REAT. Due to the complexity of the library, in this study, we limited our analysis to peaks with a height of 30 or greater that were associated with genes expressed in the AVC. This focused our analysis on 520 peaks associated with 647 genes. 57 of these genes with high confidence MedChemExpress STA 9090 TWIST1 binding sites were differentially expressed in the Twist1 null AVC by Tag-seq. These novel putative targets of TWIST1 represented a variety of functions critical for cell differentiation. For example, the TWIST1 target Chd9 is a chromatin modifier and a regulator of transcription, while Eif3h is an elongation factor involved in gene translation. Dagla is a diacylglycerol lipase involved in neuronal cell proliferation and function. Finally, Iffo2 is an intermediate filament and Tgfbi is an ECM component and modifier that causes a postnatal growth defect and increased frequency of tumors when mutated in mice. Up-regulated genes bound by TWIST1 included the two pore channel Tpcn1; the Rho activating protein, Abra, which has been implicated in cardiac hypertrophy; the kinase Sik1; and the uncharacterized genes Gatsl2 and Wdr75. To confirm our ChIP-seq results, we performed ChIP-qPCR validation on 17 novel TWIST1 binding sites using primers within the ChIP-seq peak regions. We used the known TWIST1 target DNM3os as a positive control and the promoter region of Foxa2 as a negative control. We found ChIP-qPCR enrichment for all novel TWIST1 bound regions analyzed as compared to the negative control. Significantly, our novel TWIST1 targets identified in the embryonic heart were also bound by TWIST1 in the developing limb suggesting that they are bound by TWIST1 in several cellular contexts. Taken together these results suggest that TWIST1 plays a critical role in endocardial cushion development, by directly regulating spatially and temporally restricted gene expression. Discussion We have used a combination of Tag-seq and ChIP-seq to examine the in vivo functions of TWIST1 in the E10.5 developing mouse heart valves. By comparing genome-wide analysis of gene expression 
changes in the Twist1 null AVC with spatial expression data in the E10.5 heart, we identified dramatic changes that occur in the AVC in the absence of TWIST1. Furthermore, using ChIP in vivo in the E10.5 heart, we identified 17 novel direct target genes of TWIST1 with expression changes in the Twist1 mutant embryos. Identification of AVC- and OFT-enriched Genes In this study, we describe the generation and analysis of five Tag-seq libraries from the atria, ventricles, OFT, and wild-type and Twist1 null AVCs of the developing E10.5 mouse heart. These Tag-seq libraries were sequenced to a depth of over 7 million tags per library. Using these Tag-seq libraries we identified 725 genes Twist1 Targets in Embryonic Heart Valves enriched in both the AVC and OFT, which PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22205151 included 123 transcriptional regulators. The majority of AVC-enriched genes overlapped with the OFT-enriched genes, highlighting the shared mechanisms underlying the development of the valves in these two regions. However, there were some notable exceptions of genes enriched in the OFT but not the AVC, and vice versa, indicative of gene expression differences underlying unique AVC and OFT developmental processes. Although both the AVC and OFT form valves to control blood flow, the OFT is also critical in the formation of the main arteries leaving the left ventricle. Accordingly, Gene Ontology categorization identified vasculature development