Fig. 5

Proportion of inter-/intra-TAD chromatin loops and distribution of RNA expression of individual genes in lens cells. (a) Schematic diagram showing four possible loop-TAD anchor arrangements. Inter- is defined where both loop anchors connect two separate TADs. Intra- is defined where both loop anchors are within a single TAD. Loops with anchors that were found between TADs were defined as “Not in TAD”. Loops where one anchor lies within a given TAD and the other lies outside of the TAD were defined as “1 anchor in TAD”. (b) Quantitative analysis of four types of chromatin loops. ES cells show a higher number of Inter-TAD chromatin loops (n = 560) than lens epithelium (n = 94) and fiber cells (n = 240). Lens epithelial cells show the highest number of loops where anchors are not within a TAD boundary (n = 4,463). (c) Boxplot showing top differentially expressed coding and non-coding transcripts with fragments per kilobase of transcript per million mapped reads (FPKM). The top expressed genes in the lens epithelium mostly include small nuclear RNAs and αA-crystallin (Cryaa) gene whereas lens fiber cells show high expression of multiple crystallin genes