Developmental hourglass and heterochronic shifts in fin and limb development

Abstract

How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls.

The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation

“…We tested two previously published Tn5 sequence bias correction methods, HINT-ATAC [55] and BaG-Foot [56], as well as a new method we developed in this study. Tn5 DNA sequence preferences were inferred from ATAC-Seq libraries prepared by transposing purified mouse genomic DNA with Tn5 (GSM2981009 [51], GSM1550786 [52], GSM4048700 [53], and GSM2333650/GSM2333651 [54]).…”

“…We shifted the position of the cut to the center of the overhang by adding +4bp/-4bp if the read mapped to +/-strand respectively. Tn5 sequence bias was estimated from ATAC-Seq libraries prepared from purified mouse genomic DNA from independent studies [51][52][53][54] and removed from the final counts (Section 4). Finally, corrected Tn5 cut counts were normalized to each sample's library size.…”

The little skate genome and the evolutionary emergence of wing-like fins

“…We identified 193 and 117 genes preferentially expressed in pectoral and pelvic fins, respectively (Supplementary Table 4 ), including several transcription factors and components of different signalling pathways. To identify changes in the appendage gene regulatory network, we compared differentially expressed genes in skate fins with corresponding mouse fore- and hindlimb RNA-seq data 35 , 36 (Fig. 5a and Supplementary Fig.…”

Squalomix: shark and ray genome analysis consortium and its data sharing platform

“…Remarkably, cell culture in cartilaginous fishes, which was long thought difficult because of their high body fluid osmolarity, was enabled by modifying the culture medium with balancing osmolytes ( Uno et al , 2020 ). Our cytological expertise also allowed various epigenomic analyses that benefit from whole genome sequencing, on transcription factor binding with ChIP-seq ( Hara et al , 2018 ) and chromatin openness with ATAC-seq, in addition to long-range DNA interactions with Hi-C ( Kadota et al , 2020 ; Onimaru et al , 2021 ). These techniques contributed to biological analyses based on the draft genome sequences of three shark species ( Hara et al , 2018 ), which launched the Squalomix Consortium.…”