RNA-seq, ChIP-seq and ATAC-seq analysis of MKL1 blocked cells during reprogramming

Actins and regulators of actin dynamics generate contractile forces providing major mechanical and structural support for the cell. Whether and how they actively participate in cell fate control is not clear. Here, we report the actin responsive transcription factor complex MKL1/SRF, the major transcriptional regulator of large numbers of actin cytoskeletal genes, as an important regulator of genomic accessibility and cell fate outcome. Somatic cells with weaker MKL1/SRF activity progress toward pluripotency efficiently while sustained MKL1/SRF activity at a level seen in typical fibroblasts is sufficient to stall cells on their trajectory toward pluripotency. This altered cell fate outcome is associated with an overactive actin cytoskeleton, which connects to chromatin via the LINC complex, preventing its conversion into a relaxed, open conformation that allows sufficient accessibility to pluripotency-inducing transcription factors. Interfering with actin polymerization at appropriate times promotes pluripotency induction. Thus, we reveal a previously unappreciated aspect of cell fate control exerted by the actin based cytoskeletal system. Transcriptome of reprogramming cells at day 6 or day 25 with or without constitutively active MKL1 (caMKL1) were compared. Cells of both conditions at day 25 were also analyzed for Oct4 and SRF binding by ChIP-seq. Cells of both conditions at day 25, as well as starting MEFs were analyzed for histone modifications H3K4me3, H3K27ac and H3K27me3. WT ES cells with or without caMKL1 expression, and SRFf/f and SRFdelta/delta iPS cells were compared for chromatin accessibility by ATAC-seq analysis.