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High-Throughput Protein Production Combined with High- Throughput SELEX Identifies an Extensive Atlas of Ciona robusta Transcription Factor DNA-Binding Specificities

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High-Throughput Protein Production and Purification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2025))

Abstract

Transcription factors (TFs) control gene transcription, binding to specific DNA motifs located in cis-regulatory elements across the genome. The identification of TF-binding motifs is thus an important aspect to understand the role of TFs in gene regulation. SELEX, Systematic Evolution of Ligands by EXponential enrichment, is an efficient in vitro method, which can be used to determine the DNA-binding specificity of TFs. Thanks to the development of high-throughput (HT) DNA cloning system and protein production technology, the classical SELEX assay has be extended to high-throughput scale (HT-SELEX).

We report here the detailed protocol for the cloning, production, and purification of 420 Ciona robusta DNA BD. 263 Ciona robusta TF DNA-binding domain proteins were purified in milligram quantities and analyzed by HT-SELEX. The identification of 139 recognition sequences generates an atlas of protein-DNA-binding specificities that is crucial for the understanding of the gene regulatory network (GRN) of Ciona robusta. Overall, our analysis suggests that the Ciona robusta repertoire of sequence-specific transcription factors comprises less than 500 genes. The protocols for high-throughput protein production and HT-SELEX described in this article for the study of Ciona robusta TF DNA-binding specificity are generic and have been successfully applied to a wide range of TFs from other species, including human, mouse, and Drosophila.

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Acknowledgments

This work was supported by a Grant-in-Aid from French ANR grants (Chor_Reg_Net, ANR-05-BLAN-015; Chor-Evo-Net, 0ANR-08-BLAN-0067-01) and an FP6 EU grant (Transcode, LSHG-CT-2004-511990). PL and RV were members or CNRS. KN was supported by the ANR (Chor_Reg_Net), and by CNRS. Thanks to Drs. Jussi Taipale and Arttu Jolma to support NGS sequencing. This work was supported by the French Infrastructure for Integrated Structural Biology (FRISBI, ANR-10-INBS-05).

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Author notes

  1. Daniel Sobral

    Present address: Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal

  2. Kazuhiro R. Nitta and Renaud Vincentelli contributed equally to this work.

Authors and Affiliations

  1. Institute of Developmental Biology of Marseille (IBDM), Aix-Marseille Université/CNRS, Marseille cedex 9, France

    Kazuhiro R. Nitta, Edwin Jacox, Yukio Ohtsuka, Daniel Sobral & Patrick Lemaire

  2. Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan

    Kazuhiro R. Nitta

  3. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, CNRS, Aix-Marseille Université, Marseille cedex 9, France

    Agnès Cimino & Christian Cambillau

  4. Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier/CNRS, Montpellier cedex 5, France

    Edwin Jacox & Patrick Lemaire

  5. Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

    Yukio Ohtsuka

  6. Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan

    Yutaka Satou

  7. Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille cedex 9, France

    Renaud Vincentelli

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  1. Kazuhiro R. Nitta
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  9. Patrick Lemaire
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Correspondence to Patrick Lemaire .

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  1. Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille cedex 9, France

    Renaud Vincentelli

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Nitta, K.R. et al. (2019). High-Throughput Protein Production Combined with High- Throughput SELEX Identifies an Extensive Atlas of Ciona robusta Transcription Factor DNA-Binding Specificities. In: Vincentelli, R. (eds) High-Throughput Protein Production and Purification. Methods in Molecular Biology, vol 2025. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9624-7_23

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  • DOI: https://doi.org/10.1007/978-1-4939-9624-7_23

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9623-0

  • Online ISBN: 978-1-4939-9624-7

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