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- Title
CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung.
- Authors
Stuart, William D.; Fink-Baldauf, Iris M.; Tomoshige, Koichi; Guo, Minzhe; Maeda, Yutaka
- Abstract
The transcription factor NKX2-1/TTF-1 is involved in lung pathophysiology, including breathing, innate defense and tumorigenesis. To understand the mechanism by which NKX2-1 regulates genes involved in such pathophysiology, we have previously performed ChIP-seq and identified genome-wide NKX2-1-binding sites, which revealed that NKX2-1 binds to not only proximal promoter regions but also multiple intra- and inter-genic regions of the genes regulated by NKX2-1. However, the roles of such regions, especially non-proximal ones, bound by NKX2-1 have not yet been determined. Here, using CRISPRi (CRISPR/dCas9-KRAB), we scrutinize the functional roles of 19 regions/sites bound by NKX2-1, which are located in genes involved in breathing and innate defense (SFTPB, LAMP3, SFTPA1, SFTPA2) and lung tumorigenesis (MYBPH, LMO3, CD274/PD-L1). Notably, the CRISPRi approach reveals that a portion of NKX2-1-binding sites are functionally indispensable while the rest are dispensable for the expression of the genes, indicating that functional roles of NKX2-1-binding sites are unequally yoked. The transcription factor NKX2-1 is a key regulator of lung pathophysiology, but the importance of its binding sites outside of proximal promoter regions is unclear. Here, William Stuart and Iris Fink-Baldauf et al. use CRISPRi to interrogate 19 NKX2-1 binding sites and identify specific sites important for breathing, innate immune defense, and tumorigenesis.
- Subjects
NEOPLASTIC cell transformation; CRISPRS; GENE expression; RESPIRATION; TRANSCRIPTION factors
- Publication
Communications Biology, 2021, Vol 4, Issue 1, p1
- ISSN
2399-3642
- Publication type
Article
- DOI
10.1038/s42003-021-02083-4