Atrial fibrillation (AF) is the most common type of cardiac arrhythmia, characterized by an irregular heartbeat due to uncoordinated electrical activity in the atria. The Tbx5 locus has been implicated by genome wide association studies (GWAS), and our laboratory has previously shown that the absence of Tbx5 leads to spontaneous and sustained AF. We will utilize this Tbx5-deficient mouse model to further characterize the regulatory mechanisms important for cardiac rhythm and the molecular mechanisms driving the pathophysiology of atrial fibrillation.Cardiac rhythm is a dose-sensitive physiologic process, therefore stable gene expression is imperative for proper cardiac function. Precise gene regulation is reliant on feedback mechanisms to maintain accurate gene expression, and miRNAs are a canonical feedback mechanism for steady gene expression. In Chapter 1, our laboratory performed small RNA profiling of Tbx5-deficient mice to define candidate miRNAs involved in the TBX5-dependent gene regulatory network important for the maintenance of cardiac rhythm. Many of the miRNAs identified were interrogated in a high-throughput screen, which linked arrhythmogenic phenotypes to several miRNAs. Whole mouse and cellular electrophysiology studies were focused on a single miRNA candidate, miR-10b, and demonstrated its mis-regulation leads to atrial fibrillation susceptibility. This work supports a model where TBX5 regulates the expression of miRNAs critical for maintaining appropriate gene expression levels important in cardiac rhythm. Atrial fibrillation also has a strong epidemiologic link with heart failure, as these two cardiac diseases are associated with increased incidence of each other. In Chapter 2, we revealed remarkable correlation between the differentially expressed genes in the atria of AF and heart failure mouse models, and identified shared transcription factors as candidates important in driving the pathophysiology of cardiac disease. We also identified the conservation of differential ncRNA transcripts in both of these disparate disease models. Based on the knowledge that noncoding RNAs (ncRNAs) are transcribed from regulatory elements, it supports the paradigm of a common disease-specific gene regulatory network that mediates the physiologic consequences of disease. These differential non-coding RNA transcripts identified a TBX5-dependent candidate regulatory element downstream of Klf15, an important regulator in cardiac hypertrophy. We also identified a ncRNA transcript upstream of Sox9 that is up-regulated in both disease models, and may uncover a disease-response essential for coping with atrial dysfunction. In summary, our studies have identified crucial transcriptional changes in atrial fibrillation and heart failure, along with the shared regulatory mechanisms critical in driving these changes. Finally, in Chapter 4 we performed a time course deletion of Tbx5 in an effort to identify the earliest transcriptional changes in this atrial fibrillation mouse model. Interestingly, the removal of Tbx5 leads to an early response at Day 3 and Day 6, which is very different from the response at Day 10 and Day 17 of the time course. In an effort to identify significant gene expression changes between Tbx5 KO and WT throughout the time course we performed maSigPro analysis, which has provided us with candidate genes important in driving the pathophysiology of atrial fibrillation.