Analysis of transcribed sequences from young and mature zebrafish thrombocytes

Abstract

The zebrafish is an excellent model system to study thrombocyte function and development. Due to the difficulties in separating young and mature thrombocytes, comparative transcriptomics between these two cell types has not been performed. It is important to study these differences in order to understand the mechanism of thrombocyte maturation. Here, we performed single-cell RNA sequencing of the young and mature zebrafish thrombocytes and compared the two datasets for young and mature thrombocyte transcripts. We found a total of 9143 genes expressed cumulatively in both young and mature thrombocytes, and among these, 72% of zebrafish thrombocyte-expressed genes have human orthologs according to the Ensembl human genome annotation. We also found 397 uniquely expressed genes in young and 2153 uniquely expressed genes in mature thrombocytes. Of these 397 and 2153 genes, 272 and 1620 corresponded to human orthologous genes, respectively. Of all genes expressed in both young and mature thrombocytes, 4224 have been reported to be expressed in human megakaryocytes, and 1603 were found in platelets. Among these orthologs, 156 transcription factor transcripts in thrombocytes were found in megakaryocytes and 60 transcription factor transcripts were found in platelets including a few already known factors such as Nfe2 and Nfe212a (related to Nfe2) that are present in both megakaryocytes, and platelets. These results indicate that thrombocytes have more megakaryocyte features and since platelets are megakaryocyte fragments, platelets also appear to be thrombocyte equivalents. In conclusion, our study delineates the differential gene expression patterns of young and mature thrombocytes, highlighting the processes regulating thrombocyte maturation. Future knockdown studies of these young and mature thrombocyte-specific genes are feasible and will provide the basis for understanding megakaryocyte maturation.

Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish

“…We include the full lists of differentially expressed genes for all dot plots generated in this fashion as supplemental datasets: Tables S1 (adult thymus), S2 (adult and juvenile thymus), S5 (TECs), S13 (T and NK-like cells), and S15 (B cells). Additionally, we provide a summary table of the lineage defining genes mentioned in our results section and how they relate to past work in zebrafish and known mammalian lineage markers in Table S18 ( Agulleiro et al, 2010 ; Athanasiadis et al, 2017 ; Avagyan et al, 2021 ; Bachem et al, 2012 ; Bajoghli et al, 2009 ; Balla et al, 2010 ; Baracho et al, 2014 ; Baran-Gale et al, 2020 ; Baranov et al, 2016 ; Barbier et al, 2019 ; Baron et al, 2019 ; Barratt and Weitz, 2021 ; Bautista et al, 2021 ; Beetz et al, 2007 ; Ben-Moshe et al, 2010 ; Bhandari et al, 2016 ; Boller and Grosschedl, 2014 ; Bouwman et al, 2021 ; Brahler et al, 2018 ; Burda et al, 2010 ; Butko et al, 2015 ; Cadieux et al, 2005 ; Calvete, 1994 ; Carmona et al, 2017 ; Challen et al, 2014 ; Chan et al, 1997 ; Chen et al, 2021 ; Chong et al, 1995 ; Chopin et al, 2019 ; Dale and Topczewski, 2011 ; Danger et al, 2022 ; Danilova et al, 2005 ; De Decker et al, 2021 ; Dee et al, 2016 ; Di et al, 2017 ; Donovan et al, 2013 ; Ellmeier et al, 2013 ; Fallatah et al, 2022 ; Farahani and Xaymardan, 2015 ; Ferrero et al, 2020 ; Fu et al, 2009 ; Ganis et al, 2012 ; Garcia et al, 2018 ; ...…”

Role of MicroRNAs and their Downstream Target Transcription Factors in Zebrafish Thrombopoiesis

“…Piggyback hybrid knockdowns of microRNAs in adult zebra sh and estimation of total thrombocyte counts Previous work from our laboratory has identi ed genes expressed in zebra sh thrombocytes through RNASeq analysis by 10X genomic sequencing to identify the genes involved in thrombocyte differentiation and function (24). Fifteen miRNA genes were found among these expressed genes (mir-101a, mir-29b-1, mir-451a, mir-7148, let-7a-5, let-7ba-6, let-7b, let-7g-1, mir-144, mir-223, mir-142a, mir-30b, mir-16b, mir-457b, and mir-142b).…”

Role of microRNAs and their downstream target transcription factors in zebrafish thrombopoiesis

“…Previous work from our laboratory has identified genes expressed in zebrafish thrombocytes through RNASeq analysis by 10X genomic sequencing to identify the genes involved in thrombocyte differentiation and function 24 . A total of fifteen miRNA genes were found among these expressed genes ( mir-101a, mir-29b-1, mir-451a, mir-7148, let-7a-5, let-7ba-6, let-7b, let-7g-1, mir-144, mir-223, mir-142a, mir-30b, mir-16b, mir-457b, and mir-142b ).…”