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In this study, we used the Doxycycline (Dox) regulated, tetracycline-responsive (Tet-Off) promoter system to sequentially reduce or titrate gene expression levels of the essential yeast transcription factor\n                  <jats:italic>Repressor Activator Protein 1<\/jats:italic>\n                  (\n                  <jats:italic>RAP1<\/jats:italic>\n                  ) similar to a hypomorph allele series, across three distinct environments: Yeast Peptone Dextrose (YPD) media, YPD media with Heat Shock (HS), and Yeast Peptone Acetate (YPAC) media. We then performed RNA sequencing (RNA Seq) to assess global transcriptional responses to\n                  <jats:italic>RAP1<\/jats:italic>\n                  reduction in these different growth environments. Our analysis first focused on the independent effects of varying\n                  <jats:italic>RAP1<\/jats:italic>\n                  expression levels within and across environments. We then explored GxE interactions, revealing a subset of genes with significant consequences of reduced levels of\n                  <jats:italic>RAP1<\/jats:italic>\n                  and environment-specific expression patterns. Notably, many genes exhibited opposite effects of\n                  <jats:italic>RAP1<\/jats:italic>\n                  titration on gene expression when yeast were grown in YPAC media compared to YPD media and\/or HS, suggesting environment-dependent regulatory architecture. This design reveals how cells integrate internal transcriptional and regulatory changes with external environmental cues, providing a deeper view of GxE architecture. Using Weighted Gene Co-expression Network Analysis (WGCNA), we identified co-regulated gene modules, and by combining this with transcription factor motif enrichment tests, our study identified candidate regulators driving their dynamics. Our findings demonstrate that gene regulatory networks can vary dramatically depending on the environmental context an organism experiences, which can then influence the specific phenotypes produced by a particular genetic perturbation. This illustrates the complexity of genotype\u2013environment interactions and the importance of studying gene function in multiple environments to gain a truly comprehensive understanding of a gene\u2019s sometimes numerous and diverse functions.\n                <\/jats:p>","DOI":"10.64898\/2026.05.06.723246","type":"posted-content","created":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T04:25:16Z","timestamp":1778387116000},"source":"Crossref","is-referenced-by-count":0,"title":["Environmental Regulation and Gene-by-Environment Interaction Influence\n                  <i>RAP1<\/i>\n                  Activity and its Impact on Gene Expression"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2800-4559","authenticated-orcid":false,"given":"Siddhant","family":"Kalra","sequence":"first","affiliation":[{"name":"Department of Biology, Wesleyan University, Middletown, CT 06457, United States of 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