Kok et al, 2026, PLOS Genetics
This repo contains the code and (meta)data used for the analysis of the data and generation of figures. The sequencing data is deposited in GEO under the accession numbers: GSE302386, GSE302387, GSE302388
The following pipelines where used:
- nf-core/MNase_seq (https://nf-co.re/mnaseseq/1.0.0/)
- RNA_seq_processing (in this repo under scripts)
- PRO_seq (https://github.com/JAJ256/PROseq_alignment.sh)
- nf-core/ChIP_seq (https://nf-co.re/chipseq/2.1.0/)
- Long-read (in this repo under pipelines)
The folder Files contains different types of files used for the pipeline:
- Curated contains curated lists, eg genes involved in meosis, nested genes etc,
- Meta contains meta data about the differnet experiments
- Output contains files generated by pipelines or during analysis.
NOTE: The gtf/gff files for the antisense detected from the pacbio long reads are available as output/annos/merged_default_antisense.gff/gtf
Here is the workflow for the figures.
Fig. |
Data |
Processing | Intermediate | Analysis/Plot | Extra files for analysis |
|---|---|---|---|---|---|
1B |
MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | MNase_plotting.Rmd | output/anno/plusonenuc_filtered_WT.bed(*) |
| 1C | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | MNase_plotting.Rmd | output/anno/plusonenuc_filtered_WT.bed(*) |
| 1D | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_remodelers.Rmd | meta/Figure_1.xlsx |
| 2A | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | meta/Figure_2.xlsx |
| 2B | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | meta/Figure_2.xlsx |
| 2C | PRO-seq | PRO_seq_pipeline | NA | PRO_seq_CHD1.Rmd | curated/pcg.gtf |
| 2D | PRO-seq | PRO_seq_pipeline | NA | PRO_seq_CHD1.Rmd | curated/pcg.gtf |
| 3A | PRO-seq | PRO_seq_pipeline | NA | PRO_seq_CHD1.Rmd | output/anno/DE_antisense.gff |
| 3B | PRO-seq | PRO_seq_pipeline | NA | PRO_seq_CHD1.Rmd | output/anno/DE_antisense.gff |
| 3D | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | MNase_plotting.Rmd | output/anno/as_genes.bed(*) |
| 3E | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | PRO_seq_CHD1.Rmd | output/anno/as_genes.bed(*) |
| 3F | MNase-seq | MNase_seq_nfcore, PRO_seq_pipeline | MNase_computematrix.sh | PRO_seq_CHD1.Rmd | output/anno/as_genes.bed(*), output/anno/DE_antisense.gff |
| 3G | NA | NA | NA | Revision_code.Rmd | output/tabs/TATA.tsv |
| 4A | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | meta/Figure_2.xlsx, curated/sexualreproductionlist.tsv, curated/earlymeiotic.txt, curated/middlemeiotic.txt, curated/latemeiotic.txt |
| 4B | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | curated/sexualreproductionlist.tsv, curated/earlymeiotic.txt, curated/middlemeiotic.txt, curated/latemeiotic.txt |
| 4E | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | curated/earlymeiotic.txt, curated/middlemeiotic.txt, curated/latemeiotic.txt, curated/nested_genes.csv, output/tab/pcg_sig_up.csv |
| 4F | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | curated/earlymeiotic.txt, curated/middlemeiotic.txt, curated/latemeiotic.txt, curated/nested_genes.csv |
| 5C | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_tailswaps.Rmd | meta/metadata_tailswap.xlsx |
| 5D | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_tailswaps.Rmd | meta/metadata_tailswap.xlsx |
| 7A | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | NA | curated/pcg.bed(*) |
| 7B | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | ChIP_seq_CHD1.Rmd | curated/pcg.bed(*), output/tab/Quartile_hrp1_scaled.tab, output/tab/Quartile_hrp3_scaled.tab, output/tab/Quartile_H2Bub_scaled.tab |
| 7C | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | Revision_code.Rmd | output/tab/myc_scaled.tab, curated/pcg.bed(*) |
| 7D | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | Revision_code.Rmd | output/tab/totals_in_genes.tsv, output/tab/totals_genome.tsv, curated/pcg.bed(*) |
| 7E | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | NA | curated/pcg.bed(*) |
| 7F | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | MNase_plotting.Rmd | output/anno/plusonenuc_filtered_WT.bed(*) |
| 7G | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_prf1.Rmd | meta/metadata_prf1.xlsx |
(*): File is needed in Intermediate step
| Figure | Data |
Processing | Intermediate | Analysis/Plot | Extra files used |
|---|---|---|---|---|---|
| S1 | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | NA | curated/pcg.bed(*) |
| S2B–S2F | RNA-seq | RNA_seq_processing.sh | NA | RNA_seq_CHD1.Rmd | meta/Figure_2.xlsx |
| S3A | Iso-seq | Long_read | NA | supp_figure_pairs.R | NA |
| S3B | PRO-seq | PRO_seq_pipeline | NA | PRO_seq_CHD1.Rmd | curated/pcg.gtf |
| S3E | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | NA | output/tab/mnase_q1.tsv, output/tab/mnase_q2.tsv, output/tab/mnase_q3.tsv, output/tab/mnase_q4.tsv |
| S3F | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | Revision_code.Rmd | output/tab/mnase_q1.tsv, output/tab/mnase_q2.tsv, output/tab/mnase_q3.tsv, output/tab/mnase_q4.tsv |
| S3G | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | MNase_plotting.Rmd | output/anno/as_genes.bed(*) |
| S4A | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | NA | NA |
| S4B | MNase-seq | MNase_seq_nfcore | NA | GC_analysis.Rmd | NA |
| S4C | MNase-seq | MNase_seq_nfcore | MNase_computematrix.sh | NA | NA |
| S4E | Iso-seq | Long_read (main.nf) | NA | supp_figure_pairs.R | NA |
| S5A | NA | NA | NA | Revision_code.Rmd | curated/genotype_antisense_upstream.fasta, curated/spombe_pcg_upstream.fasta, curated/random_500bp.fasta |
| S5C | NA | NA | NA | Revision_code.Rmd | curated/genotype_antisense_upstream.fasta, scurated/pombe_pcg_upstream.fasta |
| S5D | NA | NA | NA | Revision_code.Rmd | output/tab/TATA_pcg.tsv |
| S5F | NA | NA | NA | Revision_code.Rmd | output/tab/tomtom_test.csv |
| S6A | mRNA-seq | RNA_seq_processing.sh | RNA_seq_remodelers.Rmd | meta/Figure_1.xlsx | |
| S6B | mRNA-seq | RNA_seq_processing.sh | RNA_seq_remodelers.Rmd | meta/Figure_1.xlsx, curated/sexualreproductionlist.txt | |
| S10A | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | ChIP_seq_CHD1.Rmd | curated/pcg.bed(*) |
| S10B | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | ChIP_seq_CHD1.Rmd | curated/pcg.bed(*) |
| S10D | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | Revision_code.Rmd | output/tab/Q1_gene_signal.tsv, output/tab/Q2_gene_signal.tsv, output/tab/Q3_gene_signal.tsv, output/tab/Q4_gene_signal.tsv |
| S10E | ChIP-seq | ChIP_seq_nfcore | ChIP_seq_computematrix.sh | ChIP_seq_CHD1.Rmd | curated/pcg.bed(*), output/tab/mean_tpm.txt |
| S10F | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_prf1.Rmd | meta/metadata_prf1.xlsx |
| S10G | mRNA-seq | RNA_seq_processing.sh | NA | RNA_seq_prf1.Rmd | meta/metadata_prf1.xlsx |
| S11 | Iso-seq, mRNA-seq | Long_read (review.nf) | sense_process.R | supp_figure_sense.R | NA |
(*): File is needed in Intermediate step