Reconstruction of gene regulatory modules from RNA silencing of IFN-α modulators: Experimental set-up and inference method

Angela Grassi, Barbara Di Camillo, Francesco Ciccarese, Valentina Agnusdei, Paola Zanovello, Alberto Amadori, Lorenzo Finesso, Stefano Indraccolo, Gianna Maria Toffolo

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: Inference of gene regulation from expression data may help to unravel regulatory mechanisms involved in complex diseases or in the action of specific drugs. A challenging task for many researchers working in the field of systems biology is to build up an experiment with a limited budget and produce a dataset suitable to reconstruct putative regulatory modules worth of biological validation. Results: Here, we focus on small-scale gene expression screens and we introduce a novel experimental set-up and a customized method of analysis to make inference on regulatory modules starting from genetic perturbation data, e.g. knockdown and overexpression data. To illustrate the utility of our strategy, it was applied to produce and analyze a dataset of quantitative real-time RT-PCR data, in which interferon-α (IFN-α) transcriptional response in endothelial cells is investigated by RNA silencing of two candidate IFN-α modulators, STAT1 and IFIH1. A putative regulatory module was reconstructed by our method, revealing an intriguing feed-forward loop, in which STAT1 regulates IFIH1 and they both negatively regulate IFNAR1. STAT1 regulation on IFNAR1 was object of experimental validation at the protein level. Conclusions: Detailed description of the experimental set-up and of the analysis procedure is reported, with the intent to be of inspiration for other scientists who want to realize similar experiments to reconstruct gene regulatory modules starting from perturbations of possible regulators. Application of our approach to the study of IFN-α transcriptional response modulators in endothelial cells has led to many interesting novel findings and new biological hypotheses worth of validation.

Original languageEnglish
Article number228
JournalBMC Genomics
Volume17
Issue number1
DOIs
Publication statusPublished - Mar 12 2016

Fingerprint

Gene Regulatory Networks
RNA Interference
Interferons
Endothelial Cells
Systems Biology
Gene Expression Regulation
Budgets
Real-Time Polymerase Chain Reaction
Research Personnel
Gene Expression
Pharmaceutical Preparations
Proteins
Datasets

Keywords

  • Experimental set-up
  • Gene regulatory modules
  • IFN-α modulators
  • RNA silencing
  • Small-scale gene expression screens

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Reconstruction of gene regulatory modules from RNA silencing of IFN-α modulators : Experimental set-up and inference method. / Grassi, Angela; Di Camillo, Barbara; Ciccarese, Francesco; Agnusdei, Valentina; Zanovello, Paola; Amadori, Alberto; Finesso, Lorenzo; Indraccolo, Stefano; Toffolo, Gianna Maria.

In: BMC Genomics, Vol. 17, No. 1, 228, 12.03.2016.

Research output: Contribution to journalArticle

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