Abstract Estrogen exerts diverse biological effects in multiple tissues in both animals and humans. Much of the accumulated knowledge on the role of estrogen receptor (ER) in the heart has been obtained from studies using ovariectomized mice, whole body ER gene knock-out animal models, ex vivo heart studies, or from isolated cardiac myocytes. In light of the wide systemic influence of ER signaling in regulating a host of biological functions in multiple tissues, it is difficult to infer the direct role of ER on the heart. Therefore, we developed a mouse model with a cardiomyocyte-specific deletion of the ERα allele (cs-ERα^−/−). Male and female cs-ERα^−/− mice with age/sex-matched wild type controls were examined for differences in cardiac structure and function by echocardiogram and differential gene expression microarray analysis. Our study revealed sex-differences in structural parameters in the hearts of cs-ERα^−/− mice, with minimal functional differences. Analysis of microarray data revealed differential variations in the expression of 208 genes affecting multiple transcriptional networks. Furthermore, we report sex-specific differences in the expression of 56 genes. Overall, we developed a mouse model with cardiac-specific deletion of ERα to characterize the role of ERα in the heart independent of systemic effects. Our results suggest that ERα is involved in controlling the expression of diverse genes and networks in the cardiomyocyte in a sex-dependent manner. Introduction Estrogen receptors (ER) are involved in multiple biological processes in a variety of tissues including the cardiovascular system, adipose tissue, and sex organs [37][1]. Generally, the actions of ERs are triggered upon binding of estrogens such as 17-β estradiol (E2), the predominant active form of estrogen [38][2]. Upon ligand binding, ERs mediate their response by two possible modes of action: genomic, which elicits a slow response, and non-genomic, which induces a rapid response. Genomic activation of ERs initiate transcription factors either by direct DNA interaction through estrogen response elements (ERE) or through ER-DNA indirect interactions by tethering with known transcription factors bound to the DNA [39][3]. The non-genomic actions, on the other hand, are mostly membrane-initiated and involve signaling cascades, such as the mitogen-activated protein kinase (MAPK) pathway, the cyclic adenosine mono-phosphate/protein kinase A (cAMP/PKA) pathway, or the endothelial nitric oxide synthase (eNOS) pathway [40][4]–[41][6]. ERs have been implicated in several pathophysiological conditions including diabetes and obesity with implications for cardiovascular disease [42][1], [43][7]. In the heart, cardiomyocytes express both sub-types of ER, ERα and ERβ, with significantly higher levels of ERα [44][8]–[45][10]. Mice with whole-body deletion of ERα have been shown to exhibit altered cardiac substrate preference, particularly uptake and maintenance of glucose in the heart [46][11]. Indeed, whole-body ERα knockout mice are obese and insulin resistant [47][12]–[48][14] and exhibit diminished rates of fatty acid (FA) oxidation in skeletal muscle [49][13]. ERα is also thought to possess cardio-protective properties, due to its ability to up-regulate expression of ApoE, an apolipoprotein that increases clearance of low density lipoproteins (LDL) from circulation [50][15], [51][16]. Similarly, ERβ has been reported to mediate sex-differences in ischemia/reperfusion injury [52][17], [53][18] as well as protect against left-ventricular hypertrophy (LVH) in females [54][19]. Interestingly, ERα and ERβ have also been reported to differentially modulate the expression of inflammatory markers, in particular that of inducible nitric oxide synthase (iNOS) [55][20]. Nevertheless, to date, the studies describing the role of ERs on the cardiovascular system were based on whole-body ER knockouts or on the effects of ER ligands, such as estrogen, on the heart, but with the caveat that such ER ligands also affect peripheral tissues. In light of the wide influence of ER signaling in regulating physiologic functions in multiple tissues, including systemic energy homeostasis, and considering that peripheral substrates can induce cardio-metabolic remodeling, it is difficult to infer the direct role of ER on the heart using whole-body KO models. As a first step in characterizing the role of ERs in the heart, independent of systemic effects of ERs, we have generated a mouse model with a cardiomyocyte-specific deletion of ERα (cs- ERα^−/−. The availability of mice with cs-ERα^−/− will enable, for the first time, to investigate the role of ERα in cardiac tissue independent of peripheral effects. In addition, since ERs are important therapeutic targets, development of in vivo models of selective modulation (such as cardiac specific deletion) will enable better understanding of ER effects in specific tissue [56][21], [57][22]. To that end, we characterized basal cardiac structure and function, and performed gene expression microarray profiling to determine differentially affected networks and pathways in male and female mice. Statistically validated results from the microarray analyses were used for pathway analysis, with emphasis on transcriptional factors and receptor networks (for deciphering genomic actions of ERα). Our findings indicate that cs- ERα^−/− manifests significant variations in the expression profile of genes involved in metabolism, cell growth and differentiation, muscle architecture, and relaxation. Finally, we delineate sex differences associated with the absence of ERα in the heart and identify key transcriptional/receptor hubs that are involved in ERα mediated regulation/signaling in cardiac tissue. Materials and Methods All experiments were conducted according to a protocol approved by the animal experiment committee at Washington University School of Medicine in Saint Louis (IACUC Animal Welfare Assurance # A-3381-01) and in accordance to ‘Principles of laboratory animal care’ (NIH pub no. 85–23, revised 1985; [58]http://grants1.nih.gov/grants/olaw/references/phspol.htm). Animals