Frédéric Flamant, Yanis Zekri, Romain Guyot
When bound to thyroid hormone, the nuclear receptor TRα1 activates the transcription of a number of genes in many cell types. It mainly acts by binding DNA as a heterodimer with retinoid X receptors at specific response elements related to the DR4 consensus sequence. However, the number of DR4-like elements in the genome exceed by far the number of occupied sites, indicating that minor variations in nucleotides composition deeply influence the DNA-binding capacity and transactivation activity of TRα1. An improved protocol of synthetic self-transcribing active regulatory region sequencing was used to quantitatively assess the transcriptional activity of thousands of synthetic sites in parallel. This functional screen highlights a strong correlation between the affinity of the heterodimers for DNA and their capacity to mediate the thyroid hormone response.
Frédéric Flamant, Yanis Zekri, Romain Guyot. Functional Definition of Thyroid Hormone Response Elements Based on a Synthetic STARR-seq Screen. 2022-06-09. https://doi.org/10.1210/endocr/bqac084
A degenerate DR4-like response-element library (5′NGGTCANNNNRGGNNA3′; 32,768 possible combinations) was cloned into the hSTARR-seq-ORI vector and transfected into HEK293 cells. The deposited data contain input-library counts and vector-transcript output counts for 600 ng and 1,200 ng library transfections with or without T3.
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 9 files (ZIP)GSE196145_family.soft.gzGSE196145_RAW.tarGSE196145_series_matrix.txt.gzGSM5861241_Counts_lib1.txt.gzGSM5861242_Counts_lib2.txt.gzGSM5861243_Counts_lib3.txt.gzGSM5861244_Counts_lib4.txt.gzGSM5861245_Counts_lib7.txt.gzsource_manifest.txt