Finding lncRNAs in bone marrow and fetal liver erythroid progenitor cells in mice

Abstract

Red blood cell development is crucial to the survival of all mammals and occurs primarily in the liver during embryogenesis and then in the bone marrow during adulthood. In spite of the different microenvironments of the liver and bone marrow, current research shows that the majority of protein-coding genes important to crythropoiesis are expressed during both the fetal and adult developmental stage and the difference between red blood cells from the two stages remains unknown. Differences in the expression of long non-coding genes, which are more tissue and developmental stage specific than coding genes, may play a role in the production of red blood cells in the two tissues but also have not been studied. In this paper, we analyze RNA-seq, ChIP-seq, and DNase-seq experimental data in order to shed light on the differences and similarities in gene expression of both coding and non-coding genes, chromatin markings and promoter and enhancer activity, and transcription factor motifs between fetal and adult red blood cell progenitors. We find that solute carriers make up many of the differentially expressed genes, most notably Glut1, and that there is no clear difference in chromatin markings near transcription start sites of differentially expressed genes. Further work will analyze enriched transcription factor motifs inside DNase-I footprints generated in this work to determine which transcription factors may be responsible for differential gene expression.