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Transcriptome and epigenome in the cortical neurons transfected with Gata1

ABSTRACT: Gata1, a member of the GATA transcription factor family, has been considered as an important factor in the hematopoietic system. As a transcriptional regulator, Gata1 has a crucial role in differentiation of blood cells such as erythrocytes, megakaryocytes, eosinophils, and dendritic cells. Recently, a novel function of Gata1 has been demonstrated in the central nervous system. Gata1, a stress-inducible gene in the brain, has been shown to increase the expression in the dorsolateral prefrontal cortex of patients with depression and function as a transcriptional repressor of synapse-related genes. In this study, we investigated the global alteration in gene expression by Gata1 using ChIPseq, mRNAseq, and smallRNAseq. From the result of ChIPseq for histone marks H3K4me3 and H3K27me3, we have identified 1127 and 4881 unique peaks respectively in the gene promoter region in the cultured cortical neurons overexpressed with Gata1 compared to the control. We also identified 113 differentially expressed mRNAs and 82 miRNAs in cultured neurons transfected with Gata1 through the mRNAseq and smallRNAseq. Through the three-sequencing data analysis, we have profiled genes that might be affected by Gata1 in the cultured cortical neurons. Gene ontology (GO) analysis revealed that Gata1 might be associated with the immune-related function. These results will provide a better understanding of the regulatory mechanisms of Gata1 that affects the pathophysiological status, such as depression.

ORGANISM(S): Mus musculus

PROVIDER: GSE181679 | GEO | 2024/08/06

REPOSITORIES: GEO

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Project description:The 3' untranslated region (3'UTR) of mRNA plays several important roles in post-transcriptional gene regulation. Some of its functions include regulating mRNA stability by polyadenylation and microRNAs. However, the overall function of the Gata1 3’UTR in mammals has not been defined. In this study, we used CRISPR/CAS9 technology to knock out the sequence of the mouse Gata1 3’UTR. We found a defect in erythropoiesis in mutant mice, evidenced by macrocytic anemia at the baseline. Ablation of Gata1 3’UTR also resulted in a reduced number of erythroid precursors that might be associated with the cell cycle, especially G2/M disruption in fetal livers. Mechanistically, deletion of the Gata1 3’UTR destabilizes the Gata1 mRNA and ultimately reduces Gata1 protein levels. The low stability of the Gata1 mRNA is unlikely to be caused by the loss of binding of microRNAs or lack of polyadenylation; rather, in part, by the dissociation of AU-rich elements in the 3’UTR with a trans-activating factor Elavl1. Specifically, we transcribed Gata1 3’UTR in vitro and performed an RNA pulldown assay followed by mass spectrometry to profile the proteins that bind the 3’UTR. Gene Ontology analysis demonstrated that several proteins specifically targeting the 3’UTR were found to potentially bind Gata1 3’UTR, among which Elavl1 was in almost all categories related to mRNA stabilization. Western blotting and RNA immunoprecipitation confirmed the direct interaction of Gata1 3’UTR with Elavl1. Manipulation of Elavl1 activity and protein levels by the small molecule inhibitor Dihydro-tanshinone-I and Elavl1 overexpression in fetal liver erythroblasts confirmed Elavl1 as a stabilizing factor for Gata1 mRNA. Our findings shed light on the functional significance of the 3’UTR of Gata1 mRNA in the context of erythroid development. More importantly, our findings highlight the complexity and diversity of regulatory mechanisms that govern Gata1 mRNA stability and precise expression at the post-transcriptional levels. In addition, our findings prove that miRNAs are not always essential in vivo for controlling transcription factor levels to maintain body homeostasis.

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Transcriptome and epigenome in the cortical neurons transfected with Gata1

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