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Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

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Abstract

Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.

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Authors and Affiliations

  1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China

    Nan Ding, Yanming Li, Jian Shi, Zhaojun Zhang & Xiangdong Fang

  2. Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China

    Jiafei Xi, Xiaoyan Xie, Yanhua Li, Fang Fang, Sihan Wang, Wen Yue & Xuetao Pei

  3. University of Chinese Academy of Sciences, Beijing, 100049, China

    Nan Ding & Jian Shi

  4. South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China

    Jiafei Xi, Xiaoyan Xie, Yanhua Li, Fang Fang, Sihan Wang, Wen Yue & Xuetao Pei

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  1. Nan Ding
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  2. Jiafei Xi
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  3. Yanming Li
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  9. Sihan Wang
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  10. Wen Yue
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  11. Xuetao Pei
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Correspondence to Xuetao Pei or Xiangdong Fang.

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Ding, N., Xi, J., Li, Y. et al. Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation. Front. Med. 10, 297–310 (2016). https://doi.org/10.1007/s11684-016-0452-0

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