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| Status |
Public on Aug 07, 2023 |
| Title |
Revisiting chromatin packaging in mouse sperm [Hi-C] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.
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| Overall design |
3D genome profiling in mouse sperm samples that are pre-treated with Dnase or DTT using Hi-C
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| Contributor(s) |
Yin Q, Yang C, Strelkova OS, Sun Y, Gopalan S, Yang L, Dekker J, Fazzio TG, Li XZ, Gibcus J, Rando OJ |
| Citation missing |
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| Submission date |
Aug 07, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Qiangzong Yin |
| E-mail(s) |
qiangzong.yin@umassmed.edu
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| Organization name |
UMass Chan Medical School
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| Department |
Biochemistry and Molecular Biotechnology
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| Lab |
Dr. Oliver Rando's lab
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| Street address |
364 Plantation St LRB940
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE226689 |
Revisiting chromatin packaging in mouse sperm |
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| Relations |
| BioProject |
PRJNA1003038 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE240248_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of BW, MCOOL, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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