POL Scientific / JBM / Volume 11 / Issue 2 / DOI: 10.14440/jbm.2024.0009
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Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells

Zhiheng Liu1 Lirong Zhang2* Yupeng Chen1,2*
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1 Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China
2 Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
JBM 2024 , 11(2), e99010015; https://doi.org/10.14440/jbm.2024.0009
Submitted: 31 May 2024 | Revised: 21 June 2024 | Accepted: 25 June 2024 | Published: 10 July 2024
© 2024 by the Journal of Biological Methods published by POL Scientific. Licensee POL Scientific, USA. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

Spatiotemporal regulation of gene expression is essential for maintaining cellular homeostasis throughout kidney development and disease progression. Transcription factors (TFs) and epigenetic modifications play pivotal roles in controlling gene expression. Profiling chromatin modifications across the genome, along with the distribution and target regulation by TFs in specific kidney cell types, is crucial for understanding the dynamic changes in gene expression. Here, we presented a comprehensive workflow for epigenomic, cistromic, and transcriptomic analyses of primary kidney tubular cells. Specifically, our methodologies included the isolation of primary kidney tubular epithelial cells, RNA extraction, assay for transposase-accessible chromatin using sequencing, ultra-low-input micrococcal nuclease-based native chromatin immunoprecipitation, cleavage under targets and release using nuclease, and subsequent bioinformatic analysis. This protocol provides a methodological framework for investigating the roles of TFs and epigenetic modifications in kidney development and diseases.

Keywords
Epigenomic
Cistromic
Transcriptomic
Kidney disease
Funding
This study was supported by Tianjin Municipal Education Commission (Grant No.: 2022ZD054).
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Conflict of interest
The authors declare no conflict of interest.
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Journal of Biological Methods, Electronic ISSN: 2326-9901 Print ISSN: TAB, Published by POL Scientific