Small RNA Sequencing

Abstract

The Antarctic icefish, a family (Channichthyidae) of teleosts  within the perciform suborder Notothenioidei, are the only known  vertebrates without oxygen‐transporting haemoglobins and that are  largely devoid of circulating erythrocytes. To elucidate the evo‐devo  mechanisms underpinning the suppressed erythropoiesis in the icefish, we  conducted comparative studies on the transcriptomes and microRNA omes  of the primary haematopoietic tissues between an icefish (Chionodraco hamatus ) and two red‐blooded notothenioids (Trematomus bernacchii  and Gymnodraco acuticeps ).  We identified substantial remodelling of the haematopoietic programs in  the icefish through which erythropoiesis is selectively suppressed.  Experimental verification showed that erythropoietic suppression in the  icefish may be attributable to the upregulation of TGF ‐β signalling,  which coincides with reductions in multiple transcription factors  essential for erythropoiesis and the upregulation of hundreds of  microRNA s, the majority (> 80%) of which potentially target  erythropoiesis regulating factors. Of the six microRNA s selected for  verification, three miRNA s (miR‐152, miR‐1388 and miR‐16b) demonstrated  suppressive functions on GATA 1 and ALAS 2, which are two factors  important for erythroid differentiation, resulting in reduced numbers of  erythroids in microinjected zebra fish embryos. Codon substitution  analyses of the genes of the TGF ‐β superfamily revealed signs of  positive selection in TGF ‐ β1  and endoglin  in  the lineages leading to Antarctic notothenioids. Both genes are  previously known to function in erythropoietic suppression. These  findings implied a general trend of erythropoietic suppression in the  cold‐adapted notothenioid lineages through evolutionary modulation of  the multi‐functional TGF ‐β signalling pathway. This trend is more  pronounced in the haemoglobin‐less icefish, which may pre‐emptively  hinder the otherwise defective erythroids from production.