Additional file 1 of Transcription initiation of distant core promoters in a large-sized genome of an insect
Creators: name: Liu, Qing
name: Jiang, Feng
name: Zhang, Jie
name: Li, Xiao
name: Kang, Le
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Nucleotide composition of OTSSs and nucleotide distribution of sequencing reads. Figure S2. Distribution of identified OTSSs in different genomic regions. Figure S3. Correlation of the number of tissues involved and the identified OTSSs. Figure S4. Distribution of the distance between the identified OTSSs and start codon. Figure S5. Width distribution of transcription start site clusters (TSCs) in different genomic regions. Figure S6. Consensus 25-bp sequences surrounding the dominant TSSs in different genomic regions. Figure S7. A significant enrichment of the TGAG motif and its 1-bp-substitution variants in the 1-bp-wide TSCs. Figure S8. Mis-hybridization of the 5′ oligo-capping adaptors and internal RNA sites results in overrepresentation of the TGAG motif. Figure S9. False TSCs derived from internal signals in the possible truncated mRNAs. Figure S10. Density histogram of the 3′ end of insert fragments along the mRNA transcript with lognormal fit. Figure S11. Percentage of removed TSCs by the 3′ end distribution of insert fragments. Figure S12. Quantification reproducibility for individual TSCs for two biological replicates. Figure S13. Number of identified TSCs per annotated protein-coding gene in the migratory locust and fruit fly. Figure S14. Summary of Drosophila core promoter elements in the core promoters of locusts and fruit flies. Figure S15. CpG distribution in the 4-kb flanking region of transcription start sites. Figure S16. Normalized CpG contents of locusts and fruit flies. Figure S17. Mean AT contents in the 10 to 50 bp regions upstream of dominant OTSSs of core promoters in locusts and fruit flies. Figure S18. Distribution of the tissue-specificity index (tau) of genic TSCs in locusts. Figure S19. Scatterplot of enriched GO terms of ubiquitously (Tau = 0) and restricted (tau = 1) TSC expression of locust core promoters. Figure S20. Correlation between TSC expression and OTSS diversity via binscatter estimation. Figure S21. The alternative usage of core promoters (promoter shifting) in the ovary sample when compared to the muscle sample as a control. Figure S22. The alternative usage of core promoters (promoter shifting) of protein-coding genes in different tissue or organ samples when compared to the muscle samples as controls in locusts. Figure S23. Distant transcription initiation in locusts and fruit flies. Figure S4. Mean intron length in mRNA leaders of locusts and fruit flies. Figure S25. Consensus sequences of the 25 bps surrounding the dominant TSSs. Figure S26. Meta-profile of TSCs over the gene body of protein-coding genes in the official gene sets. Figure S27. The density distribution of distances from the annotated start codon of protein-coding genes to the upstream genic core promoters. Figure S28. The abundance distribution of the distances from the TFBSs to the dominant transcription starting site (TSS) in protein-coding genes. Table S1. Sequencing data generated in this study for locusts. Table S2. Overrepresented motifs of TGAG and its variants in the 1-bp-wide TSCs located in the intergenic region. Table S3. Over-represented motifs of TGAG and its variants in the non-1-bp-wide TSCs located in the intergenic region. Table S4. Overrepresented motifs of TGAG and its variants in the 1-bp-wide TSCs located in the intronic region. Table S5. Over-represented motifs of TGAG and its variants in the non-1-bp-wide TSCs located in the intronic region. Table S6. Over-represented motifs of TGAG and its variants in the 1-bp-wide TSCs located in the coding sequence (CDS) region. Table S7. Overrepresented motifs of TGAG and its variants in the non-1-bp-wide TSCs located in the coding sequence (CDS) region. Table S8. Consensus sequences of Drosophila core promoter elements. Table S9. Sequencing data generated in this study for the arthropod species. Table S10. The identified TSCs in the arthropod species.