Palmitoyltransferase ZDHHC19 regulates histone-to-protamine exchange during spermiogenesis in mice
Data files
Dec 23, 2025 version files 69.32 GB
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KO_1_R1.fastq.gz
4.55 GB
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KO_1_R2.fastq.gz
4.50 GB
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KO_2_R1.fastq.gz
4.71 GB
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KO_2_R2.fastq.gz
4.45 GB
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Macs2_v1.zip
1.65 GB
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MD5.txt
944 B
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Migr_1_R1.fastq.gz
3.43 GB
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Migr_1_R2.fastq.gz
3.22 GB
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Migr_2_R1.fastq.gz
4.46 GB
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Migr_2_R2.fastq.gz
4.28 GB
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README.md
3.34 KB
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Wt_1_R1.fastq.gz
4.76 GB
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Wt_1_R2.fastq.gz
4.75 GB
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Wt_2_R1.fastq.gz
4.88 GB
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Wt_2_R2.fastq.gz
4.62 GB
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ZDHC19_1_R1.fastq.gz
4.29 GB
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ZDHC19_1_R2.fastq.gz
4.31 GB
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ZDHC19_2_R1.fastq.gz
3.29 GB
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ZDHC19_2_R2.fastq.gz
3.17 GB
Abstract
Spermiogenesis, the final phase of spermatogenesis, involves replacing histones by protamines, a process known as histone-to-protamine exchange, which is crucial for chromatin condensation. While this exchange is essential, the precise mechanisms remain incompletely understood. In this study, we discovered that the palmitoyltransferase ZDHHC19 functions as a key regulator of mouse spermiogenesis. Loss of Zdhhc19 leads to male infertility and abnormal sperm morphology. Zdhhc19-deficient sperm exhibit impaired histone-to-protamine exchange, leading to retention of histones and misdistribution of protamines. Similarly, the palmitoyltransferase catalytic site mutant Zdhhc19 C142S knock-in mice show reduced fertility, sperm abnormalities, and histone retention. Mechanistically, ZDHHC19 mediates histone H3 palmitoylation at cysteine 110, weakening H3-H4 interactions and reducing its affinity for DNA. Palmitoylation of H3 facilitates histone-to-protamine exchange. This study highlights the essential role of ZDHHC19's palmitoyl-transferase activity in histone-to-protamine exchange during spermiogenesis and underscores the broader significance of histone palmitoylation in chromatin remodeling.
Dataset DOI: 10.5061/dryad.xd2547dv6
Description of the data and file structure
This dataset contains the ATAC-seq of GC1 cells overexpressing Migr1 (vector) or WT-ZDHHC19 protein, and sorted wild-type and Zdhhc19-/- mouse (10 weeks) haploid spermatids. Raw reads were quality-filtered using Trimmomatic with the default parameters. ATAC-seq paired-end data were aligned to the reference mouse genome (GRCm38/mm10) using the BWA program. MD5 checksums are included for all FASTQ files to validate data integrity. MACS2 files are included for Peak Calling Results.
Files and variables
File: Migr_1_R1.fastq.gz
Description: ATAC-seq of GC1 cells transfected Migr1 (vector)
File: Migr_2_R1.fastq.gz
Description: ATAC-seq of GC1 cells transfected Migr1 (vector)
File: Migr_1_R2.fastq.gz
Description: ATAC-seq of GC1 cells transfected Migr1 (vector)
File: ZDHC19_1_R1.fastq.gz
Description: ATAC-seq of GC1 cells transfected WT-ZDHHC19 protein
File: Migr_2_R2.fastq.gz
Description: ATAC-seq of GC1 cells transfected Migr1 (vector)
File: ZDHC19_1_R2.fastq.gz
Description: ATAC-seq of GC1 cells transfected WT-ZDHHC19 protein
File: ZDHC19_2_R1.fastq.gz
Description: ATAC-seq of GC1 cells transfected WT-ZDHHC19 protein
File: KO_1_R1.fastq.gz
Description: ATAC-seq of sorted Zdhhc19-/- mouse haploid spermatids
File: Wt_1_R1.fastq.gz
Description: ATAC-seq of sorted wild-type mouse haploid spermatids
File: MD5.txt
Description: MD5 checksums for validation of all FASTQ files
File: ZDHC19_2_R2.fastq.gz
Description: ATAC-seq of GC1 cells transfected WT-ZDHHC19 protein
File: KO_1_R2.fastq.gz
Description: ATAC-seq of sorted Zdhhc19-/- mouse haploid spermatids
File: Wt_1_R2.fastq.gz
Description: ATAC-seq of sorted wild-type mouse haploid spermatids
File: KO_2_R1.fastq.gz
Description: ATAC-seq of sorted Zdhhc19-/- mouse haploid spermatids
File: Wt_2_R1.fastq.gz
Description: ATAC-seq of sorted wild-type mouse haploid spermatids
File: KO_2_R2.fastq.gz
Description: ATAC-seq of sorted Zdhhc19-/- mouse haploid spermatids
File: Macs2_v1.zip
Description: MACS2 Peak Calling Results, analyzed by MACS2 software. The file named "All_peakNum.xls" is the peak count summary for all samples.
For each sample, there are two file types.
- .narrowPeak File: This is a peak coordinate file in the narrowPeak format. It can be opened and viewed using software like Excel or a standard text editor.
- .bw File: This is a file in the bigWig (bw) format. It can be uploaded to visualization tools such as the UCSC Genome Browser or IGV (Integrative Genomics Viewer) to visually display the distribution of sequencing reads across a reference genome.
File: Wt_2_R2.fastq.gz
Description: ATAC-seq of sorted wild-type mouse haploid spermatids
Code/software
The ATAC-seq data were aligned to the reference mouse genome (GRCm38/mm10) using the BWA program. The peak calling profiles were analyzed by the MACS2 software, and the heatmaps were drawn by the deeptools tool.
Access information
NA
Haploid spermatids and spermatocytes were sorted by FACS. In brief, adult mouse testes were put in PBS at 33°C for collagenase and trypsin digestion. After filtering, single germ cells were stained with 5 μg/ml Hoechst 33342 at 33°C for 40 min. Then, the two populations were separated and sorted by FACS (BD, Aria II, Influx) according to signals in 630/30 and 460/50 excited by 355nm. 630/30high 460/50high population represents spermatocytes, and 630/30low 460/50low population represents haploid spermatids. In haploid spermatids, the FSChigh population represents round spermatids and the FSClow population represents elongated spermatids.