Proteomic and network analysis of proteins regulated by REX1 in human embryonic stem cells.
Recent studies have suggested that REX1 (reduced expression 1) plays an important role in pluripotency, proliferation, and differentiation. However, the molecular mechanisms involved in REX1-dependent regulation of diverse cellular processes remain unclear. To elucidate the regulatory functions of REX1 in human embryonic stem cells (hESCs), comparative proteomic analysis was performed on REX1 RNAi specifically silenced hESCs. Analysis of the proteome via nano-LC-MS/MS identified 140 differentially expressed proteins (DEPs) displaying a >2-fold difference in expression level between control and REX1 knockdown (KD) hESCs, which were then compared with transcriptome data and validated by quantitative real-time RT-PCR and Western blotting. These DEPs were analyzed by GO, pathway, and functional clustering analyses to determine the molecular functions of the proteins and pathways regulated by REX1. The REX1 KD-mediated DEPs mapped to major biological processes involved in the regulation of ribosome-mediated translation and mitochondrial function. Functional network analysis revealed a highly interconnected network among these DEPs and indicated that these interconnected proteins are predominantly involved in translation and the regulation of mitochondrial organization. These findings regarding REX1-mediated regulatory network have revealed the contributions of REX1 to maintaining the status of hESCs and have improved our understanding of the molecular events that underlie the fundamental properties of hESCs.
Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahangno, Yuseong-gu, Daejeon, Republic of Korea.|Department of functional genomics, University of Science & Technology, Gajungro, Yuseong-gu, Daejeon, Republic of Korea.
Mi-Young
MY
Son
Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahangno, Yuseong-gu, Daejeon, Republic of Korea.
Jae Eun
JE
Kwak
Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahangno, Yuseong-gu, Daejeon, Republic of Korea.
Young-Dae
YD
Kim
Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahangno, Yuseong-gu, Daejeon, Republic of Korea.|Department of functional genomics, University of Science & Technology, Gajungro, Yuseong-gu, Daejeon, Republic of Korea.
Yee Sook
YS
Cho
D015153:Blotting, Western; D000066449:Human Embryonic Stem Cells / Q000378:metabolism*; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D034622:RNA Interference
D051741:Kruppel-Like Transcription Factors; C507976:ZFP42 protein, human
Cell biology; Human embryonic stem cells; Pluripotency; Quantitative proteomics; REX1