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ChIP-seq analysis of androgen receptor binding in epididymis of ArKI mice

ABSTRACT: ChIP-seq analysis of androgen receptor binding in epididymis of ArKI mice

PROVIDER: PRJNA495852 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8035301.fastq.gz	Fastqsanger.gz
	SRR8035302.fastq.gz	Fastqsanger.gz
	SRR8035303.fastq.gz	Fastqsanger.gz
	SRR8035304.fastq.gz	Fastqsanger.gz
	SRR8035305.fastq.gz	Fastqsanger.gz

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ChIP-seq analysis of androgen receptor binding in epididymis of ArKI mice

Project description:To analyze how SUMOylation of AR affects its chromatin binding, we generated a mouse model (ArKI) in which the two conserved SUMO acceptor lysines of androgen receptor (AR) were permanently abolished by converting them to arginines (ArK381R, K500R). ChIP-seq was used to analyse how the lack of AR SUMOylation affects the chromatin binding of AR in epididymis.

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Project description:We report the in vivo androgen receptor (AR) binding sites in murine prostate, epididymis and kidney in response to physiological androgen testosterone using ChIP-sequencing and gene expression profiling by microarray. From AR cistrome analysis, we identified tissue-specific collaborating factors i.e. FoxA1 in prostate, Hnf4a in kidney and AP2a in epididymis and validated by ChIP-seq. The ChIP experiments have been performed using antibodies specific to AR, FoxA1, Hnf4a, AP-2a and IgG non-specific antibody as a negative control. Examination of AR binding sites in murine androgen-responsive tissues prostate, epididymis and kidney using ChIP-seq. Further analysis of AR cistromes led to identification of tissue-specific collaborating factors and these collaborating factors are validated by ChIP-seq from the same tissues. Two parallel IgG samples were sequenced, merged together and used as a control data set. Parallel ChIP-seq samples were sequenced and merged for each replicate wherever required to contain approximately the same amount of reads across all tissues and conditions. All ChIP-seq experiments are performed in biological duplicates except for the castrated conditions.

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Project description:We report the in vivo androgen receptor (AR) binding sites in caput epididymis of intact SPARKI and wild-type mice using ChIP-sequencing. SPARKI (specificity affecting androgen receptor knock-in) mouse line has the second zinc finger of AR replaced by that of glucocorticoid receptors. In vivo analysis of SPARKI and wild-type AR genome-wide binding sites identified cis-element with less stringent sequence requirements that specify selective AR-binding sites. The ChIP experiments have been performed using antibody specific to AR and IgG non-specific antibody as a negative control. Examination of AR binding sites in epididymis of wild-type and SPARKI mice using ChIP-seq. Two biological replicates from intact wild-type and SPARKI mice and two control IgG samples were sequenced and used in peak calling. To increase the depth of the analysis, replicate ChIP-seq samples were merged and the concatanated samples were used in peak calling.

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Project description:The androgen receptor (AR) has a pivotal role in regulating gene expression in the male reproductive system. Due to the involvement of AR in prostate cancer, its role is best studied in the prostate gland epithelium and prostate cancer cell lines. Here we investigate the transcriptional program of AR in normal human epididymis epithelial (HEE) cells. After AR stimulation of caput HEE cells with the synthetic androgen R1881, AR targets were revealed with RNA-sequencing. Next, AR occupancy genome-wide was determined in control or R1881-stimulated HEE cells by chromatin immunoprecipitation and deep sequencing (ChIP-seq). The results identify about 200 genes that are differentially expressed (DEGs) in HEE cells after AR activation. Some of these DEGs show occupancy of AR at their promoters or cis-regulatory elements suggesting direct regulation. However there is little overlap in AR-associated DEGs between HEE and prostate epithelial cells. Inspection of over-represented motifs in AR ChIP-seq peaks identified CAAT-enhancer binding protein beta (CEBPB) and Runt-related transcription factor 1 (RUNX1) as potential co-factors, with no evidence for FOXA1, which is an important co-factor in the prostate epithelium. CEBPB and RUNX1 ChIP-seq in HEE cells showed that both these factors often occupied AR-binding sites, though rarely simultaneously. Further analysis at a single AR-regulated locus (FK506-binding protein 5, FKPB5) suggests that RUNX1 may inhibit AR occupancy, while CEBP appears to be a co-activator. These data suggest a novel AR transcriptional network governs differentiated functions of the human epididymis epithelium.

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