ArticleNucleic acids research2013
Nanobody(R)-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- NanoTag is an improved method to map interactions between DNA and proteins not requiring IgG.Scientific reports · 2025Article
- Discovery of nanobodies: a comprehensive review of their applications and potential over the past five years.Journal of nanobiotechnology · 2024Review
- Studying the characteristics of nanobody CDR regions based on sequence analysis in combination with 3D structures.Journal, genetic engineering & biotechnology · 2022Article
- A comprehensive comparison between camelid nanobodies and single chain variable fragments.Biomarker research · 2021Review
- Camelid Single-Domain Antibodies for the Development of Potent Diagnosis Platforms.Molecular diagnosis & therapy · 2021Review
- A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.Nature communications · 2019Article
- YtrAFrontiers in microbiology · 2019Article
- A Two-Step Approach for the Design and Generation of Nanobodies.International journal of molecular sciences · 2018Article
- Selectable high-yield recombinant protein production in human cells using a GFP/YFP nanobody affinity support.Protein science : a publication of the Protein Society · 2018Article
- Structural Basis for the Specific Neutralization of Stx2a with a Camelid Single Domain Antibody Fragment.Toxins · 2018Article
- Institute collection and analysis of Nanobodies (iCAN): a comprehensive database and analysis platform for nanobodies.BMC genomics · 2017Article
- Joining the in vitro immunization of alpaca lymphocytes and phage display: rapid and cost effective pipeline for sdAb synthesis.Microbial cell factories · 2017Article
- The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.BMC genomics · 2016Article
- Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications.International journal of nanomedicine · 2016Review
- Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies.The Biochemical journal · 2014Article
- The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation.BMC genomics · 2013Article
- Host and viral transcriptional regulators in Sulfolobus: an overview.Extremophiles : life under extreme conditions · 2013Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanobodies® are single-domain antibody fragments derived from camelid heavy-chain antibodies. Because of their small size, straightforward production in Escherichia coli, easy tailoring, high affinity, specificity, stability and solubility, nanobodies® have been exploited in various biotechnological applications. A major challenge in the post-genomics and post-proteomics era is the identification of regulatory networks involving nucleic acid-protein and protein-protein interactions. Here, we apply a nanobody® in chromatin immunoprecipitation followed by DNA microarray hybridization (ChIP-chip) for genome-wide identification of DNA-protein interactions. The Lrp-like regulator Ss-LrpB, arguably one of the best-studied specific transcription factors of the hyperthermophilic archaeon Sulfolobus solfataricus, was chosen for this proof-of-principle nanobody®-assisted ChIP. Three distinct Ss-LrpB-specific nanobodies®, each interacting with a different epitope, were generated for ChIP. Genome-wide ChIP-chip with one of these nanobodies® identified the well-established Ss-LrpB binding sites and revealed several unknown target sequences. Furthermore, these ChIP-chip profiles revealed auxiliary operator sites in the open reading frame of Ss-lrpB. Our work introduces nanobodies® as a novel class of affinity reagents for ChIP. Taking into account the unique characteristics of nanobodies®, in particular, their short generation time, nanobody®-based ChIP is expected to further streamline ChIP-chip and ChIP-Seq experiments, especially in organisms with no (or limited) possibility of genetic manipulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.