Liver transcriptome data of Esr1 knockout male rats reveals altered expression of genes involved in carbohydrate and lipid metabolism

Estrogens are traditionally considered to be female sex steroid hormones and most of the studies examining estrogen regulation of metabolic function in the liver have been conducted in females. However, the liver expresses high levels of estrogen receptor alpha (ESR1) in both males and females, which mediates the hepatic response to estrogens. In this data article, we investigated whether metabolic disorders in Esr1 knockout (Esr1-/-) male rats were linked with loss of transcriptional regulation by ESR1 in liver. To identify the ESR1 regulated genes in the mutant liver, RNA-sequencing was performed on liver RNAs purified from young male rats. The raw data were analyzed using the CLC Genomics Workbench and high-quality RNA-sequencing reads were aligned to the Rattus norvegicus genome. Transcriptome data obtained from Esr1-/- liver RNAs were compared to that of wild type rats. Based on an absolute fold change of 2 with a p-value ≤ 0.05, a total of 618 differentially expressed genes were identified in the Esr1-/- male liver. Pathway analyses demonstrated that the majority of differentially expressed genes are regulators of carbohydrate and lipid metabolism in the liver. These differentially expressed genes and their potential roles were further examined in a companion manuscript, “Disruption of ESR1 alters the expression of genes regulating hepatic lipid and carbohydrate metabolism in male rats” (Khristi et al., 2018).


a b s t r a c t
Estrogens are traditionally considered to be female sex steroid hormones and most of the studies examining estrogen regulation of metabolic function in the liver have been conducted in females. However, the liver expresses high levels of estrogen receptor alpha (ESR1) in both males and females, which mediates the hepatic response to estrogens. In this data article, we investigated whether metabolic disorders in Esr1 knockout (Esr1-/-) male rats were linked with loss of transcriptional regulation by ESR1 in liver. To identify the ESR1 regulated genes in the mutant liver, RNAsequencing was performed on liver RNAs purified from young male rats. The raw data were analyzed using the CLC Genomics Workbench and high-quality RNA-sequencing reads were aligned to the Rattus norvegicus genome. Transcriptome data obtained from Esr1-/-liver RNAs were compared to that of wild type rats. Based on an absolute fold change of 2 with a p-value r 0.05, a total of 618 differentially expressed genes were identified in the Esr1-/-male liver. Pathway analyses demonstrated that the

Value of the data
This data article provides liver transcriptomic analyses of Esr1-/-male rats. Pathway analyses of the differentially expressed genes in the Esr1-/-liver show their involvement in carbohydrate and lipid metabolism.
Differentially expressed genes are also linked to development of obesity, hepatic steatosis, and other liver diseases.

Data
In this data article, we present analyzed RNA-seq data showing the differentially expressed genes in the Esr1-/-male liver (Table S1). Bioinformatic analyses show that these differentially expressed genes are linked to pathways of carbohydrate metabolism (Table 1, Fig. 1), lipid metabolism ( Table 2, Fig. 2) and hepatic diseases including hepatic steatosis, necrosis of the liver, and obesity (Fig. 3).

Esr1 knockout rats
The Holtzman Sprague-Dawley (HSD) Esr1-mutant rat model was generated by targeted deletion of exon 3 in the Esr1 gene [2]. Deletion of exon 3 caused a frameshift and null mutation in the ESR1 coding sequence [2]. All animals were screened for the presence of the mutation by PCR using tail-tip DNA samples (REDExtract-N-Amp Tissue PCR Kit, Sigma-Aldrich) and primers targeting the flanking intron sequences [2]. All procedures were performed in accordance with the protocols approved by the University of Kansas Medical Center Animal Care and Use Committee.

Sample collection from wild type and Esr1-/-rats
Liver tissues were collected from 10 to 12-week-old Esr1-/-and age matched wild type male rats. The tissue samples were collected immediately after euthanization, cut into small species, snap frozen in liquid nitrogen, and stored at À 80°C until they were processed for RNA extraction. Total RNA from liver tissues was extracted using TRI Reagent (Millipore-Sigma) following the manufacturer's instructions. RNA quality was assessed using the Agilent Bioanalyzer and samples with a RIN score Z 9 were included in the RNA-seq library preparation.

Library preparation and RNA-sequencing
The library preparation and sequencing of RNA was performed at the Genome Sequencing facility of the University of Kansas Medical Center. Five hundred nanogram of liver total RNA was used for the RNA-seq library preparation. Libraries were prepared using a TruSeq Stranded mRNA kit (Illumina) following the manufacturer's instructions. Briefly, mRNA was enriched from total RNA by oligo-dT magnetic beads, purified, and chemically fragmented. The first strand of cDNA was synthesized using random hexamer primers and reverse transcriptase. Then, double stranded (ds) cDNA was generated by removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP. ds cDNA was purified from the second strand reaction mix by AMPure XP beads (Beckman Coulter). The cDNA ends were blunted and poly (A) tails were added to the 3' ends. Finally, after ligation of indexing adaptors (Illumina), the suitable DNA fragments were selected for PCR