Cargando…
CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung
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-bind...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115294/ https://www.ncbi.nlm.nih.gov/pubmed/33980985 http://dx.doi.org/10.1038/s42003-021-02083-4 |
_version_ | 1783691203537010688 |
---|---|
author | Stuart, William D. Fink-Baldauf, Iris M. Tomoshige, Koichi Guo, Minzhe Maeda, Yutaka |
author_facet | Stuart, William D. Fink-Baldauf, Iris M. Tomoshige, Koichi Guo, Minzhe Maeda, Yutaka |
author_sort | Stuart, William D. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8115294 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-81152942021-05-12 CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung Stuart, William D. Fink-Baldauf, Iris M. Tomoshige, Koichi Guo, Minzhe Maeda, Yutaka Commun Biol Article 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. Nature Publishing Group UK 2021-05-12 /pmc/articles/PMC8115294/ /pubmed/33980985 http://dx.doi.org/10.1038/s42003-021-02083-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Stuart, William D. Fink-Baldauf, Iris M. Tomoshige, Koichi Guo, Minzhe Maeda, Yutaka CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung |
title | CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung |
title_full | CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung |
title_fullStr | CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung |
title_full_unstemmed | CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung |
title_short | CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung |
title_sort | crispri-mediated functional analysis of nkx2-1-binding sites in the lung |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115294/ https://www.ncbi.nlm.nih.gov/pubmed/33980985 http://dx.doi.org/10.1038/s42003-021-02083-4 |
work_keys_str_mv | AT stuartwilliamd crisprimediatedfunctionalanalysisofnkx21bindingsitesinthelung AT finkbaldaufirism crisprimediatedfunctionalanalysisofnkx21bindingsitesinthelung AT tomoshigekoichi crisprimediatedfunctionalanalysisofnkx21bindingsitesinthelung AT guominzhe crisprimediatedfunctionalanalysisofnkx21bindingsitesinthelung AT maedayutaka crisprimediatedfunctionalanalysisofnkx21bindingsitesinthelung |