Journal: Nucleic Acids Research

Article Title: Transient SUMOylation inhibition in human pre-adipocytes stably imprints a transcriptional beiging fate

doi: 10.1093/nar/gkag232

Figure Lengend Snippet: Stable mobilization of CEBPs and PPARG upon transient TAK-981 treatment in pre-adipocytes. ( A ) ATAC-seq experimental layout in hTERT A41hWAT-SVF pre-adipocytes. Time series analysis and hierarchical clustering of significant variations in chromatin accessibility at day 0 (D0), 12 h (12h), and day (D7) after TAK-981 treatment. ( C ) GOBP analysis of ATAC-seq clusters 2 and 6 revealed in panel (B). See and for an analysis of all clusters. ( D – F ) Volcano plots displaying the results of ATAC-seq inferred differential TF activity analyses performed at D0, 12h, and D7 after TAK-981 or DMSO treatment. Colored dots indicate significant differentially mobilized TFs (TAK-981 versus DMSO). Differential binding score >0.05 and pAdj <0.001. ( G ) Time series analysis inferred TF activity over time (TAK-981 versus DMSO) at D0, 12h, and D7 after TAK-981 treatment. ( H ) Western blot analysis of CEBPB SUMOylation in DMSO and TAK-981-treated cells. ( I ) Western blot analysis of CEBPB and PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hTERT A41hWAT-SVF pre-adipocytes. ( J ) Western blot analysis of PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hASCs.

Article Snippet: Samples for assay for transposase-accessible chromatin sequencing (ATAC-seq) were prepared based on previously published protocols with the Illumina ATAC-seq library preparation kit (20034197) [ – ].

Techniques: Activity Assay, Binding Assay, Western Blot

Journal: Frontiers in Plant Science

Article Title: Integration of ATAC-seq and RNA-seq unveils transcription factors involved in low-nitrogen tolerance in cucumber

doi: 10.3389/fpls.2026.1798277

Figure Lengend Snippet: Integration of ATAC-seq and RNA-seq to decipher the core transcriptional regulatory network driving early low-nitrogen adaptation in C52. (A) Heatmap illustrating the genome-wide enrichment of ATAC-seq signals around Transcription Start Sites (TSS) in C13 and C52 leaves under normal (NN) and low nitrogen (LN, 4 h) conditions. The distinct enrichment patterns confirm high library quality and the effective capture of open chromatin regions. (B) UpSet plot visualizing the intersection between Differentially Accessible Regions (DARs) and Differentially Expressed Genes (DEGs) across different comparisons. The partial overlap indicates a complex, multilayered relationship between chromatin remodeling and transcriptional output. (C) Venn diagram showing the consensus of transcription factor (TF) binding motifs predicted by three complementary algorithms (HOMER, MEME-ChIP, and PlantTFDB) within the flanking sequences (± 1 kb) of DARs in C52. (D) The inferred Transcriptional Regulatory Network (TRN) for the early N-starvation response in C52. The network comprises a core layer (DAR-DEG intersections) and an extended layer (DAR-only). Circular nodes represent candidate TFs, and square nodes represent downstream target genes. Node size is proportional to the total degree of connectivity (in-degree + out-degree), reflecting regulatory importance. Edge thickness indicates the statistical confidence (E-value) of the Motif-TF match. Node colors correspond to distinct WGCNA modules (e.g., CsTGA7 co-segregates with CsDMR6 and CsFTIP7 ). (E) Expression heatmap of candidate TFs under NN and LN conditions. Key stress-responsive families (bZIP, AP2/ERF, WRKY) are highlighted, with Cs TGA7 showing significant upregulation and CsERF118 showing downregulation ( P < 0.05). (F) Integrative visualization of chromatin accessibility (IGV tracks) and relative gene expression (bar charts) for four core target genes (Cs DMR6 , CsFTIP7 , CsAHG1 , CsSDR3b ). Red boxes highlight regulatory regions where chromatin accessibility decreased under low (N) Note the divergent transcriptional outcomes: CsDMR6 and CsSDR3b were downregulated (concordant), whereas CsFTIP7 and CsAHG1 were upregulated (discordant), suggesting diverse chromatin-based regulatory mechanisms.

Article Snippet: Following transposition, equimolar amounts of Adapter 1 and Adapter 2 were added, and the library was amplified by PCR using the ATAC-seq Novogene Kit (Novogene, China).

Techniques: RNA Sequencing, Genome Wide, Binding Assay, Expressing, Gene Expression