Precise modulation of transcription factor levels identifies features underlying dosage sensitivity

Abstract

Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.

Dosage amplification dictates oncogenic regulation by theNKX2-1lineage factor in lung adenocarcinoma

“…Prior studies of c-MYC 14 or SOX9 17 suggest either linear or buffered responses to dosage modulation. In the case of SOX9, most changes in chromatin accessibility occur in the increase from 0% to 25% of wild-type SOX9 dosage.…”

“…For the c-MYC oncogene in Burkitt’s lymphoma, a linear model of transcriptional amplification was identified 14 , however this result was later found to be due to a specific role for c-MYC as a selective transcriptional activator of metabolic processes like ribosome biogenesis 16 . For the SOX9 lineage factor in a craniofacial developmental context, a buffered model of dosage regulation was found, where most changes in chromatin accessibility occurred from 0-25% of wild-type SOX9 dosage 17 . To date, the role of dosage modulation in oncogene regulation for amplified oncogenic TFs has not been characterized, to the best of our knowledge.…”

Trans-eQTL hotspots shape complex traits by modulating cellular states

“…This strategy is similar to analyses of allelic series at a given gene in human populations, in which alleles of varying molecular severity, ranging from knockouts to subtle cis -eQTLs, are assayed for their effects on a complex trait to create dose-response curves (Dendrou et al, 2016; Plenge et al, 2013). Related genetic strategies and synthetic approaches have been used to relate the expression level of several focal genes to yeast fitness (Arita et al, 2021; Duveau et al, 2018; Keren et al, 2016; Metzger et al, 2015) and human gene regulation (Freimer et al, 2022; Naqvi et al, 2023). Here, we applied this logic to independent, mostly trans -acting eQTLs across the genome and to dozens of traits.…”

A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression.

“…The dynamic interactions that regulate DNA-protein recognition passing through chromatin status and interaction of TFs with nucleosomes (34,35), eventually lead to rates of association and dissociation of DNA-binding proteins to and from DNA, which in turn determine cell-specific transcriptional activity (36)(37)(38). Therefore, the high to low affinity ranges of DNA-protein interactions (the number and types of TFBSs and TF concentrations and types (39)(40)(41)) account of gene expression from noise (42) to gene expression programs (43,44). However, it is unknown whether evolution has generated an additional level of DNA-protein interaction in gene regulation.…”