Additional file 1 of Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci
Creators: name: Lima, Alex Ranieri Jerônimo
name: Silva, Herbert Guimarães de
 Sousa
name: Poubel, Saloe
name: Rosón, Juliana Nunes
name: de Lima, Loyze Paola Oliveira
name: Costa-Silva, Héllida Marina
name: Gonçalves, Camila Silva
name: Galante, Pedro A. F.
name: Holetz, Fabiola
name: Motta, Maria Cristina Machado M.
name: Silber, Ariel M.
name: Elias, M. Carolina
name: da Cunha, Julia Pinheiro Chagas
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. A. Data summary for sequenced samples (EPI – epimastigote; META – metacyclic trypomastigote) and control for each replicate and read pairs. B. FastQC mean quality scores of sequenced samples. C. Scheme of the pipeline used to explore the FAIRE-seq data. D. Number of mapped reads against the Trypanosoma cruzi Dm28c genome for each dataset (biological replicates). Blue bars represent total dataset reads; orange bars indicate the mapped reads; gray bars show the remaining mapped reads with MAPQ scores above 10. The percentage is relative to the total reads of each dataset (blue bars). Spearman correlation (E) and PCA (F) of read counts for each dataset (biological replicates) from epimastigote (EPI), metacyclic trypomastigote (metacyclic) life forms and control samples generated with deepTools. Figure S2. A. Representative IGV snapshot of FAIRE-seq data mapped against the T. cruzi Dm28c genome (contig PRFA01000010). The data were normalized using RPGC (see Materials and Methods in main text). Epimastigote biological replicates (EPI-1 and EPI-2) are shown in red, and metacyclic trypomastigote biological replicates (META-1 and META-2) are shown in blue. Datasets not filtered with MAPQ score 10 are labeled as “WithoutQ10”. At the genomic features, repeat regions are represented in yellow. The dashed rectangle highlights a long repeat region and its low coverage upon MAPQ10 removal. B. IGV snapshots of two contigs comparing the raw mapped FAIRE read profile to the removal of multimapped reads (Q10 - arrows) in epimastigotes and metacyclic trypomastigotes. Core and disruptive genomic compartments are shown as red and green tracks, respectively. Figure S3. A. Superposition of FAIRE-seq (red) and MNase-seq (blue) in epimastigotes. The y-axis represents RPGC normalized tag counts for FAIRE-seq on the right side and MNase-seq on the left side. The profile CDSs transcribed by RNA Pol II is showed. B. Comparison of core and disruptive compartments of MNase-seq data using RPGC counts in epimastigotes (red) and trypomastigotes (blue). The median values for epimastigores were 2.04 and 1.09 for the core and disruptive compartments, respectively; for trypomastigote, the median values were 2.13 and 1.14. *** Wilcoxon-Mann-Whitney test with p-value = 0.001. C. RPGC tag counts at multigenic family genes and other CDSs transcribed by RNA Pol II for epimastigotes (red) and metacyclic trypomastigotes (blue). D. Summary plots for virulence factors in epimastigotes and metacyclics. *** Wilcoxon-Mann-Whitney test with p-value = 0.001. Figure S4. A. Landscape profile of cSSR (blue) and dSSR (green) showing median values in RPGC log2 ratio of epimastigotes/metacyclics (left). Start and End represent the first and last bases of each feature, respectively. Boxplots showing RPCG counts for dSSR (upper) and cSSR (lower) for epimastigotes (red) and metacyclics (blue). *** Wilcoxon-Mann–Whitney test with p value = 0.001. B. The percentage of bases of multifamily genes for each polycistron according to clustering is shown in Figure 4D. In B, clusterization was performed considering 1 kb upstream and downstream from the polycistron, while in C, clusterization considered only the PTU. Statistical analysis was performed using the Wilcoxon-Mann-Whitney test (*** p-value = 0.001; * p-value = 0.05). D. Landscape profiles of all CDSs (upper) and clustering based on the RPGC log2 ratio of epimastigotes/metacyclics (lower). Figure S5. Genes classified as high, medium and low expressed based on TPM values for epimastigote (red) and metacyclic trypomastigote (blue) life forms. *** Wilcoxon-Mann-Whitney test with p-value = 0.001. Figure S6. A. IGV snapshots of FAIRE-seq enrichment in epimastigotes (duplicates – red) compared to metacyclics (duplicates – blue) in three different loci. tDNAs are highlighted in yellow rectangles. B. Number of tRNA genes in each cluster. The tRNA genes grouped in each cluster after hierarchical clustering, as shown in Figure 6C, were counted and plotted in column graphics according to R group classification of the amino acids. C. Representative scheme of tRNA gene localization at divergent, convergent and codirectional PTUs. The arrows indicate the sense of transcription in each PTU. D. Quantification of tRNA-FISH UUC (Glu),GUC (Asp) in epimastigote (blue) and metacyclic (green) forms. Mean gray values represent intensity per area. Unpaired T-test: ** (p-value &gt; 0.05), and *** (p-value &lt; 0.0001). E. Quantification of tRNA-Northern blot UUC and GUC in Epi (blue) and MT (green) forms. The expression levels are represented by intensity per area (Mean gray values). Unpaired T-test: * (p-value &lt; 0.05), and *** (p-value &lt; 0.0001). ns, non-significant.