processes. Compiling evidence indicates that part of this regulation happens at the transcriptional level through subtle adjustments in the expression of core clock genes. Thus, to better understand the network and identify the molecular mechanisms of clock input pathways, it is imperative to determine how core clock genes are regulated. For this purpose we developed reagents for an unbiased approach to identify transcription factors (TFs) interacting with the promoters of core clock genes. At the center of this approach lies the yeast one-hybrid (Y1H) assay in which a pool of proteins fused to the GAL4 transcriptional activation domain are tested for their ability to interact with a selected promoter fragment in yeast cells. Taking advantage of the fact that Arabidopsis TF genes are well annotated, we generated a comprehensive TF clone collection (TF ORFeome) and used it to replace the standard cDNA pool strategy traditionally used in Y1H screens. The use of this TF clone collection substantially accelerates the comprehensive discovery of promoter-specific DNA binding activities among all Arabidopsis TFs. Considering that this strategy can be extended to the study of the promoter interactome of any Arabidopsis gene, we developed a low throughput protocol that can be universally implemented to screen the ~2000 TF clone library.
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Affiliation(s)
- Ghislain Breton
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Steve A Kay
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90089, USA.
| | - José L Pruneda-Paz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Center for Chronobiology, University of California San Diego, La Jolla, CA, 92093, USA.
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36
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Rastegar S, Strähle U. The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes. GENETICS, GENOMICS AND FISH PHENOMICS 2016; 95:195-216. [DOI: 10.1016/bs.adgen.2016.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Zolotarev NA, Kyrchanova OV, Maksimenko OG, Georgiev PG. Recruiting insulator protein ZIPIC of Drosophila melanogaster to minor binding sites in vivo depends on other DNA-binding transcription factors. Mol Biol 2015. [DOI: 10.1134/s0026893315060242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Abstract
The underlying physical properties of microfluidic tools have led to new biological insights through the development of microsystems that can manipulate, mimic and measure biology at a resolution that has not been possible with macroscale tools. Microsystems readily handle sub-microlitre volumes, precisely route predictable laminar fluid flows and match both perturbations and measurements to the length scales and timescales of biological systems. The advent of fabrication techniques that do not require highly specialized engineering facilities is fuelling the broad dissemination of microfluidic systems and their adaptation to specific biological questions. We describe how our understanding of molecular and cell biology is being and will continue to be advanced by precision microfluidic approaches and posit that microfluidic tools - in conjunction with advanced imaging, bioinformatics and molecular biology approaches - will transform biology into a precision science.
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Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A. Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature 2015; 528:147-51. [PMID: 26550828 DOI: 10.1038/nature15545] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/02/2015] [Indexed: 12/25/2022]
Abstract
One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.
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Affiliation(s)
- Gerald Stampfel
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Tomáš Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Olga Frank
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Sebastian Wienerroither
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Franziska Reiter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
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Külshammer E, Mundorf J, Kilinc M, Frommolt P, Wagle P, Uhlirova M. Interplay among Drosophila transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy. Dis Model Mech 2015; 8:1279-93. [PMID: 26398940 PMCID: PMC4610234 DOI: 10.1242/dmm.020719] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/28/2015] [Indexed: 12/16/2022] Open
Abstract
Cancer initiation and maintenance of the transformed cell state depend on altered cellular signaling and aberrant activities of transcription factors (TFs) that drive pathological gene expression in response to cooperating genetic lesions. Deciphering the roles of interacting TFs is therefore central to understanding carcinogenesis and for designing cancer therapies. Here, we use an unbiased genomic approach to define a TF network that triggers an abnormal gene expression program promoting malignancy of clonal tumors, generated in Drosophila imaginal disc epithelium by gain of oncogenic Ras (RasV12) and loss of the tumor suppressor Scribble (scrib1). We show that malignant transformation of the rasV12scrib1 tumors requires TFs of distinct families, namely the bZIP protein Fos, the ETS-domain factor Ets21c and the nuclear receptor Ftz-F1, all acting downstream of Jun-N-terminal kinase (JNK). Depleting any of the three TFs improves viability of tumor-bearing larvae, and this positive effect can be enhanced further by their combined removal. Although both Fos and Ftz-F1 synergistically contribute to rasV12scrib1 tumor invasiveness, only Fos is required for JNK-induced differentiation defects and Matrix metalloprotease (MMP1) upregulation. In contrast, the Fos-dimerizing partner Jun is dispensable for JNK to exert its effects in rasV12scrib1 tumors. Interestingly, Ets21c and Ftz-F1 are transcriptionally induced in these tumors in a JNK- and Fos-dependent manner, thereby demonstrating a hierarchy within the tripartite TF network, with Fos acting as the most upstream JNK effector. Of the three TFs, only Ets21c can efficiently substitute for loss of polarity and cooperate with RasV12 in inducing malignant clones that, like rasV12scrib1 tumors, invade other tissues and overexpress MMP1 and the Drosophila insulin-like peptide 8 (Dilp8). While rasV12ets21c tumors require JNK for invasiveness, the JNK activity is dispensable for their growth. In conclusion, our study delineates both unique and overlapping functions of distinct TFs that cooperatively promote aberrant expression of target genes, leading to malignant tumor phenotypes. Summary: This study provides genetic evidence that malignancy driven by oncogenic Ras and loss of polarity requires transcription factors of three distinct protein families, acting in synergy downstream of JNK signaling.
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Affiliation(s)
- Eva Külshammer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Juliane Mundorf
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Merve Kilinc
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Peter Frommolt
- Bioinformatics Facility, CECAD Research Center, University of Cologne, 50931 Cologne, Germany
| | - Prerana Wagle
- Bioinformatics Facility, CECAD Research Center, University of Cologne, 50931 Cologne, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
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MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJM. Transcription Factor Activity Mapping of a Tissue-Specific in vivo Gene Regulatory Network. Cell Syst 2015; 1:152-162. [PMID: 26430702 DOI: 10.1016/j.cels.2015.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A wealth of physical interaction data between transcription factors (TFs) and DNA has been generated, but these interactions often do not have apparent regulatory consequences. Thus, equating physical interaction data with gene regulatory networks (GRNs) is problematic. Here, we comprehensively assay TF activity, rather than binding, to construct a network of gene regulatory interactions in the C. elegans intestine. By manually observing the in vivo tissue-specific knockdown of 921 TFs on a panel of 19 fluorescent transcriptional reporters, we identified a GRN of 411 interactions between 19 promoters and 177 TFs. This GRN shows only modest overlap with physical interactions, indicating that many regulatory interactions are indirect. We applied nested effects modeling to uncover information flow between TFs in the intestine that converges on a small set of physical TF-promoter interactions. We found numerous cell nonautonomous regulatory interactions, illustrating tissue-to-tissue communication. Altogether, our study illuminates the complexity of gene regulation in the context of a living animal.
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Affiliation(s)
- Lesley T MacNeil
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - H Efsun Arda
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gabrielle E Giese
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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42
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Bauke AC, Sasse S, Matzat T, Klämbt C. A transcriptional network controlling glial development in the Drosophila visual system. Development 2015; 142:2184-93. [DOI: 10.1242/dev.119750] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/28/2015] [Indexed: 01/07/2023]
Abstract
In the nervous system, glial cells need to be specified from a set of progenitor cells. In the developing Drosophila eye, perineurial glia proliferate and differentiate as wrapping glia in response to a neuronal signal conveyed by the FGF receptor pathway. To unravel the underlying transcriptional network we silenced all genes encoding predicted DNA-binding proteins in glial cells using RNAi. Dref and other factors of the TATA box-binding protein-related factor 2 (TRF2) complex were previously predicted to be involved in cellular metabolism and cell growth. Silencing of these genes impaired early glia proliferation and subsequent differentiation. Dref controls proliferation via activation of the Pdm3 transcription factor, whereas glial differentiation is regulated via Dref and the homeodomain protein Cut. Cut expression is controlled independently of Dref by FGF receptor activity. Loss- and gain-of-function studies show that Cut is required for glial differentiation and is sufficient to instruct the formation of membrane protrusions, a hallmark of wrapping glial morphology. Our work discloses a network of transcriptional regulators controlling the progression of a naïve perineurial glia towards the fully differentiated wrapping glia.
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Affiliation(s)
- Ann-Christin Bauke
- Institute of Neurobiology, University of Münster, Münster 48149, Germany
| | - Sofia Sasse
- Institute of Neurobiology, University of Münster, Münster 48149, Germany
| | - Till Matzat
- Institute of Neurobiology, University of Münster, Münster 48149, Germany
| | - Christian Klämbt
- Institute of Neurobiology, University of Münster, Münster 48149, Germany
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43
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Garcia-Cordero JL, Maerkl SJ. Mechanically Induced Trapping of Molecular Interactions and Its Applications. ACTA ACUST UNITED AC 2015; 21:356-67. [PMID: 25805850 DOI: 10.1177/2211068215578586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Indexed: 12/21/2022]
Abstract
Measuring binding affinities and association/dissociation rates of molecular interactions is important for a quantitative understanding of cellular mechanisms. Many low-throughput methods have been developed throughout the years to obtain these parameters. Acquiring data with higher accuracy and throughput is, however, necessary to characterize complex biological networks. Here, we provide an overview of a high-throughput microfluidic method based on mechanically induced trapping of molecular interactions (MITOMI). MITOMI can be used to obtain affinity constants and kinetic rates of hundreds of protein-ligand interactions in parallel. It has been used in dozens of studies to measure binding affinities of transcription factors, map protein interaction networks, identify pharmacological inhibitors, and perform high-throughput, low-cost molecular diagnostics. This article covers the technological aspects of MITOMI and its applications.
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Affiliation(s)
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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44
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Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:59-84. [PMID: 25704908 PMCID: PMC4339228 DOI: 10.1002/wdev.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/04/2014] [Accepted: 11/16/2014] [Indexed: 11/08/2022]
Abstract
UNLABELLED Gene expression is regulated through the activity of transcription factors (TFs) and chromatin-modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods have led to an explosion of both computational and empirical methods for CRM discovery in model and nonmodel organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against TFs or histone post-translational modifications, identification of nucleosome-depleted 'open' chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted TF-binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Kushal Suryamohan
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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45
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Fast and continuous-flow detection and separation of DNA complexes and DNA in nanofluidic chip format. Methods Mol Biol 2015. [PMID: 25673486 DOI: 10.1007/978-1-4939-2353-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fast separation of DNA and detection of protein/DNA complexes are important in many state-of-the-art molecular medicine technologies, like the production of gene vaccines or medical diagnostics. Here, we describe a nanofluidic chip-based technique for fast, efficient, and virtually label-free detection and separation of protein/DNA and drug/DNA complexes and topological DNA variants. The mechanism is based on a continuous-flow dielectrophoresis at a nanoslit and allows efficient separation of small DNA fragments (<7,000 base pairs) and fast detection of DNA complexes within 1 min.
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46
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Schertel C, Albarca M, Rockel-Bauer C, Kelley NW, Bischof J, Hens K, van Nimwegen E, Basler K, Deplancke B. A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome Res 2015; 25:514-23. [PMID: 25568052 PMCID: PMC4381523 DOI: 10.1101/gr.181305.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 01/07/2015] [Indexed: 12/31/2022]
Abstract
Transcription factors (TFs) are key regulators of cell fate. The estimated 755 genes that encode DNA binding domain-containing proteins comprise ∼ 5% of all Drosophila genes. However, the majority has remained uncharacterized so far due to the lack of proper genetic tools. We generated 594 site-directed transgenic Drosophila lines that contain integrations of individual UAS-TF constructs to facilitate spatiotemporally controlled misexpression in vivo. All transgenes were expressed in the developing wing, and two-thirds induced specific phenotypic defects. In vivo knockdown of the same genes yielded a phenotype for 50%, with both methods indicating a great potential for misexpression to characterize novel functions in wing growth, patterning, and development. Thus, our UAS-TF library provides an important addition to the genetic toolbox of Drosophila research, enabling the identification of several novel wing development-related TFs. In parallel, we established the chromatin landscape of wing imaginal discs by ChIP-seq analyses of five chromatin marks and RNA Pol II. Subsequent clustering revealed six distinct chromatin states, with two clusters showing enrichment for both active and repressive marks. TFs that carry such "bivalent" chromatin are highly enriched for causing misexpression phenotypes in the wing, and analysis of existing expression data shows that these TFs tend to be differentially expressed across the wing disc. Thus, bivalently marked chromatin can be used as a marker for spatially regulated TFs that are functionally relevant in a developing tissue.
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Affiliation(s)
- Claus Schertel
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Monica Albarca
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Claudia Rockel-Bauer
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Nicholas W Kelley
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
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47
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Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EEM, Taipale J. Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. eLife 2015; 4:e04837. [PMID: 25779349 PMCID: PMC4362205 DOI: 10.7554/elife.04837] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/09/2015] [Indexed: 02/07/2023] Open
Abstract
Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latter has been difficult to assess, as previous systematic analyses of TF binding specificity have been performed using different methods in different species. To address this, we determined the binding specificities of 242 Drosophila TFs, and compared them to human and mouse data. This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences. The few human TFs with divergent specificities function in cell types not found in fruit flies, suggesting that evolution of TF specificities contributes to emergence of novel types of differentiated cells.
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Affiliation(s)
- Kazuhiro R Nitta
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Arttu Jolma
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden,Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Yimeng Yin
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Morgunova
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Teemu Kivioja
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Junaid Akhtar
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Korneel Hens
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Jarkko Toivonen
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden,Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland,For correspondence:
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Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH. Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data. J Proteomics 2014; 108:269-83. [DOI: 10.1016/j.jprot.2014.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/14/2014] [Accepted: 05/17/2014] [Indexed: 02/07/2023]
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49
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Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep 2014; 8:622-32. [PMID: 25043187 DOI: 10.1016/j.celrep.2014.06.033] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/28/2014] [Accepted: 06/19/2014] [Indexed: 12/31/2022] Open
Abstract
Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs) bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.
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Affiliation(s)
- Jose L Pruneda-Paz
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ghislain Breton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dawn H Nagel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - S Earl Kang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katia Bonaldi
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colleen J Doherty
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Ravelo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mary Galli
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve A Kay
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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Kloke A, Fiebach AR, Zhang S, Drechsel L, Niekrawietz S, Hoehl MM, Kneusel R, Panthel K, Steigert J, von Stetten F, Zengerle R, Paust N. The LabTube - a novel microfluidic platform for assay automation in laboratory centrifuges. LAB ON A CHIP 2014; 14:1527-1537. [PMID: 24590165 DOI: 10.1039/c3lc51261d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Assay automation is the key for successful transformation of modern biotechnology into routine workflows. Yet, it requires considerable investment in processing devices and auxiliary infrastructure, which is not cost-efficient for laboratories with low or medium sample throughput or point-of-care testing. To close this gap, we present the LabTube platform, which is based on assay specific disposable cartridges for processing in laboratory centrifuges. LabTube cartridges comprise interfaces for sample loading and downstream applications and fluidic unit operations for release of prestored reagents, mixing, and solid phase extraction. Process control is achieved by a centrifugally-actuated ballpen mechanism. To demonstrate the workflow and functionality of the LabTube platform, we show two LabTube automated sample preparation assays from laboratory routines: DNA extractions from whole blood and purification of His-tagged proteins. Equal DNA and protein yields were observed compared to manual reference runs, while LabTube automation could significantly reduce the hands-on-time to one minute per extraction.
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Affiliation(s)
- A Kloke
- HSG-IMIT - Institut für Mikro- und Informationstechnik, Georges-Köhler-Allee 103, 79110 Freiburg, Germany.
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