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( A ) Schematic of the human TP53 gene. The sequence deleted in dUTR cells is shown in blue. Tracks of binding sites for miRNAs, RNA-binding proteins, and lncRNAs are depicted below (see also ). URE, U-rich element. CRISPR/Cas9-mediated deletions at the nucleotide level are shown in . ( B ) Northern blot analysis of TP53 mRNA from WT and dUTR HEK293 cells. A probe that hybridizes to the TP53 coding region (CDS) reveals expression of a shortened TP53 mRNA in dUTR cells. The size difference is consistent with the length of the CRISPR/Cas9-induced deletion. A probe designed to bind the TP53 3′UTR does not produce a signal in the mRNA of dUTR cells, confirming deletion of this sequence element. The band of 18S rRNA is used as a loading control. * indicates an unspecific band originating from ribosomal RNA. ( C ) TP53 mRNA expression measured by RT-qPCR with a primer pair located in the 3′UTR in the indicated samples derived from HCT116 cells. KO, HCT116 TP53 -/- cells. Data are shown as mean +s.d. of n = 5 independent experiments after normalization to GAPDH . Statistical analysis using ANOVA and Tukey’s post-hoc test with ***p<0.001, ns, not significant. ( D ) TP53 mRNA expression measured by RT-qPCR with a primer pair located in the CDS in the indicated samples derived from HCT116 cells. Data are shown as mean +s.d. of n = 5 independent experiments after normalization to GAPDH . Statistical analysis using ANOVA and Tukey’s post-hoc test with ***p<0.001, ns, not significant. ( E ) Experimental setup to estimate TP53 mRNA half-life. Metabolic labeling with <t>4-thiouridine</t> <t>(4sU)</t> was used to enrich newly transcribed mRNAs. The newly transcribed RNAs were thiol-alkylated and biotinylated, followed by Streptavidin pull-down. Their relative abundance was measured using RT-qPCR. ( F ) TP53 mRNA half-life obtained by 4sU labeling as described in (E) is shown for the indicated samples derived from HCT116 cells in the presence or absence of etoposide for 4 hr (Eto, 20 µM). Shown is mean + s.d. from n = 3 independent experiments. Statistical analysis using ANOVA and Tukey’s post-hoc test with *p<0.05, **p<0.01, ns, not significant.

4 Thiouridine, supplied by Valiant Co Ltd, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/0215213405/4-Thiouridine/pmc08137139-327-8-10
Average 91 stars, based on 5 article reviews

4 thiouridine - by Bioz Stars, 2026-09

91/100 stars

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1) Product Images from "Endogenous p53 expression in human and mouse is not regulated by its 3′UTR"

Article Title: Endogenous p53 expression in human and mouse is not regulated by its 3′UTR

Journal: eLife

doi: 10.7554/eLife.65700

Figure Legend Snippet: ( A ) Schematic of the human TP53 gene. The sequence deleted in dUTR cells is shown in blue. Tracks of binding sites for miRNAs, RNA-binding proteins, and lncRNAs are depicted below (see also ). URE, U-rich element. CRISPR/Cas9-mediated deletions at the nucleotide level are shown in . ( B ) Northern blot analysis of TP53 mRNA from WT and dUTR HEK293 cells. A probe that hybridizes to the TP53 coding region (CDS) reveals expression of a shortened TP53 mRNA in dUTR cells. The size difference is consistent with the length of the CRISPR/Cas9-induced deletion. A probe designed to bind the TP53 3′UTR does not produce a signal in the mRNA of dUTR cells, confirming deletion of this sequence element. The band of 18S rRNA is used as a loading control. * indicates an unspecific band originating from ribosomal RNA. ( C ) TP53 mRNA expression measured by RT-qPCR with a primer pair located in the 3′UTR in the indicated samples derived from HCT116 cells. KO, HCT116 TP53 -/- cells. Data are shown as mean +s.d. of n = 5 independent experiments after normalization to GAPDH . Statistical analysis using ANOVA and Tukey’s post-hoc test with ***p<0.001, ns, not significant. ( D ) TP53 mRNA expression measured by RT-qPCR with a primer pair located in the CDS in the indicated samples derived from HCT116 cells. Data are shown as mean +s.d. of n = 5 independent experiments after normalization to GAPDH . Statistical analysis using ANOVA and Tukey’s post-hoc test with ***p<0.001, ns, not significant. ( E ) Experimental setup to estimate TP53 mRNA half-life. Metabolic labeling with 4-thiouridine (4sU) was used to enrich newly transcribed mRNAs. The newly transcribed RNAs were thiol-alkylated and biotinylated, followed by Streptavidin pull-down. Their relative abundance was measured using RT-qPCR. ( F ) TP53 mRNA half-life obtained by 4sU labeling as described in (E) is shown for the indicated samples derived from HCT116 cells in the presence or absence of etoposide for 4 hr (Eto, 20 µM). Shown is mean + s.d. from n = 3 independent experiments. Statistical analysis using ANOVA and Tukey’s post-hoc test with *p<0.05, **p<0.01, ns, not significant.

Techniques Used: Sequencing, Binding Assay, RNA Binding Assay, CRISPR, Northern Blot, Expressing, Quantitative RT-PCR, Derivative Assay, Labeling

other:

Article Title: Local administration of 4-Thiouridine, a novel molecule with potent anti-inflammatory properties, protects against experimental colitis and arthritis.
Article Snippet: Previous studies in a rat model of Sephadex induced lung inflammation showed that 4-Thiouridine (4SU), a thiol substituted nucleoside, was very effective in reducing edema, leukocyte influx and TNF levels in bronchoalvelolar lavage fluid.. However, little is known about the factors and mechanisms underlying these effects.. In the present study, we have used two separate mouse models of chronic inflammation, a model of dextran sulphate sodium (DSS) induced colitis and a model of antigen induced arthritis, to evaluate the anti-inflammatory effect of 4-thiouridine.

Article Title: Endogenous p53 expression in human and mouse is not regulated by its 3′UTR
Article Snippet: Chemical compound, drug , 4-Thiouridine , MP Biomedicals , MP215213425 , .

Cell Culture:

Article Title: Enriching s 4 U-RNA using methane thiosulfonate (MTS) chemistry
Article Snippet: .. list-behavior=simple prefix-word= mark-type=none max-label-size=0 Cultured cells (e.g., HEK293T cells; at least 1 × 10 6 ) DMEM high glucose (Invitrogen, cat. no. 11965-092) Fetal bovine serum (Invitrogen, cat. no. 16000-044) Penicillin/streptomycin (Millipore, cat. no. TMS-AB2-C) 4-thiouridine (MP Biomedicals, cat. no. 0215213405 TRIzol reagent (Life Technologies, cat. no 15596-026) Chloroform (AmericanBio, cat. no. AB00350-00500) Kimwipes (Kimberly Clark, cat. no. 730830) RNeasy Mini Kit (Qiagen, cat. no. {"type":"entrez-protein","attrs":{"text":"Q74106","term_id":"75593227","term_text":"Q74106"}} Q74106 ) 100% ethanol (AmericanBio, cat. no. AB04010-00500) 10x TURBO DNase reaction buffer TURBO DNase (Life Technologies, cat. no. AM2238) DTT (VWR International, cat. no. EM-3860) DEPC-Treated Water (Life Technologies, cat. no. AM9906) HEPES free acid (DOT Scientific, cat. no. DSH75030-250) EDTA disodium salt (Sigma Aldrich, cat. no. E5134-500G) Dimethyl formamide (J.T. .. Baker, cat. no. 9344-13) MTSEA-biotin-XX (Biotium, cat. no. 89139-636) Chloroform: Isoamyl alcohol (Fisher Scientific, cat. no. 3160-450ML) Phase-lock gel tube, heavy 1.5 mL (5-Prime, cat. no. FP2302820) Glycogen (AmericanBio, cat. no AB00670-00020) Dynabeads MyOne Streptavidin C1 magnetic beads (Life Technologies, cat. no. 65001) Tris•HCl (Fisher Scientific, cat. no. T5941-500G) Sodium chloride (Sigma Aldrich, cat. no. S9888-2.5KG) Tween-20 (Mp Biomedicals Inc., cat. no. ICN19484180) β-mercaptoethanol (Sigma Aldrich, cat. no. M3148-25ML) Qubit RNA HS assay kit (Thermo Fisher Scientific, cat. no. {"type":"entrez-protein","attrs":{"text":"Q32855","term_id":"75280862","term_text":"Q32855"}} Q32855 ) Ambion century plus RNA marker (Thermo Fisher Scientific, cat. no. AM7145) MAXIscript T7 transcription kit (Thermo Fisher Scientific, cat. no. AM1312) Cy5-CTP (GE Healthcare, cat. no. 25-8010-87) 4-thiouridine-5’-triphosphate (s 4 UTP) (Trilink Bio, cat. no. N-1025) SequaGel UreaGel 29:1 Denaturing Gel System (National Diagnostics, cat. no. EC-829) Gel cassettes 1.0 mm (Life Sciences, cat. no. NC2010) list-behavior=simple prefix-word= mark-type=none max-label-size=0 Nanodrop 2000c Spectrophotometer (Thermo Fisher Scientific, cat. no. ND-2000c) MagRack 6 magnetic stand (GE Healthcare, cat. no. 28948964) DynaMag 96 side (Life Technologies, cat. no. 12331D) Qubit 3.0 Fluorometer (Thermo Fisher Scientific, cat. no. {"type":"entrez-protein","attrs":{"text":"Q33216","term_id":"75101668","term_text":"Q33216"}} Q33216 ) Rotator (Glas-Col, cat. no. 099A MR1512) Typhoon FLA 9500 (GE Healthcare) Metabolic labeling of cells and isolation of total cellular RNA In this section we describe the metabolic labeling of HEK293T RNA with s 4 U.

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Biological and canonical tRNA strand reads aligned against reference sequences. (A) tRNA fMet , (B) tRNA Phe , and (C) tRNA Lys . In each panel (i) is base coverage along the reference sequence at each position (coverage plot) and (ii) is a randomly selected subset of individual aligned nanopore reads. The total numbers of aligned reads are shown to the left of the coverage plots. The positions of expected modifications on biological tRNA 3 are indicated above the coverage plots and are abbreviated: 4 = 4-thiouridine; D = Dihydrouridine; B = 2′- O -methylcytidine; 7 = 7-methylguanosine; T = 5-methyluridine; P = pseudouridine; X = 3-(3-amino-3-carboxypropyl)uridine; * = 2-methylthio-N6-isopentenyladenosine; S = 5-methyl-aminomethyl-2-thiouridine; and 6 = N6-threonylcarbamoyl-adenosine. Gray columns in the coverage plots indicate positions along the reference where 80% or more of the quality weighted reads are the expected canonical nucleotide. At positions where the value is under the 80% threshold, the proportion of each nucleotide call is shown in color where U(T) = red, A = green, C = blue, and G = gold. Similarly, the rows of individual aligned reads (A–C, ii) are gray at positions matching the reference and colored (using the previously mentioned convention) at positions with mismatches. The black horizontal bars in the aligned reads indicate a deletion, and purple bars indicate an insertion. The rows of aligned reads are presented as they were displayed on IGV.

Journal: ACS Nano

Article Title: Direct Nanopore Sequencing of Individual Full Length tRNA Strands

doi: 10.1021/acsnano.1c06488

Figure Lengend Snippet: Biological and canonical tRNA strand reads aligned against reference sequences. (A) tRNA fMet , (B) tRNA Phe , and (C) tRNA Lys . In each panel (i) is base coverage along the reference sequence at each position (coverage plot) and (ii) is a randomly selected subset of individual aligned nanopore reads. The total numbers of aligned reads are shown to the left of the coverage plots. The positions of expected modifications on biological tRNA 3 are indicated above the coverage plots and are abbreviated: 4 = 4-thiouridine; D = Dihydrouridine; B = 2′- O -methylcytidine; 7 = 7-methylguanosine; T = 5-methyluridine; P = pseudouridine; X = 3-(3-amino-3-carboxypropyl)uridine; * = 2-methylthio-N6-isopentenyladenosine; S = 5-methyl-aminomethyl-2-thiouridine; and 6 = N6-threonylcarbamoyl-adenosine. Gray columns in the coverage plots indicate positions along the reference where 80% or more of the quality weighted reads are the expected canonical nucleotide. At positions where the value is under the 80% threshold, the proportion of each nucleotide call is shown in color where U(T) = red, A = green, C = blue, and G = gold. Similarly, the rows of individual aligned reads (A–C, ii) are gray at positions matching the reference and colored (using the previously mentioned convention) at positions with mismatches. The black horizontal bars in the aligned reads indicate a deletion, and purple bars indicate an insertion. The rows of aligned reads are presented as they were displayed on IGV.

Article Snippet: The standards included 5-methyluridine (TCI America), B -pseudouridine (TRC Canada), uridine (Sigma), 4-thiouridine (MP Biomedicals), 2′- O -methylcytidine (Alfa Aesar), and 7-methylguanosine (Sigma).

Techniques: Sequencing

Systematic base miscalls in purified biological and canonical tRNA fMet , tRNA Lys , and tRNA Phe . The coverage plots (A–C) for biological and canonical synthetic tRNAs were generated from alignments using marginAlign. The number of aligned reads for each tRNA is shown under each coverage plot. Boxes surrounding base positions denote systematic miscalls (posterior probability of ≥30%). No systematic miscalls were identified in the synthetic canonical tRNAs. Colored bars are at positions where <80% of the quality weighted alignments match the reference. At these positions, the proportion of individual bases called are shown in color (U(T) = red, A = green, C = blue, and G = gold). The known modifications for the biological tRNAs 3 are indicated above the coverage plots. Modified nucleotides are indicated above the reference sequence with abbreviations (4 = 4-thiouridine, D = dihydrouridine, B = 2′- O -methylcytidine, 7 = 7-methylguanosine, T = 5-methyluridine, P = pseudouridine, X = 3-(3-amino-3-carboxy-propyl)uridine, * = 2-methylthio-N6- isopentenyladenosine, S = 5-methylaminomethyl-2-thiouridine, and 6 = N6-threonylcarbamoyl-adenosine). The falloff in 5′ coverage of synthetic tRNA Lys (B, lower panel) and tRNA Phe (C, lower panel) is likely due to incomplete 5′ phosphorylation of these substrates.

Journal: ACS Nano

Article Title: Direct Nanopore Sequencing of Individual Full Length tRNA Strands

doi: 10.1021/acsnano.1c06488

Figure Lengend Snippet: Systematic base miscalls in purified biological and canonical tRNA fMet , tRNA Lys , and tRNA Phe . The coverage plots (A–C) for biological and canonical synthetic tRNAs were generated from alignments using marginAlign. The number of aligned reads for each tRNA is shown under each coverage plot. Boxes surrounding base positions denote systematic miscalls (posterior probability of ≥30%). No systematic miscalls were identified in the synthetic canonical tRNAs. Colored bars are at positions where <80% of the quality weighted alignments match the reference. At these positions, the proportion of individual bases called are shown in color (U(T) = red, A = green, C = blue, and G = gold). The known modifications for the biological tRNAs 3 are indicated above the coverage plots. Modified nucleotides are indicated above the reference sequence with abbreviations (4 = 4-thiouridine, D = dihydrouridine, B = 2′- O -methylcytidine, 7 = 7-methylguanosine, T = 5-methyluridine, P = pseudouridine, X = 3-(3-amino-3-carboxy-propyl)uridine, * = 2-methylthio-N6- isopentenyladenosine, S = 5-methylaminomethyl-2-thiouridine, and 6 = N6-threonylcarbamoyl-adenosine). The falloff in 5′ coverage of synthetic tRNA Lys (B, lower panel) and tRNA Phe (C, lower panel) is likely due to incomplete 5′ phosphorylation of these substrates.

Techniques: Purification, Generated, Modification, Sequencing

Journal: eLife

Article Title: Endogenous p53 expression in human and mouse is not regulated by its 3′UTR

doi: 10.7554/eLife.65700

Figure Lengend Snippet: ( A ) Schematic of the human TP53 gene. The sequence deleted in dUTR cells is shown in blue. Tracks of binding sites for miRNAs, RNA-binding proteins, and lncRNAs are depicted below (see also ). URE, U-rich element. CRISPR/Cas9-mediated deletions at the nucleotide level are shown in . ( B ) Northern blot analysis of TP53 mRNA from WT and dUTR HEK293 cells. A probe that hybridizes to the TP53 coding region (CDS) reveals expression of a shortened TP53 mRNA in dUTR cells. The size difference is consistent with the length of the CRISPR/Cas9-induced deletion. A probe designed to bind the TP53 3′UTR does not produce a signal in the mRNA of dUTR cells, confirming deletion of this sequence element. The band of 18S rRNA is used as a loading control. * indicates an unspecific band originating from ribosomal RNA. ( C ) TP53 mRNA expression measured by RT-qPCR with a primer pair located in the 3′UTR in the indicated samples derived from HCT116 cells. KO, HCT116 TP53 -/- cells. Data are shown as mean +s.d. of n = 5 independent experiments after normalization to GAPDH . Statistical analysis using ANOVA and Tukey’s post-hoc test with ***p<0.001, ns, not significant. ( D ) TP53 mRNA expression measured by RT-qPCR with a primer pair located in the CDS in the indicated samples derived from HCT116 cells. Data are shown as mean +s.d. of n = 5 independent experiments after normalization to GAPDH . Statistical analysis using ANOVA and Tukey’s post-hoc test with ***p<0.001, ns, not significant. ( E ) Experimental setup to estimate TP53 mRNA half-life. Metabolic labeling with 4-thiouridine (4sU) was used to enrich newly transcribed mRNAs. The newly transcribed RNAs were thiol-alkylated and biotinylated, followed by Streptavidin pull-down. Their relative abundance was measured using RT-qPCR. ( F ) TP53 mRNA half-life obtained by 4sU labeling as described in (E) is shown for the indicated samples derived from HCT116 cells in the presence or absence of etoposide for 4 hr (Eto, 20 µM). Shown is mean + s.d. from n = 3 independent experiments. Statistical analysis using ANOVA and Tukey’s post-hoc test with *p<0.05, **p<0.01, ns, not significant.

Article Snippet: Chemical compound, drug , 4-Thiouridine , MP Biomedicals , MP215213425 , .

Techniques: Sequencing, Binding Assay, RNA Binding Assay, CRISPR, Northern Blot, Expressing, Quantitative RT-PCR, Derivative Assay, Labeling

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4 thiouridine (Valiant Co Ltd)

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