Genome-wide analysis of thapsigargin-induced microRNAs and their targets in NIH3T3 cells.
Disruption of the endoplasmic reticulum (ER) homeostasis is the cause of ER stress. We performed microRNA (miRNA) analysis (deep sequencing) to search for coping responses (including signaling pathways) induced by disrupted ER Ca(2 +) homeostasis. Our focus was on a specific branch of UPR namely the bi-functional protein kinase/endoribonuclease inositol-requiring element 1α (IRE1α). Activated IRE1α undergoes autophosphorylation and oligomerization, leading to the activation of the endoribonuclease domain and splicing of the mRNA encoding XBP1 specific transcription factor. This processing changes the coding reading frame, producing a potent transcription factor termed XBP1s. We utilized the XBP1 splicing luciferase reporter to screen for modulators of the IRE1α branch of the unfolded protein response (UPR). Here, we describe a detailed experimental design and bioinformatics analysis of ER Ca(2 +) depletion (thapsigargin treated)-induced microRNA (deep sequencing) profile. The data can be access at the Gene Expression Omnibus (GEO), the National Center for Biotechnology Information (NCBI), reference number GSE57138.
Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S7, Canada.
Jody
J
Groenendyk
Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada.
Xiao
X
Fan
Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada.
Zhenling
Z
Peng
Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
Yaroslav
Y
Ilnytskyy
Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada.
Lukasz
L
Kurgan
Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S7, Canada.
Marek
M
Michalak
Bioinformatics; Endoplasmic reticulum stress; MicroRNA; Unfolded protein response