Transcriptome dynamics during human erythroid differentiation and development

Yadong Yang; Hai Wang; Kai Hsin Chang; Hongzhu Qu; Zhaojun Zhang; Qian Xiong; Heyuan Qi; Peng Cui; Qiang Lin; Xiuyan Ruan; Yaran Yang; Yajuan Li; Chang Shu; Quanzhen Li; Edward K. Wakeland; Jiangwei Yan; Songnian Hu; Xiangdong Fang

doi:10.1016/j.ygeno.2013.09.005

Transcriptome dynamics during human erythroid differentiation and development

Yadong Yang, Hai Wang, Kai Hsin Chang, Hongzhu Qu, Zhaojun Zhang, Qian Xiong, Heyuan Qi, Peng Cui, Qiang Lin, Xiuyan Ruan, Yaran Yang, Yajuan Li, Chang Shu, Quanzhen Li, Edward K. Wakeland, Jiangwei Yan, Songnian Hu^*, Xiangdong Fang

^*Corresponding author for this work

Biological, Environmental Sciences and Engineering

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expressed genes decreased during differentiation, whereas the total expression intensity increased. At each of the three transitions (HESCs-ESERs, ESERs-FLERs, and FLERs-PBERs), many differentially expressed genes were observed, which were involved in maintaining pluripotency, early erythroid specification, rapid cell growth, and cell-cell adhesion and interaction. We also discovered dynamic networks and their central nodes in each transition. Our study provides a fundamental basis for further investigation of erythroid differentiation and development, and has implications in using ESERs for transfusion product in clinical settings.

Original language	English (US)
Pages (from-to)	431-441
Number of pages	11
Journal	Genomics
Volume	102
Issue number	5-6
DOIs	https://doi.org/10.1016/j.ygeno.2013.09.005
State	Published - Nov 2013

Bibliographical note

Funding Information:
The authors thank Dr. Yuxia Jiao for critically reading the manuscript. This research was supported by the “Strategic Priority Research Program” of the Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Research ( XDA01040405 to X.F.); the National Key Scientific Instrument and Equipment Development Projects of China ( 2011YQ03013404 to X.F.); the National Basic Research Program (973 Program) ( 2006CB910403 to S.H.); the National Natural Science Foundation of China ( 31371300 to Z.Z. and 31100924 to Y.L.); and the National Institute of Health grants of United States ( DK077864 to K-H.C.).

Keywords

Cell differentiation
Development
Erythropoiesis
Gene regulatory networks
High-throughput RNA sequencing

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2013.09.005

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title = "Transcriptome dynamics during human erythroid differentiation and development",

abstract = "To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expressed genes decreased during differentiation, whereas the total expression intensity increased. At each of the three transitions (HESCs-ESERs, ESERs-FLERs, and FLERs-PBERs), many differentially expressed genes were observed, which were involved in maintaining pluripotency, early erythroid specification, rapid cell growth, and cell-cell adhesion and interaction. We also discovered dynamic networks and their central nodes in each transition. Our study provides a fundamental basis for further investigation of erythroid differentiation and development, and has implications in using ESERs for transfusion product in clinical settings.",

keywords = "Cell differentiation, Development, Erythropoiesis, Gene regulatory networks, High-throughput RNA sequencing",

author = "Yadong Yang and Hai Wang and Chang, {Kai Hsin} and Hongzhu Qu and Zhaojun Zhang and Qian Xiong and Heyuan Qi and Peng Cui and Qiang Lin and Xiuyan Ruan and Yaran Yang and Yajuan Li and Chang Shu and Quanzhen Li and Wakeland, {Edward K.} and Jiangwei Yan and Songnian Hu and Xiangdong Fang",

note = "Funding Information: The authors thank Dr. Yuxia Jiao for critically reading the manuscript. This research was supported by the “Strategic Priority Research Program” of the Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Research ( XDA01040405 to X.F.); the National Key Scientific Instrument and Equipment Development Projects of China ( 2011YQ03013404 to X.F.); the National Basic Research Program (973 Program) ( 2006CB910403 to S.H.); the National Natural Science Foundation of China ( 31371300 to Z.Z. and 31100924 to Y.L.); and the National Institute of Health grants of United States ( DK077864 to K-H.C.).",

year = "2013",

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doi = "10.1016/j.ygeno.2013.09.005",

language = "English (US)",

volume = "102",

pages = "431--441",

journal = "Genomics",

issn = "0888-7543",

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T1 - Transcriptome dynamics during human erythroid differentiation and development

AU - Yang, Yadong

AU - Wang, Hai

AU - Chang, Kai Hsin

AU - Qu, Hongzhu

AU - Zhang, Zhaojun

AU - Xiong, Qian

AU - Qi, Heyuan

AU - Cui, Peng

AU - Lin, Qiang

AU - Ruan, Xiuyan

AU - Yang, Yaran

AU - Li, Yajuan

AU - Shu, Chang

AU - Li, Quanzhen

AU - Wakeland, Edward K.

AU - Yan, Jiangwei

AU - Hu, Songnian

AU - Fang, Xiangdong

N1 - Funding Information: The authors thank Dr. Yuxia Jiao for critically reading the manuscript. This research was supported by the “Strategic Priority Research Program” of the Chinese Academy of Sciences, Stem Cell and Regenerative Medicine Research ( XDA01040405 to X.F.); the National Key Scientific Instrument and Equipment Development Projects of China ( 2011YQ03013404 to X.F.); the National Basic Research Program (973 Program) ( 2006CB910403 to S.H.); the National Natural Science Foundation of China ( 31371300 to Z.Z. and 31100924 to Y.L.); and the National Institute of Health grants of United States ( DK077864 to K-H.C.).

PY - 2013/11

Y1 - 2013/11

N2 - To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expressed genes decreased during differentiation, whereas the total expression intensity increased. At each of the three transitions (HESCs-ESERs, ESERs-FLERs, and FLERs-PBERs), many differentially expressed genes were observed, which were involved in maintaining pluripotency, early erythroid specification, rapid cell growth, and cell-cell adhesion and interaction. We also discovered dynamic networks and their central nodes in each transition. Our study provides a fundamental basis for further investigation of erythroid differentiation and development, and has implications in using ESERs for transfusion product in clinical settings.

AB - To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expressed genes decreased during differentiation, whereas the total expression intensity increased. At each of the three transitions (HESCs-ESERs, ESERs-FLERs, and FLERs-PBERs), many differentially expressed genes were observed, which were involved in maintaining pluripotency, early erythroid specification, rapid cell growth, and cell-cell adhesion and interaction. We also discovered dynamic networks and their central nodes in each transition. Our study provides a fundamental basis for further investigation of erythroid differentiation and development, and has implications in using ESERs for transfusion product in clinical settings.

KW - Cell differentiation

KW - Development

KW - Erythropoiesis

KW - Gene regulatory networks

KW - High-throughput RNA sequencing

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U2 - 10.1016/j.ygeno.2013.09.005

DO - 10.1016/j.ygeno.2013.09.005

M3 - Article

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AN - SCOPUS:84890121384

SN - 0888-7543

VL - 102

SP - 431

EP - 441

JO - Genomics

JF - Genomics

IS - 5-6

ER -

Transcriptome dynamics during human erythroid differentiation and development

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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