Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis.

Yongqing Lan,Meng Li,Shuangli Mi

doi:10.3390/genes12050630

Abstract

Hematopoietic differentiation is a well-orchestrated process by many regulators such as transcription factor and long non-coding RNAs (lncRNAs). However, due to the large number of lncRNAs and the difficulty in determining their roles, the study of lncRNAs is a considerable challenge in hematopoietic differentiation. Here, through gene co-expression network analysis over RNA-seq data generated from representative types of mouse myeloid cells, we obtained a catalog of potential key lncRNAs in the context of mouse myeloid differentiation. Then, employing a widely used in vitro cell model, we screened a novel lncRNA, named Gdal1 (Granulocytic differentiation associated lncRNA 1), from this list and demonstrated that Gdal1 was required for granulocytic differentiation. Furthermore, knockdown of Cebpe, a principal transcription factor of granulocytic differentiation regulation, led to down-regulation of Gdal1, but not vice versa. In addition, expression of genes involved in myeloid differentiation and its regulation, such as Cebpa, were influenced in Gdal1 knockdown cells with differentiation blockage. We thus systematically identified myeloid differentiation associated lncRNAs and substantiated the identification by investigation of one of these lncRNAs on cellular phenotype and gene regulation levels. This study promotes our understanding of the regulation of myeloid differentiation and the characterization of roles of lncRNAs in hematopoietic system.

Highlights

Under this model of hematopoietic development, blockage in the myeloid differentiation at different stage could result in an accumulation of different immature myeloid cells in the bone marrow and peripheral blood, which is usually manifested by myeloid leukemia, leading to the concept that differentiation arrest is a causative event in malignant transformation [9]
We explored the involvement of long non-coding RNAs (lncRNAs) in the context of mouse myeloid differentiation by gene co-expression network analysis
Database and ArrayExpress database (E-MTAB-3079 and E-MTAB-2923). These types of cells were purified from mouse bone marrow as follows: c-Kit+ bone marrow cells (BMCs) were sorted by c-Kit+, hematopoietic stem cells (HSCs) were sorted by Lin−Sca1+ckit+, common myeloid progenitors (CMPs) were sorted by Lin−CD127−Sca1−c-Kit+CD16/32 lowCD34+, precursor for myeloid-macrophage progenitors (PreGMPs) were sorted by Lin−Sca1−c-kit+CD150−CD105−CD41−CD16/32−, granulocyte–macrophage progenitors (GMPs) were sorted by Lin−CD127−Sca1−c-Kit+CD16/32highCD34+, granulocytes were sorted by Gr-1+Mac-1+CD3−CD4−CD8−IgM−Ter119−, monocytes were sorted by Gr1mediumMac-1+CFMS+CD3−CD4−CD8−IgM−Ter119−, and macrophages were sorted by CD45+F4/80+CD31−Ter119−7AAD− [13,14,29]

Summary

Introduction

The production of GMPs from CMPs is directed by C/EBPα [5,6], and C/EBPε is required for the generation of mature myeloid cells from GMPs [7,8]. Under this model of hematopoietic development, blockage in the myeloid differentiation at different stage could result in an accumulation of different immature myeloid cells in the bone marrow and peripheral blood, which is usually manifested by myeloid leukemia, leading to the concept that differentiation arrest is a causative event in malignant transformation [9]. The mouse bone marrow cells derived cell model expressing an inducible MLL fusion protein such as MLL-ENL has been widely used to study myeloid differentiation or malignant transformation by many research groups given its ease of manipulation [11,12,13,14]

Methods

Results

Conclusion