Dynamic Profiles and Transcriptional Preferences of Histone Modifications During Spermiogenesis.
During spermiogenesis, extensive histone modifications take place in developing haploid spermatids besides morphological alterations of the genetic material to form compact nuclei. Better understanding on the overall transcriptional dynamics and preferences of histones and enzymes involved in histone modifications may provide valuable information to dissect the epigenetic characteristics and unique chromatin status during spermiogenesis. Using single-cell RNA-Sequencing, the expression dynamics of histone variants, writers, erasers, and readers of histone acetylation and methylation, as well as histone phosphorylation, ubiquitination, and chaperones were assessed through transcriptome profiling during spermiogenesis. This approach provided an unprecedented panoramic perspective of the involving genes in epigenetic modifier/histone variant expression during spermiogenesis. Results reported here revealed the transcriptional ranks of histones, histone modifications, and their readers during spermiogenesis, emphasizing the unique preferences of epigenetic regulation in spermatids. These findings also highlighted the impact of spermatid metabolic preferences on epigenetic modifications. Despite the observed rising trend on transcription levels of all encoding genes and histone variants, the transcriptome profile of genes in histone modifications and their readers displayed a downward expression trend, suggesting that spermatid nuclei condensation is a progressive process that occurred in tandem with a gradual decrease in overall epigenetic activity during spermiogenesis.
Pubmed ID: 33175103 RIS Download
Research resources used in this publication
- Gene Set Enrichment Analysis (RRID:SCR_003199) (software resource)
- GraphPad Prism (RRID:SCR_002798) (software resource)
- Monocle3 (RRID:SCR_018685) (software resource)
- scater (RRID:SCR_015954) (software resource)
- scanpy (RRID:SCR_018139) (software resource)
- SEURAT (RRID:SCR_007322) (software resource)
- featureCounts (RRID:SCR_012919) (software resource)
- STAR (RRID:SCR_004463) (software resource)
- fastp (RRID:SCR_016962) (software resource)
- FastQC (RRID:SCR_014583) (software resource)
Additional research tools detected in this publication
None foundAntibodies used in this publication
- SPlink Detection Kits (Biotin-Streptavidin HRP Detection Systems) (RRID:AB_2758472)
- Anti-L-lactyllysine rabbit pAb (RRID:AB_2868521)
- Succinyl-Histone H3 (Lys122) rabbit pAb (RRID:AB_2868522)
- Histone H4 (acetylated) (acetyl K8) antibody [EP1002Y] (RRID:AB_732937)
- Recombinant Anti-Histone H4 (crotonyl K8) antibody [EPR17905(R)] (RRID:AB_2868523)
- Phospho-Histone H3 (Thr3) (D5G1I) Rabbit mAb (RRID:AB_2798261)
- CDYL antibody (RRID:AB_2077197)
Associated grants
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This is a list of tools and resources that we have found mentioned in this publication.
SPlink Detection Kits (Biotin-Streptavidin HRP Detection Systems) (antibody)
RRID:AB_2758472
This unknown targets IgG
View all literature mentionsAnti-L-lactyllysine rabbit pAb (antibody)
RRID:AB_2868521
This polyclonal targets lactyllysine
View all literature mentionsSuccinyl-Histone H3 (Lys122) rabbit pAb (antibody)
RRID:AB_2868522
This polyclonal targets H3K122su
View all literature mentionsHistone H4 (acetylated) (acetyl K8) antibody [EP1002Y] (antibody)
RRID:AB_732937
This monoclonal targets Histone H4 (acetyl K8)
View all literature mentionsRecombinant Anti-Histone H4 (crotonyl K8) antibody [EPR17905(R)] (antibody)
RRID:AB_2868523
This recombinant monoclonal targets Histone H4 (crotonyl K8)
View all literature mentionsPhospho-Histone H3 (Thr3) (D5G1I) Rabbit mAb (antibody)
RRID:AB_2798261
This monoclonal targets H3
View all literature mentionsGene Set Enrichment Analysis (software resource)
RRID:SCR_003199
Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
View all literature mentionsGraphPad Prism (software resource)
RRID:SCR_002798
Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsMonocle3 (software resource)
RRID:SCR_018685
Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.
View all literature mentionsscater (software resource)
RRID:SCR_015954
Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
View all literature mentionsscanpy (software resource)
RRID:SCR_018139
Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.
View all literature mentionsSEURAT (software resource)
RRID:SCR_007322
A software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data.
View all literature mentionsfeatureCounts (software resource)
RRID:SCR_012919
A read summarization program, which counts mapped reads for the genomic features such as genes and exons.
View all literature mentionsSTAR (software resource)
RRID:SCR_004463
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsfastp (software resource)
RRID:SCR_016962
Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.
View all literature mentionsFastQC (software resource)
RRID:SCR_014583
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentions
