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This protocol was adapted from Picossi et al. (2014). A sincere thank you to Trudi A. Semeniuk for her diligent proofreading of this protocol. This work was supported by grants from National Portuguese Funding through FCT (Fundacao para a Ciencia e a Tecnologia) projects [PTDC/BIA-MIC/4418/2012, IF/00881/2013, UID/BIM/04773/2013-CBMR, UID/Multi/04326/2013-CCMAR]. MAHP current position is funded by the Australian Government through the Australian Research Council Centre of Excellence for Translational Photosynthesis (CE1401000015). JGL current position is funded by the Spanish Ministry of Economy and Economy and European Regional Development Funds(FEDER) BIO2016-77639-P (MINECO/FEDER), respectively. None of the authors have any conflicts of interest or competing interests to declare.

Analysis of institutional authors

Giner-Lamia, JoaquinAuthor

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Article

ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803

Publicated to:Bio Protoc. 8 (12): e2895- - 2018-01-01 8(12), DOI: 10.21769/BioProtoc.2895

Authors: Giner-Lamia, Joaquin; Hernandez-Prieto, Miguel A.; Futschik, Matthias E.;

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Abstract

Nitrogen is an essential nutrient for all living organisms. In cyanobacteria, a group of oxygenic photosynthetic bacteria, nitrogen homeostasis is maintained by an intricate regulatory network around the transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, the sets of genes under its control (i.e., its regulon) remain poorly defined. In this protocol, we describe the procedure for chromatin immunoprecipitation using NtcA antibodies, followed by DNA sequencing analysis (ChIP-seq) during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). This protocol can be extended to analyze any DNA-binding protein in cyanobacteria for which suitable antibodies exist.

Keywords

Chip-seqCyanobacteriaNitrogenNtcaSynechocystisTranscription

Quality index

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-05-31:

  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 14 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

    Leadership analysis of institutional authors

    This work has been carried out with international collaboration, specifically with researchers from: Australia; Portugal; United Kingdom.

    There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (GINER LAMIA, JOAQUIN) .