Transcriptional and translational regulation of sex-specific genes in mouse liver
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With the advent of high-throughput sequencing technology, modeling molecular mechanisms for gene regulatory networks has expanded to include the epigenome. Using diverse high-throughput DNA sequencing platforms, previous studies have revealed such mechanisms for sex-differential gene regulation in mouse liver. This thesis describes the contribution of transcription factor (TF) HNF6 to these models. Further, the utility of digital genomic footprinting (DGF) using the DNase-I hypersensitive sites sequencing (DNase-Seq) assay or the Assay for Transposase Accessible Chromatin (ATAC-Seq) is demonstrated. Finally, this thesis characterizes the extent of post-translational control of genes active in mouse liver using the ribosome profiling assay (Ribo-Seq), by way of translational efficiency (TE), and uses Ribo-Seq to interrogate open reading frames from previously characterized untranslated regions of protein-coding genes and in a set of liver-expressed long non-coding RNA genes for evidence of translation. First, mouse liver binding sites for HNF6 are integrated for overlap with sex-biased DNase-I hypersensitivity sites, male-biased STAT5, and female-specific CUX2 binding sites. This analysis showed how epigenetic markers, together with HNF6, target specific sets of sex-biased genes, revealing specific mechanisms involving HNF6 that contribute to the sex-specificity of gene expression in mouse liver. Next, the limited utility of the DGF technique to predict TF-DNA interactions was demonstrated using publicly available datasets for 21 TFs using DNase-seq and ATAC-seq datasets and sequencing libraries prepared using chromatin as well as purified DNA. Additionally, a simple model is proposed that benchmarks performance of DNase-seq vs. ATAC-seq for the same set of 21 TFs. Finally, the extent to which liver-expressed genes are regulated by sex-differential TE was investigated using Ribo-Seq. Limited sex-differential TE was found. Further, this assay predicted novel peptides found in previously characterized non-coding open reading frames within untranslated regions of genes that may regulate TE of upstream genes, and in a set of liver-expressed long non-coding RNAs.