Supplementary MaterialsS1 Fig: Whisker plots considering home windows spanning different regions of the long MYC UTRs. secondary structure of Motif 9 (Fig 1) annotated with data from a previous chemical mapping study of the MYC IRES [6]. Large and small arrows are for strong and weak chemical reactivities (reagents sensitive to single-stranded RNA); when arrows are in red, they conflict with the Motif 9 model (e.g. modification site occurs at a nt that is Watson-Crick paired within a helix formed by canonical Watson-Crick pairs). Circled nt indicate AMV reverse transcriptase (RT) pausing sites, which indicate structured regions.(EPS) pone.0213758.s002.eps (1.9M) GUID:?772930CF-4E27-48D3-A80A-B3E61B5B7234 S3 Fig: RNAalifold consensus secondary structure for the MAFFT alignment of vertebrate RefSeq short 3′ UTRs (S5 File). Base Tirasemtiv (CK-2017357) pairs Tirasemtiv (CK-2017357) are colored by their conservation and the observation of different pairing types (see key on figure). Circled bases indicate structure-preserving consistent and compensatory base mutations. Lines in the consensus sequence indicated that gaps are predominate at the aligned position.(EPS) pone.0213758.s003.eps (2.1M) GUID:?62193C17-C435-4273-8C3E-7069778D1B17 S4 Fig: Annotations of miRNA binding sites on ScanFold-Fold predicted motifs. A) Shows miRNA sequences above the dot-bracket structure of Motif 17 (matched brackets indicated base pairs). Seed sites and the complements on Motif 17 are colored. B) Displays miRNA seed binding sites annotated for the 2D style of Theme 17. C) Displays base-pairing between miR-24 as well as the 2D style of Theme 18. D) Displays base-pairing between miR-24 as well as the 2D style of Theme 15.(EPS) pone.0213758.s004.eps (3.5M) GUID:?DDE5C67C-AF2A-4C98-9FEC-8D3EDA85D350 S1 Desk: Correlation between metrics. Correlations between metrics for many scanning home windows (uncooked data in S1 Document). For every, relationship coefficients are reported, with ideals above 0.5 in bold.(DOCX) pone.0213758.s005.docx (25K) GUID:?B3342E5A-9048-418E-AEB3-B8218597C12C S2 Desk: Mean values of metrics for every mRNA region. For every region from the mRNA, metrics from all overlapping home windows were averaged. Right here we defined areas predicated on the coding series placement referred to for “type”:”entrez-nucleotide”,”attrs”:”text message”:”NM_002467.5″,”term_id”:”1237937914″,”term_text message”:”NM_002467.5″NM_002467.5 (nt 1161 to 2525). The home windows useful for the evaluation are available in S1 Document and were thought as comes after: 5′ UTRCwindows 1 to 1091; 5′ junctionCwindows 1092 to 1161; ORFCwindows 1162 to 2456; 3′ junctionCwindows 2457 to 2525; 3’UTRCwindows Rabbit Polyclonal to MYLIP 2526 to 4449.(DOCX) pone.0213758.s006.docx (27K) GUID:?7AC033F6-E005-4593-B6A6-22C95C1B961E S3 Desk: Matrix of t-test p-values determined for mean ideals of metrics between each mRNA region. The p-values are held by This matrix of the two-tailed t-test assuming unequal variance between your corresponding regions. P-values greater than 0.01 are bolded.(DOCX) pone.0213758.s007.docx (39K) GUID:?ED7A5587-66B0-46C6-BE60-0184765033FE S4 Table: Percentage of Motif base pairs predicted in the unconstrained Tirasemtiv (CK-2017357) global model of MYC mRNA folding (S2 File). (DOCX) pone.0213758.s008.docx (30K) GUID:?FC0FEAB7-3593-4448-93AF-95516813D09F S5 Table: gBlock sequences used for generation of pIS2-M17, pIS2-AS1, pIS2-LS1, and pIS2-LS1-CM. Base mutations, compared to WT pIS2-M17 sequence, are shown in bold.(DOCX) pone.0213758.s009.docx (28K) GUID:?34E28824-263E-4BE3-9FBF-5724E0D8C914 S1 File: Excel document containing ScanFold-Scan results. Columns ACO contain: the i and j coordinates for each mRNA sequence; the minimum free energy (MFE) G in kcal/mol; the z-score, calculated from Eq 1 (as described in the Materials and methods section); the P-value, in the z-score calculation (acts as a quality control); the ensemble diversity (ED); the fraction (f)MFE; the sequence of the window fragment; the MFE base pairs, in dot-bracket notation (pairs are matched brackets); the ensemble centroid base pairs; the frequencies of A, G, C and U; then, finally, the GC%.(XLSX) pone.0213758.s010.xlsx (1.0M) GUID:?100906DA-313D-425C-BCB9-85A05F29B09B S2 File: Dot-bracket structures. ScanFold-Fold predicted pairs for the short MYC mRNA (“type”:”entrez-nucleotide”,”attrs”:”text”:”NM_002467.5″,”term_id”:”1237937914″,”term_text”:”NM_002467.5″NM_002467.5) at -1 and -2 cutoff values, followed by the filled in motifs that were refolded with RNAfold. This is followed by the model structure of the 5′ UTR based on previous studies as well as the constrained RNAfold model for the 3′ UTR.(TXT) pone.0213758.s011.txt (24K) GUID:?2B472FD9-6B47-4236-B57B-97C4E774A7B5 S3 File: MAFFT alignment of select vertebrate MYC RefSeq mRNAs. (FA) pone.0213758.s012.fa (74K) GUID:?79FD6197-D2CA-4DB8-83BE-6071E941E138 S4 File: MYC 5 UTR sequence alignments. (FASTA) pone.0213758.s013.fasta (33K) GUID:?7EFDF85C-4EA1-4B57-8533-5DEA7414CB5C S5 File: MYC 3 UTR sequence alignments. (FASTA) pone.0213758.s014.fasta (29K) GUID:?BE70C277-EA5D-407B-94EB-873204E82B2E S6 File: Raw and processed RLU and qPCR data used for generation of Fig 3B and 3C. (XLSX) pone.0213758.s015.xlsx (42K) GUID:?F844EA5F-19DF-4D5D-BB16-66BA4237D062 S7 File: RBPMap results for Motif 17. (TXT) pone.0213758.s016.txt (15K) GUID:?B5930028-1C2A-4C07-93D0-47D61262E1FE S8 File: ScanFold-Fold log file for all base pairs. (TXT) pone.0213758.s017.txt (1.1M) GUID:?7136D7D4-0CB7-4E52-82C3-D2DD9A7EC5F1 S9 File: ScanFold-Fold log fileFinal Motif base pairs. (TXT) pone.0213758.s018.txt (161K) GUID:?DB53C4FD-69AF-4622-A714-8ABC81A8B755 Data Availability StatementAll relevant data are within the manuscript and its Supporting Information files. Abstract The gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting expression, we analyzed secondary structures in the mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished.