Fig 1.
Chromatin organization around TASs in each TriTryp.
(A) Schematic representation of TASs prediction from 5’UTR regions obtained with UTRme (Radio et al., 2017). (B) Average nucleosome occupancy (top panels), heatmaps for each region in a 1 kb window (bottom panels). The signals scored for DNA molecules in the nucleosomal-size range (120-180 bp) are represented. (C) 2D occupancy plots showing nucleosome density relative to the TAS (bottom panels) for one representative data set of T. cruzi (GSM5363006), T. brucei (GSM2407366) and L. major (GSM2179742) respectively. Red: High nucleosome density; blue: low nucleosome density.
Fig 2.
Differential sensitivity to MNase at the TASs in T. brucei.
(A) Average nucleosome occupancy and (B) heatmaps showing nucleosome density relative to the TAS for each region in a 1 kb window for procyclic forms of T. brucei exposed to different levels of MNase digestion. Red: High nucleosome density; blue: low nucleosome density. The signals scored for every DNA molecule sequenced (0-500 bp) are represented. Red: High nucleosome density; blue: low nucleosome density. The data sets used in this figure are: Low digestion (GSM5024927), intermediate digestion (GSM5024915) and high digestion (GSM5024921).
Fig 3.
TASs resistance to MNase digestion is partly mediated by a histone component.
Average H3 occupancy (top panels) and heatmaps (bottom panels) relative to the TAS for one representative experiment of MNase-ChIP-seq of histone H3 (A) T. brucei (GSM2586510) and (B) T. cruzi (SRR14691958). Red: High nucleosome density; blue: low nucleosome density.
Fig 4.
TAS resistance to MNase digestion includes non-histone components.
Average occupancy (top panels) and heatmaps (bottom panels) relative to TAS for (A) Average H3 signal obtained from H3 MNase-ChIP-seq for T. brucei (GSM2586510); (B) R-loops obtained from DRIP-seq (ERR2814820); (C) Rpb9 ChIP-seq (SRR5466331) and (D) MNase-seq (GSM2407366). The regions represented into every heatmap keep the sorting following the distribution of the R-loop signal from higher (Red) to lower (Blue) density.
Fig 5.
Chromatin organization at TASs in single and multi-copy gene families.
(A) Average histone H3 occupancy (top panel) and heatmaps (bottom panels) in a 1 kb window relative to the TAS for single (green) and multi-copy genes (blue) using T. cruzi histone H3 IP (SRR14691958). Red: High histone H3 density; blue: low histone H3 density. (B) Average FAIRE-seq signals were represented relative to the TAS in a 1 kb window for single (green) and multi-copy genes (blue) of T. cruzi using public data (SRR15902298) (left) and (SRR15902297) (right), respectively. (C) Average dinucleotide frequency for AA/TT/AT/TA (purple), CG/CC/GC/CG (orange) and other possible combinations (light blue) in a 100 bp window relative to the TAS for single and multi-copy genes.
Fig 6.
Differential protection at the TAS at single and multi-copy genes in Trypanosomes.
Schematic representation illustrating the proposed model of chromatin organization at the TAS in TriTryps. Consistent with lower levels of gene expression, multi-copy genes are encoded at genomic regions that are usually less accessible and their TAS are mostly covered by nucleosomes, while single-copy genes, that are transcribed more frequently, display a more open chromatin at the TAS. Moreover, TAS region at single-copy genes harbors R-loops, generated during the co-transcriptional maturation of transcripts, and some trans-splicing factors (TSF) interact through them.