Journal: Cancers

Article Title: Integrated ATAC-Seq and RNA-Seq Analyses Identify the Motif CGTTTCCGGT as an Arginine Deficiency-Responsive DNA Element in Cancer Cells

doi: 10.3390/cancers18050772

Figure Lengend Snippet: ATAC-seq and RNA-seq indicate downregulation of C11orf54 under arginine deprivation ( a ) Pearson correlation heatmap of RNA-seq samples from control and AF groups. ( b ) Volcano plot showing differentially expressed genes (DEGs) between control and AF groups. ( c ) Heatmap of DEGs in control and AF groups based on RNA-seq analysis. ( d ) Scatter plot showing the relationship between promoter chromatin accessibility (ATAC-seq signal) and gene expression (RNA-seq log 2 fold change) between AF and control groups. Dashed lines indicate the thresholds of |log 2 FC| = 1. ( e ) Genome browser tracks showing ATAC-seq signal at the C11orf54 locus in control and AF groups. ( f ) ATAC-seq motif analysis indicating enrichment of ETV5 -binding motifs near the C11orf54 locus. ( g ) Predicted ETV5 binding sites within the C11orf54 promoter region based on the JASPAR database. Three biological replicates per condition were used for both ATAC-seq and RNA-seq ( n = 3).

Article Snippet: Membranes were blocked with 5% non-fat milk in TBST (Tris-buffered saline containing 0.1% Tween-20) for 1 h at room temperature, then incubated overnight at 4 °C with primary antibodies: rabbit anti- C11orf54 (Proteintech, Wuhan, China, Cat. No. #23251-1-AP, 1:1000) and rabbit anti-GAPDH (Huabio, Hangzhou, China, Cat. No. ET1601-4, 1:5000).

Techniques: RNA Sequencing, Control, Gene Expression, Binding Assay

Journal: Cancers

Article Title: Integrated ATAC-Seq and RNA-Seq Analyses Identify the Motif CGTTTCCGGT as an Arginine Deficiency-Responsive DNA Element in Cancer Cells

doi: 10.3390/cancers18050772

Figure Lengend Snippet: Arginine deprivation reduces C11orf54 expression and promoter activity. ( a ) Relative mRNA and protein expression levels of C11orf54 in control and AF groups. Uncropped Western blot images are shown in . ( b ) Schematic representation of the C11orf54 promoter luciferase reporter construct (−938 to −100 bp). ( c ) Luciferase reporter assay showing C11orf54 promoter activity in control and AF groups. Data are presented as mean ± SD ( n = 3). Statistical significance was determined as * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: Membranes were blocked with 5% non-fat milk in TBST (Tris-buffered saline containing 0.1% Tween-20) for 1 h at room temperature, then incubated overnight at 4 °C with primary antibodies: rabbit anti- C11orf54 (Proteintech, Wuhan, China, Cat. No. #23251-1-AP, 1:1000) and rabbit anti-GAPDH (Huabio, Hangzhou, China, Cat. No. ET1601-4, 1:5000).

Techniques: Expressing, Activity Assay, Control, Western Blot, Luciferase, Construct, Reporter Assay