E-GEOD-49516 - Long Intergenic Non-Coding RNA HOTAIRM1 Regulates Cell Cycle Progression During Myeloid Maturation in NB4 Promyelocytic Leukemia Cells
Released on 30 April 2014, last updated on 6 May 2014
HOTAIRM1 is a long intergenic non-coding RNA located in the human HOXA gene cluster, with gene expression highly specific for maturing myeloid cells, particularly during all-trans retinoic acid (ATRA) induction of granolopoiesis in NB4, a human t(15;17) acute promyelocytic leukemia (APL) cell line. We sought to assess the impact of HOTAIR knockdown on the global programme of gene expression underlying the granulocytic maturing process in NB4 cells. The knockdown of HOTAIRM1 resulted in a less differentiated expression profile in the NB4 cells after 4 days of ATRA-induced granulocytic differentiation, with retained expression of many otherwise ATRA-suppressed cell cycle and DNA replication genes, as well as abated induction of cell surface leukocyte activation and defense response genes. The shRNA expressing vector targeting the HOTAIRM1 transcript and the control vector expressing scrambled shRNA sequence were generated based on the pLKO.3G vector backbone (Addgene). The stable cell lines derived from NB4 cells transfected with lentiviral vectors were selected by FACS sorting of GFP selection marker positive cells and isolation of single cell derived clones on soft agar plates. Biologically duplicated total RNA samples were prepared from HOTAIRM1 knockdown and the scrambled shRNA expressing control cells, plus one total RNA from each of wild type NB4 cells and HOTAIRM1 knockdown (by a different shRNA construct) cells, before and after 96 hours of ATRA (0.5 uM) induced granulocytic differentiation.
transcription profiling by array
Peter Newburger, Xueqing Zhang