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Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation <t>sequencing</t> (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction <t>(ChIP-qPCR,</t> two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate
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Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation <t>sequencing</t> (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction <t>(ChIP-qPCR,</t> two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate
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Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation <t>sequencing</t> (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction <t>(ChIP-qPCR,</t> two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate
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page 7 23 chip seq a simplechip enzymatic chromatin ip kit  (Cell Signaling Technology Inc)
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Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation <t>sequencing</t> (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction <t>(ChIP-qPCR,</t> two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate
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Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation <t>sequencing</t> (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction <t>(ChIP-qPCR,</t> two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate
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chip seq sample preparation kit  (Cell Signaling Technology Inc)
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Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation sequencing (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR, two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate

Journal: Genome Biology

Article Title: Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma

doi: 10.1186/s13059-024-03383-8

Figure Lengend Snippet: Lactylation-driven expression of an oncogene set. a A heatmap depicts alterations in lactylation-associated gene expression and chromatin accessibility pre- and post-lactate treatment in the oral squamous cell carcinoma (OSCC) cell line CAL27. b Correlation analysis between lactylation-driven gene expression levels and chromatin accessibility. c Variations in lactylation-driven genes and chromatin accessibility in CAL27 cells exposed to high lactate concentrations. d Enrichment analysis of lactylation-driven genes and gene sets positively and negatively correlated with chromatin accessibility via single-sample gene set enrichment analysis (ssGSEA). e Intersection analysis of lactylation-driven gene sets positively correlated with chromatin accessibility and differentially expressed genes, determined by cleavage under targets and tagmentation sequencing (CUT&TAG-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq). f Validation of increased lactylation enrichment in the promoter regions of CASP3 and TPR in OSCC tissues through chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR, two-tailed unpaired Student’s t -test, ** P < 0.01) and prediction of promoter sequences potentially affected by lactylation. g Validation of elevated expression of CASP3 , HSP90AA1 , HSP90B1 , TPR , RAS , and CCND1 in OSCC tissues through reverse transcription-quantitative polymerase chain reaction (RT-qPCR, two-tailed paired Student’s t -test, * P < 0.05; ** P < 0.01). Lac: lactate

Article Snippet: ChIP sequencing (ChIP-seq) was conducted using a ChIP-seq kit (9005S, Cell Signaling Technology) according to the provided protocol.

Techniques: Expressing, Gene Expression, Sequencing, Next-Generation Sequencing, RNA Sequencing, Biomarker Discovery, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, ChIP-qPCR, Two Tailed Test, Reverse Transcription, Quantitative RT-PCR

Journal: Cell Reports

Article Title: Integrator-Dependent and Allosteric/Intrinsic Mechanisms Ensure Efficient Termination of snRNA Transcription

doi: 10.1016/j.celrep.2020.108319

Figure Lengend Snippet:

Article Snippet: ChIP-seq Sample preparation kit , Cell Signaling Technologies , 9003S.

Techniques: Recombinant, Sample Prep, Sequencing, Plasmid Preparation, Gene Expression, Control, RNA Sequencing, Western Blot, Software