Integrative Cistromic and Transcriptomic Analyses Identify CREB Target Genes in Cystic Renal Epithelial Cells.

Abstract

BACKGROUND:

Genome-wide mapping of transcription factor (TF) binding sites is essential to identify a TF's direct target genes in kidney development and diseases. However, due to the cellular complexity of the kidney and limited numbers of a given cell type, it has been challenging to determine the binding sites of a TF in vivo. cAMP response element-binding protein (CREB) is phosphorylated and hyperactive in autosomal dominant polycystic kidney disease (ADPKD). We focus on CREB as an example to profile genomic loci bound by a TF and to identify its target genes using low numbers of specific kidney cells.

METHODS:

Cleavage under targets and release using nuclease (CUT&RUN) assays were performed with Dolichos biflorus agglutinin (DBA)-positive tubular epithelial cells from normal and ADPKD mouse kidneys. Pharmacologic inhibition of CREB with 666-15 and genetic inhibition with A-CREB were undertaken using ADPKD mouse models.

RESULTS:

CUT&RUN to profile genome-wide distribution of phosphorylated CREB (p-CREB) indicated correlation of p-CREB binding with active histone modifications (H3K4me3 and H3K27ac) in cystic epithelial cells. Integrative analysis with CUT&RUN and RNA-sequencing revealed CREB direct targets, including genes involved in ribosome biogenesis and protein synthesis. Pharmacologic and genetic inhibition of CREB suppressed cyst growth in ADPKD mouse models.

CONCLUSIONS:

CREB promotes cystogenesis by activating ribosome biogenesis genes. CUT&RUN, coupled with transcriptomic analysis, enables interrogation of TF binding and identification of direct TF targets from a low number of specific kidney cells.

• Authors: Zhiheng Liu, Yunjing Liu, Lin Dang, Meijuan Geng, Yongzhan Sun, Yi Lu, Zhongze Fang, Hui Xiong, Yupeng Chen
• Journal: Journal of the American Society of Nephrology : JASN (J Am Soc Nephrol) Vol. 32 Issue 10 Pg. 2529-2541 (10 2021) ISSN: 1533-3450 [Electronic] United States
• PMID: 34162733 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2021 by the American Society of Nephrology.

Chemical References

• 666-15 compound
• Anilides
• Creb1 protein, mouse
• Cyclic AMP Response Element-Binding Protein
• Histones
• Naphthalenes
• histone H3 trimethyl Lys4

Topics

• Anilides (pharmacology)
• Animals
• Blood Urea Nitrogen
• Cell Line
• Cyclic AMP Response Element-Binding Protein (antagonists & inhibitors, genetics, metabolism)
• Disease Progression
• Epithelial Cells (metabolism)
• Female
• Gene Expression Profiling
• Gene Expression Regulation
• Histones (metabolism)
• Kidney Tubules (metabolism, pathology)
• Male
• Mice
• Naphthalenes (pharmacology)
• Phosphorylation
• Polycystic Kidney, Autosomal Dominant (genetics, metabolism, pathology)
• Sequence Analysis, RNA