TY - JOUR
T1 - Integrative analysis of DNA methylation and mRNA expression during differentiation of umbilical cord blood derived mononuclear cells to endothelial cells
AU - Jeong, Yoonjeong
AU - Jun, Yukyung
AU - Kim, Jihye
AU - Park, Hyojin
AU - Choi, Kyu Sung
AU - Zhang, Haiying
AU - Park, Jeong Ae
AU - Kwon, Ja Young
AU - Kim, Young Myeong
AU - Lee, Sanghyuk
AU - Kwon, Young Guen
N1 - Funding Information:
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology [ NRF-2015R1A2A1A05001859 ; NRF2013M3A9B6046563 ; NRF-2015K1A4A3047851 ; NRF-2015M3A9B6066967 ], by the Bio and Medical Technology Development Program of the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (MEST) [ NRF-2015M3A9B6066967 ], by a grant from the Korea Health 21 R&D Project, Ministry of Health and Welfare of the Republic of Korea [ H16C1501 ], and by the Technology Innovation Program of the Ministry of Trade, Industry and Energy , Republic of Korea [Grant 10050154 ].
Publisher Copyright:
© 2017 The Authors
PY - 2017/11/30
Y1 - 2017/11/30
N2 - Differentiation of umbilical cord blood derived mononuclear cells to endothelial cells is accompanied by massive changes in gene expression. Although methylation and demethylation of DNA likely play crucial roles in regulating gene expression, their interplay during differentiation remains elusive. To address this question, we performed deep sequencing of DNA methylation and mRNA expression to profile global changes in promoter methylation and gene expression during differentiation from mononuclear cells to outgrowing cells. We identified 61 downregulated genes with hypermethylation, including CD74, VAV1, TLR8, and NCF4, as well as 21 upregulated genes with hypomethylation, including ECSCR, MCAM, PGF, and ARHGEF15. Interestingly, gene ontology analysis showed that downregulated genes with hypermethylation were enriched in immune-related functions, and upregulated genes with hypomethylation were enriched in the developmental process and angiogenesis, indicating the important roles of DNA methylation in regulating differentiation. We performed polymerase chain reaction analyses and bisulfite sequencing of representative genes (CD74, VAV1, ECSCR, and MCAM) to verify the negative correlation between DNA methylation and gene expression. Further, inhibition of DNA methyltransferase and demethylase activities using 5′-aza-dc and shRNAs, specific for TET1 and TET2 mRNAs, respectively, revealed that DNA methylation was the main regulator of the reversible expression of functionally important genes. Collectively, our findings implicate DNA methylation as a critical regulator of gene expression during umbilical cord blood derived mononuclear cells to endothelial cell differentiation.
AB - Differentiation of umbilical cord blood derived mononuclear cells to endothelial cells is accompanied by massive changes in gene expression. Although methylation and demethylation of DNA likely play crucial roles in regulating gene expression, their interplay during differentiation remains elusive. To address this question, we performed deep sequencing of DNA methylation and mRNA expression to profile global changes in promoter methylation and gene expression during differentiation from mononuclear cells to outgrowing cells. We identified 61 downregulated genes with hypermethylation, including CD74, VAV1, TLR8, and NCF4, as well as 21 upregulated genes with hypomethylation, including ECSCR, MCAM, PGF, and ARHGEF15. Interestingly, gene ontology analysis showed that downregulated genes with hypermethylation were enriched in immune-related functions, and upregulated genes with hypomethylation were enriched in the developmental process and angiogenesis, indicating the important roles of DNA methylation in regulating differentiation. We performed polymerase chain reaction analyses and bisulfite sequencing of representative genes (CD74, VAV1, ECSCR, and MCAM) to verify the negative correlation between DNA methylation and gene expression. Further, inhibition of DNA methyltransferase and demethylase activities using 5′-aza-dc and shRNAs, specific for TET1 and TET2 mRNAs, respectively, revealed that DNA methylation was the main regulator of the reversible expression of functionally important genes. Collectively, our findings implicate DNA methylation as a critical regulator of gene expression during umbilical cord blood derived mononuclear cells to endothelial cell differentiation.
KW - DNA methylation
KW - Differentiation
KW - Endothelial cells
KW - Gene discovery
KW - MeDIP seq
KW - Promoter CpG islands
KW - RNA seq
KW - Umbilical cord blood derived mononuclear cell
UR - http://www.scopus.com/inward/record.url?scp=85031103190&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2017.09.006
DO - 10.1016/j.gene.2017.09.006
M3 - Article
C2 - 28887159
AN - SCOPUS:85031103190
SN - 0378-1119
VL - 635
SP - 48
EP - 60
JO - Gene
JF - Gene
ER -