Identification of transcription start site and a differentially methylated region in the 5′-flanking area of Bcl11b. (A) RNA-seq on early T cells identified the actual TSS (red) of Bcl11b transcripts, which is about 640 bp upstream of the annotated one (blue). RNA-seq data from ref. 9, transcription factor binding sites from refs. 3, 9, 24,-26. (B) The DNA methylation of three CpG islands on the Bcl11b locus was measured by bisulfite-DNA sequencing. IS1, CpG island 1. IS2, CpG island 2. IS3 and IS4, 2 representative regions on CpG island 4. Because of technical issues, the methylation of an additional CpG island in intron 2 was not analyzed. The closed dots represent methylated CpG sites, and the open dots represented unmethylated sites. The positions of the CpG islands are relative to the annotated TSS of Bcl11b.