Genome-wide Analysis of Smad7-Mediated Transcription in Mouse Embryonic Stem Cells [RNA-Seq]

Smad7 has been identified as a negative regulator of the transforming growth factor TGF-ß pathway by direct interaction with the TGF-ß type I receptor (TßR-I). Although Smad7 has also been shown to play TGF-ß unrelated functions in the cytoplasm and in the nucleus, a comprehensive analysis of its nuclear function has not yet been performed. Here we show that in ESCs Smad7 is mainly nuclear and acts as a general transcription factor regulating a number of genes unrelated to the TGF-ß pathway. Loss of Smad7 results in the downregulation of several key stemness master regulators, including Pou5f1 and Zfp42, and in the upregulation of developmental genes, with consequent loss of the stem phenotype. Integrative analysis of genome-wide mapping data for Smad7 and ESC self-renewal and pluripotency transcriptional regulators revealed that Smad7 co-occupies promoters of highly expressed key stemness regulators genes, by binding to a specific consensus response element NCGGAAMM. Altogether, our data establishes Smad7 as new integral component of the regulatory circuitry that controls ESC identity. Overall design: RNA-seq transcriptome profiling of Control and Smad7 silenced mouse Embryonic Stem Cells (ESC). 8 samples, 2 different shRNAs were used for the knockdown of Smad7, 2 biological replicates for each condition.