Predict Potential γ- And β-globin Gene Expression Regulators Based On Transcriptomics Analysis

Hematopoiesis is a process in which hematopoietic stem and progenitor cells gradually differentiate and mature into lymphocytes,macrophages,red blood cells,and other blood cells,under strict and fine regulation of the hematopoietic microenvironment and various regulatory factors.The site of hematopoietic development also changes during different stages of embryonic development.The yolk sac is the site of hematopoiesis in the early stages of embryonic development.The fetal liver is the hematopoietic site of the fetus and the bone marrow is the hematopoietic site of the fetus after birth.With the changes of hematopoietic sites,globin in erythrocytes have undergone significant changes in their expression at different stages of development.The P-globin gene cluster expresses the ε-globin gene during yolk sac hematopoiesis,and mainly expresses γ-globin during fetal liver hematopoiesis.In the bone marrow hematopoiesis before birth,the β-globin gene is gradually increased,and the y-globin gene expression is gradually decreased.After birth,β-globin gene is mainly expressed.The process is subject to strict spatial and temporal regulation,and is a complex and delicate process.(3-hemoglobinopathies(β-thalassemia and sickle cell anemia)due to mutations in the coding structure of adult β-globin genes or reduced expression levels are the largest single-gene inherited diseases in the world.In adulthood y-globin gene expression can relieve the symptoms of P-hemoglobin disease and achieve the purpose of treating β-hemoglobin disease.Therefore,the study of β-globin gene expression,especially the expression of γ-to β-switching,has great significance not only in basic research but also in clinical application.Currently it is known that KLF1 and BCL11A play major roles in the regulation ofγ-to β-globin gene switching.BCL11A is the major regulator of y-globin gene expression,and KLF1 is the main regulator of β-globin gene expression.In addition,KLF1 can also inhibit y-globin gene expression indirectly by activating the expression of BCL11A.However,knockout of KLF1 and BCL11A does not effectively turn on y-globin gene expression in adulthood,suggesting that more regulatory factors are involved in the expression of γ-to β-globin gene.This study is based on RNA-seq data analysis to predict potential regulatory factors regulating globin gene expression.Through the GEO database,we obtained RNA-seq data of erythroid cells which were derived from peripheral blood/fetal liver-originated CD34+ HSPCs and were induced to differentiate for 11 days and 14 days(Database 1).We also obtained RNA-seq data of erythroid cells which were derived from peripheral blood/umbilical cord-originated CD34+ HSPCs and were induced to differentiate into different stages(proerythroblast,early basophilic erythroblast,late basophilic erythroblast,polychromatophilic erythroblast,orthochromatic erythroblast)(Database 2).In view of that different globin genes are expressed in erythroid cells from different sources(in erythroid cells at all stages derived from peripheral blood,β-globin gene are mainly expressed,while in erythroid cells at all stages derived from fetal liver or umbilical cord,γ-globin genes are abundantly expressed),we compared the differential expression genes from different sources(for database 1 we compared peripheral blood/fetal liver;and for database 2 we compared peripheral blood/umbilical cord)at each stage,aiming to find differential expression genes associated with globin gene expression.We performed pathway analysis for differentially expressed genes at all stages.We found that the differentially expressed genes varies at different stages.After the intersection of differentially expressed genes at different stages,we obtained the differentially expressed genes that persisted in all stages.Through these genes and their upstream regulatory factors,we have predicted potential γ-and β-globin gene expression regulators.A total of 205 potential regulatory factors were predicted,of which the first three co-presence factors were MAPK1,TNF,and IFNG.