Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response

The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA-sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g-/- zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type, hnf4g-/-, and hnf4a-/-;hnf4g-/- zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10-15 pooled gastrointestinal tracts, and 4 biological replicates per treatment group were sequenced. mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1) WTCV, WTGF, hnf4g-/-CV, hnf4g-/-GF 2) WTCR, hnf4g-/-CR, hnf4a-/-;hnf4g-/-CR