Gabriele Baniulyte, Abby A McCann, Dana L Woodstock, Morgan A Sammons
The p53 family of transcription factors (p53, p63 and p73) regulate diverse organismal processes including tumor suppression, maintenance of genome integrity and the development of skin and limbs. Crosstalk between transcription factors with highly similar DNA binding profiles, like those in the p53 family, can dramatically alter gene regulation. While p53 is primarily associated with transcriptional activation, p63 mediates both activation and repression. The specific mechanisms controlling p63-dependent gene regulatory activity are not well understood. Here, we use massively parallel reporter assays (MPRA) to investigate how local DNA sequence context influences p63-dependent transcriptional activity. Most regulatory elements with a p63 response element motif (p63RE) activate transcription, although binding of the p63 paralog, p53, drives a substantial proportion of that activity. p63RE sequence content and co-enrichment with other known activating and repressing transcription factors, including lineage-specific factors, correlates with differential p63RE-mediated activities. p63 isoforms dramatically alter transcriptional behavior, primarily shifting inactive regulatory elements towards high p63-dependent activity. Our analysis provides novel insight into how local sequence and cellular context influences p63-dependent behaviors and highlights the key, yet still understudied, role of transcription factor paralogs and isoforms in controlling gene regulatory element activity.
Gabriele Baniulyte, Abby A McCann, Dana L Woodstock, Morgan A Sammons. Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity. 2024-11-20. https://doi.org/10.1093/nar/gkae1143
The five-variant p63-bound regulatory-element library was assayed in HaCaT transformed keratinocytes to examine epithelial-context dependence of p63RE activity. This processed table uses the author-filtered WT/mut matched subset and retains one row per enhancer family.
The same five-variant p63-bound regulatory-element STARR-seq MPRA library was assayed in MCF10A TP53−/− cells to isolate p63-dependent activity from p53 activity. Each retained row is an enhancer family containing WT, p63RE mutant, p63RE shuffle, flanking-region shuffle, and full-sequence shuffle measurements.
The five-variant p63-bound regulatory-element library was assayed in SCC25 head-and-neck squamous cell carcinoma cells to examine epithelial-context dependence of p63RE activity. This processed table uses the author-filtered WT/mut matched subset and retains one row per enhancer family.
The p63-bound regulatory-element STARR-seq library was assayed in an MCF10A derivative with doxycycline-induced TAp63β expression to test p63 isoform-dependent activity. This processed table contains the author-filtered WT/mut matched subset and one row per enhancer family.
A five-variant STARR-seq MPRA library of 17,310 human p63-bound regulatory elements was transiently assayed in TP53+/+ MCF10A cells. Each retained row is an enhancer family containing WT, p63RE mutant, p63RE shuffle, flanking-region shuffle, and full-sequence shuffle measurements.
The p63-bound regulatory-element STARR-seq library was assayed in an MCF10A derivative carrying doxycycline-induced β-glucuronidase (GUS) as the overexpression control. This processed table contains the author-filtered WT/mut matched subset and one row per enhancer family.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 11 files (ZIP)gkae1143_supplementary_archive.zipGSE266670_p63enh_starrseq_raw_counts.csv.gzGSE266670_RAW.tarGSM8516686_p63enh_starrseq_raw_counts_SCC25rep4.csv.gzsupplementary_tables/Supplemental_Figure_Legends.docxsupplementary_tables/Table_S1.xlsxsupplementary_tables/Table_S2.xlsxsupplementary_tables/Table_S3.xlsxsupplementary_tables/Table_S4.xlsxsupplementary_tables/Table_S5.xlsxsupplementary_tables/Table_S6.xlsx