Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish

H. William Detrich,John H. Postlethwait,Thomas Desvignes

doi:10.1016/j.margen.2016.04.013

Abstract

White-blooded Antarctic crocodile icefish are the only vertebrates known to lack functional hemoglobin genes and red blood cells throughout their lives. We do not yet know, however, whether extinction of hemoglobin genes preceded loss of red blood cells or vice versa, nor whether erythropoiesis regulators disappeared along with hemoglobin genes in this erythrocyte-null clade. Several microRNAs, which we here call erythromiRs, are expressed primarily in developing red blood cells in zebrafish, mouse, and humans. Abrogating some erythromiRs, like mir144 and mir451a, leads to profound anemia, demonstrating a functional role in erythropoiesis. Here, we tested two not mutually exclusive hypotheses: 1) that the loss of one or more erythromiR genes extinguished the erythropoietic program of icefish and/or led to the loss of globin gene expression through pseudogenization; and 2) that some erythromiR genes were secondarily lost after the loss of functional hemoglobin and red blood cells in icefish. We explored small RNA transcriptomes generated from the hematopoietic kidney marrow of four Antarctic notothenioids: two red-blooded species (bullhead notothen Notothenia coriiceps and emerald notothen Trematomus bernacchii) and two white-blooded icefish (blackfin icefish Chaenocephalus aceratus and hooknose icefish Chionodraco hamatus). The N. coriiceps genome assembly anchored analyses. Results showed that, like the two red-blooded species, the blackfin icefish genome possessed and the marrow expressed all known erythromiRs. This result indicates that loss of hemoglobin and red blood cells in icefish was not caused by loss of known erythromiR genes. Furthermore, expression of only one erythromiR, mir96, appears to have been lost after the loss of red blood cells and hemoglobin—expression was not detected in the erythropoietic organ of hooknose icefish but was present in blackfin icefish. All other erythromiRs investigated, including mir144 and mir451a, were expressed by all four species and thus are present in the genomes of at least the two white-blooded icefish. Our results rule out the hypothesis that genomic loss of any known erythromiRs extinguished erythropoiesis in icefish, and suggest that after the loss of red blood cells, few erythromiRs experienced secondary loss. Results suggest that functions independent of erythropoiesis maintained erythromiRs, thereby highlighting the evolutionary resilience of miRNA genes in vertebrate genomes.

Highlights

Since the first report by the Norwegian biologist Ditlef Rustad of a fish with “colorless blood” that he caught near the sub-Antarctic Bouvet Island (Bouvetøya) in December 1927 and the confirmation in 1954 by Johan Ruud that this species, the blackfin icefish Chaenocephalus aceratus, lacks both red blood cells and hemoglobin (Hb) (Ruud, 1954), the “crocodile icefish” of the Southern Ocean have puzzled physiologists
The hypothesis that the loss of erythropoietic miRNAs led to the loss of red blood cells and hemoglobin in white-blooded icefish predicts that red-blooded notothenioids would possess erythromiRs known from other vertebrates but white-blooded icefish would lack one or more of them
We first examined whether miRNAs currently known to be important in erythropoiesis in vertebrates were expressed in erythropoietic organs of red-blooded and white-blooded notothenioids

Summary

Introduction

Since the first report by the Norwegian biologist Ditlef Rustad of a fish with “colorless blood” that he caught near the sub-Antarctic Bouvet Island (Bouvetøya) in December 1927 and the confirmation in 1954 by Johan Ruud that this species, the blackfin icefish Chaenocephalus aceratus, lacks both red blood cells and hemoglobin (Hb) (Ruud, 1954), the “crocodile icefish” of the Southern Ocean have puzzled physiologists. Icefish comprise the only vertebrate clade whose members lack red blood cells and the oxygen transport protein hemoglobin throughout their life cycles Spurred by these seminal observations, contemporary molecular biologists and physiologists have sought to understand the evolutionary mechanism(s) that led to the loss of mature red blood cells and hemoglobin in icefish and the physiological traits that enable these unique vertebrates to survive without oxygen-binding proteins in their blood (Braasch et al, 2015; Cheng and Detrich, 2007; Holeton, 1970; Kock, 2005a, 2005b; Near et al, 2006; Sidell and O’Brien, 2006). Several other teleost lineages have lost cardiac myoglobin expression, including the circum-Arctic threespined stickleback (Gasterosteus aculeatus), which possesses a pseudogenized myoglobin gene (Hoffmann et al, 2011; Macqueen et al, 2014)

Methods

Results

Conclusion