(A) Six-week-old C57BL/6J sires were fed either a control or high-fat diet (CON or HFD, respectively) for 8–10 weeks. Males were then time-mated with CON-fed C57BL/6J females to generate …
(A) Heatmap of log2 normalized counts for obesity-sensitive regions in sperm (n=1760). Columns (samples) and rows (genomic regions) are arranged by hierarchical clustering with complete-linkage …
(A) Histogram showing frequency distributions of read abundances of genome-wide 150 bp windows. The vertical red line indicates the cut-off where windows with low read counts were filtered out …
(A) Top 10 significantly enriched known motifs at obesity-sensitive regions with increased histone H3 lysine 4 tri-methylation (H3K4me3) enrichment in high-fat diet (HFD)-sperm. Motifs are clustered …
(A–B) Upset plots showing annotations for tissue-specific enhancers overlapping with differentially expressed histone H3 lysine 4 tri-methylation (deH3K4me3) regions with decreased enrichment in …
(A–B) Heatmaps of normalized counts scaled by row (z-score) for transcripts that code for the detected differentially expressed genes (Lancaster p<0.05) in female (A, n=2035 genes) and male (B, …
(A) Spearman correlation heatmap on variance stabilized transcripts. The color gradient represents the Spearman correlation coefficient for each sample pairwise comparison. (B–C) Principal component …
(A) Boxplots showing sample-specific proportions for the top 5 cell types with highest proportions detected in the bulk RNA-sequencing (RNA-seq) data deconvolution analysis across experimental …
(A) Principal component analysis (PCA) plot of 4346 single cells from mouse E14.5 placenta, with the 28 different cell types previously identified within the placenta (Han et al., 2018). The number …
(A) Boxplots showing sample-specific proportions for the remaining cell types detected in the bulk RNA-sequencing (RNA-seq) data deconvolution analysis across experimental groups (n=4 per sex per …
(A–F) Principal component results for female (A–C) and male (D–F) placentas. (A and D) PCA plot of cell proportions. Confidence ellipses are drawn around mean points for each experimental group. (B …
(A) Boxplots showing sample-specific proportions for the top 10 cell types with highest proportions detected in the bulk RNA-sequencing data deconvolution analysis across experimental groups (n=5 …
(A) Spearman correlation heatmap on variance stabilized transcripts. The color gradient represents the Spearman correlation coefficient for each sample pairwise comparison. (B) Principal component …
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Biological sample (Mus musculus, male) | Spermatozoa | C57BL/6J, The Jackson Laboratory | Isolated from Mus musculus (C57BL/6J) | |
Biological sample (Mus musculus) | Placenta | C57BL/6J, The Jackson Laboratory | Isolated from Mus musculus (C57BL/6J) | |
Antibody | Tri-Methyl-Histone H3 (Lys4) (C42D8) (Rabbit monoclonal) | Cell Signaling Technology | Cat#:9751 | (5 µg) |
Commercial assay or kit | ChIP DNA Clean and Concentrator | Zymo Research | Cat#:D5201 | |
Commercial assay or kit | RNeasy Mini Kit | QIAGEN | Cat#:74104 | |
Chemical compound, drug | Dithiothreitol | Bio Shop | Cat#:3483-12-3 | |
Chemical compound, drug | Micrococcal nuclease (MNase) | Roche | Cat#:10107921001 | |
Chemical compound, drug | Complete Tablets EASYpack | Roche | Cat#:04693116001 | |
Chemical compound, drug | DynaBeads, Protein A | Thermo Fisher Scientific | Cat#:10002D | |
Chemical compound, drug | Bovine Serum Albumin (BSA) | Sigma-Aldrich | Cat#:BP1600-100 | |
Chemical compound, drug | RNase A | Sigma-Aldrich | Cat#:10109169001 | |
Chemical compound, drug | Proteinase K | Sigma-Aldrich | Cat#:P2308 | |
Software, algorithm | R (version 4.0.2) | R Core Team, 2018 | ||
Software, algorithm | Python (version 3.7.4) | Van Rossum and Drake, 2009 | ||
Software, algorithm | Trimmomatic (version 0.36) | Bolger et al., 2014 | ||
Software, algorithm | Bowtie2 (version 2.3.4) | Langmead and Salzberg, 2012 | ||
Software, algorithm | SAMtools (version 1.9) | Li et al., 2009 | ||
Software, algorithm | Deeptools (version 3.2.1) | Ramírez et al., 2016 | ||
Software, algorithm | Trim Galore (version 0.5.0) | Krueger, 2015 | ||
Software, algorithm | Hisat2 (version 2.1.0) | Kim et al., 2015 | ||
Software, algorithm | Stringtie (version 2.1.2) | Pertea et al., 2015 | ||
Software, algorithm | Seaborn (version 0.9.0) | Waskom, 2021 | ||
Software, algorithm | Betareg (version 3.1–4) | Ferrari and Cribari-Neto, 2004 | ||
Software, algorithm | Csaw (version 1.22.1) | Lun and Smyth, 2016 | ||
Software, algorithm | Sva (version 3.36.0) | Leek et al., 2012; Zhang et al., 2020 | ||
Software, algorithm | topGO (version 2.40.0) | Alexa et al., 2006 | ||
Software, algorithm | trackplot | Bolger et al., 2014 | ||
Software, algorithm | Rtracklayer (version 1.48.0) | Lawrence et al., 2009 | ||
Software, algorithm | HOMER (version 4.10.4) | Heinz et al., 2010 | ||
Software, algorithm | ViSEAGO (version 1.2.0) | Brionne et al., 2019 | ||
Software, algorithm | DESeq2 (version 1.28.1) | Love et al., 2014 | ||
Software, algorithm | Aggregation (version 1.0.1) | Yi et al., 2018 | ||
Software, algorithm | Corrplot (version 0.88) | Taiyun and Simko, 2021 | ||
Software, algorithm | Pheatmap (version 1.0.12) | Kolde, 2019 | ||
Software, algorithm | Numpy (version 1.17.2) | Harris et al., 2020 | ||
Software, algorithm | Pandas (version 0.25.2) | McKinney, 2010 | ||
Software, algorithm | Pickle (version 4.0) | Van Rossum, 2020 | ||
Software, algorithm | Scanpy (version 1.8.2) | Wolf et al., 2018 | ||
Software, algorithm | Scipy (version 1.7.3) | Virtanen et al., 2020 | ||
Software, algorithm | Autogenes (version 1.0.4) | Aliee and Theis, 2021 |
Data quality statistics and gene ontology analysis.
(a) ChIP-sequencing sample information and read statistics. (b) Significant gene ontology terms enriched in high-fat diet (HFD)-sperm differentially expressed histone H3 lysine 4 tri-methylation (deH3K4me3) regions at promoters detected in our previous study and this study, related to Figure 2—figure supplement 1E. (c) Significant gene ontology terms enriched in HFD-sperm at regions showing a decrease in H3K4me3 at promoters, related to Figure 2—figure supplement 1E. (d) Significant gene ontology terms enriched in HFD-sperm at regions showing an increase in H3K4me3 at promoters, related to Figure 2—figure supplement 1E. (e) Significant gene ontology terms enriched in differentially expressed genes in female placentas derived from HFD-sires, related to Figure 4C. (f) Significant gene ontology terms enriched in differentially expressed genes in male placentas derived from HFD-sires, related to Figure 4D. (g) Reference single-cell RNA-sequencing data information (from Han et al., 2018) – number of cells per cell type, related to Figure 5—figure supplement 1.
Interactive heatmap for significant gene ontology terms enriched in high-fat diet (HFD)-sperm deH3K4me3 regions at promoters detected in our previous study (Pepin et al., 2022) and this study, related to Figure 2—figure supplement 1E.
Motif analysis, showing significantly enriched known motifs in regions gaining H3K4me3 in high-fat diet (HFD)-sperm, related to Figure 3.