Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells

Abstract

Planarians have become an established model system to study regeneration and stem cells, but the regulatory elements in the genome remain almost entirely undescribed. Here, by integrating epigenetic and expression data we use multiple sources of evidence to identify enhancer elements active in the adult stem cell populations that drive regeneration. We have used ChIP-seq data to identify regions with histone modifications consistent with enhancer identity and activity, and ATAC-seq data to identify accessible chromatin. Overlapping these signals allowed for the identification of a set of high confidence candidate enhancers predicted to be active in planarian adult stem cells. These enhancers are enriched for conserved transcription factor (TF) binding sites for TFs and TF families expressed in planarian adult stem cells. Foot-printing analyses provided further evidence that these potential TF binding sites are occupied in adult stem cells. We integrated these analyses to build testable hypotheses for the regulatory function of transcription factors in stem cells, both with respect to how pluripotency might be regulated, and to how lineage differentiation programs are controlled. Our work identifies active enhancers regulating adult stem cells and regenerative mechanisms.

Gene conversion limits the cost of asexuality in somatically immortal worms

“…We ran Orthofinder using a proteome from a new planarian annotation to isolate the orthologues of each predicted gene 48,49 . To reduce redundancy, we first ran CD-hits to collapse all peptides with 99% identity to a single transcript ID (supplementary data 4).…”

“…Thus, if a mutation is homozygous in all libraries supporting the mutation, it will have a homozygosity score of 1 and vice versa. To verify that the homozygosity score does not represent biased gene expression rather than homozygosity, we compared SNPs found in both RNAseq data to available ATAC (genomic) data 49 . This showed that when filtering for mutations supported by over 3 libraries, there is over 95% agreement between RNAseq and ATAC based methods of calling purely homozygous variants (supplementary figure 1).…”