Gene Regulatory Network Construction And Stage-specific Module Analysis In Erythropoiesis

Objectives: Erythropoiesis is a process by which the hematopoietic stem cells(HSCs)proliferate and differentiate to generate the mature red blood cells.It is precisely regulated by transcription factors.There are three stages of erythropoiesis: early erythropoiesis,terminal erythroid differentiation,and reticulocyte maturation.Dramatic phenotypic changes occur at different stages of erythropoiesis such as cell volume decreases,chromatin condensation,and increasing amounts of hemoglobin which are all accompanied by changes in gene expression.Complex interactions between transcription factors and their target genes vary at different stages.In order to understand the stage-specific transcriptional regulation at the system level in erythropoiesis,we constructed gene co-expression network of erythropoiesis based on RNA-seq data.In addition,we explored the network modules to distinguish key genes and their different distinct functions between early stage and terminal stage.Methods: Stage specific gene expression of cord blood and peripheral blood were calculated byFastQC,tophat,cuffquant,cuffdiff,cummeRbund processing procedures and filtered.Co-expression network was built by WGNCA.Network structure parameters such as degree,core,betweenness,closeness was calculated by Pajek.Network modules were used to compare between the early and terminal erythropiesis.Results: The gene co-expression network was constructedand hub geneswere identified,of which 30% had been verified by references.Four moduleswere stage-specific which include one early progenitor cell module and three late modules of terminal erythroid development.The early progenitor cell module consists of genes involved in the regulation of cell proliferation,differentiation and apoptosis pathways,including known erythropoiesis related genes such as PTPN6 and ETS2.The two terminal stage modules consists of different genes which share similar biological processes associated in regulating the autophagy,protein modification and ubiqutin-mediated processes.These related to erythroid cell maturation and cytoskeleton rearrangement.These two modules include known erythropoiesis related genes such as ULK1,AKT2,EIF4EBP2 and FOXO3.The third module of terminal stage including genes such as TAL1 and NFE2 are associated with regulation of chromatin organization,dephosphorylation,which are related to chromatin diversification and erythroid development.Conclusion: The co-expression network and module analysis showed that the early progenitor cell module was mainly about progenitor cells proliferation and differentiation,while the terminal erythroid modules were mainly about functions related to enucleation such as autophagy,chromatin condensation,and cytoskeleton rearrangement.This study greatly extends our knowledge on the gene regulatory network of early progenitor cell proliferation and the enucleation in erythropoiesis.In addition,it helps us to predict new regulatory genes which can be used to produce functional red blood cells from hematopoietic stem cell in vitro.