Identification of differentially expressed transcripts and translatants targeted by knock-down of endogenous PCBP1

• Published in: Biochimica et biophysica acta Vol. 1804; no. 10; pp. 1954 - 1964
• Main Authors: Huo, Li-Rong, Ju, Weina, Yan, Ming, Zou, Jun-Hua, Yan, Wu, He, Bing, Zhao, Xin-Liang, Jenkins, Edmund C., Brown, W. Ted, Zhong, Nanbert
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2010
• Subjects: Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Blotting, Western; Electrophoresis, Gel, Two-Dimensional; Gene Expression Profiling; Gene Knockdown Techniques; Heterogeneous-Nuclear Ribonucleoproteins - antagonists & inhibitors; Heterogeneous-Nuclear Ribonucleoproteins - genetics; Heterogeneous-Nuclear Ribonucleoproteins - metabolism; Histone proteins; Humans; Neuroblastoma - genetics; Neuroblastoma - metabolism; Neuroblastoma - pathology; Oligonucleotide Array Sequence Analysis; PCBP1; Reverse Transcriptase Polymerase Chain Reaction; RNA interference; RNA, Messenger - genetics; RNA, Small Interfering - pharmacology; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Transcriptional profile; Translational profile; Tumor Cells, Cultured; Histone proteins; RNA interference; Transcriptional profile; PCBP1; Translational profile
• ISSN: 1570-9639; 0006-3002; 1878-1454
• DOI: 10.1016/j.bbapap.2010.07.002

PCBP1 is a member of the hnRNP family and participates in the regulation of transcription and translation. Previously, we identified transcripts targeted by overexpression of exogenous PCBP1. To further determine if these altered transcripts may also be targeted by a lack of PCBP1, we depleted endogenous PCBP1 in human SH-SY5Y cells. We identified 941 transcripts with the Affymetrix and 1362 with the Agilent expression platforms. There were 375 transcripts identified by both platforms, including 328 down-regulated and 47 up-regulated. The identified transcripts could be grouped into neuronal, cell signaling, metabolic, developmental, and differentiation categories, with pathway involvement in Wnt signaling, TGF beta signaling, translation factors and nuclear receptors. A proteomic profiling study with a two-dimensional chromatographic platform showed global translational changes over a range of isoelectric points (pI) = 4.84–8.42. This study identifies the transcripts affected by knock-down of endogenous PCBP1 and compares them to the transcripts affected by overexpression of PCBP1. This study determined transcripts targeted by a lack of PCBP1. We identified 941 transcripts with the Affymetrix and 1,362 with the Agilent expression platforms. There were 375 transcripts identified by both platforms, including 328 downregulated and 47 up-regulated. The identified transcripts are grouped into neuronal, cell signaling, metabolic, developmental, and differentiation categories, with pathway involvement in Wnt signaling, TGF beta signaling, translation factors and nuclear receptors. A proteomic profiling study with a two-dimensional chromatographic platform showed global translational changes over a range of isoelectric poits (pI) = 4.84-8.42.