Identification of intergenic transcript HOTAIRM1 within the HOXA cluster. (A) Transcription mapping of the human HOXA cluster in myeloid cell lines and mature neutrophils was performed on Affymetrix ENCODE tiling arrays; each panel (labeled with cell type and conditions) presents data from at least 3 biologic repeats. Pseudo-median signals are color scaled by P value, as indicated in the right margin, to highlight the significant TARs. The median point (threshold for positive) was set to P = 10−5, based on visual inspection of well-aligned HOXA1 signals in NB4 cells. (B) Alignment of the sequence of HOTAIRM1 (mapped by 5′- and 3′-RACE), spliced ESTs, and HG_U13 probe sets with the human genome sequence for the intergenic region between HOXA1 and HOXA2 in the March 2006 human reference sequence (NCBI Build 36.1). Also shown are primer sites used for ChIP-PCR amplification of HOTAIRM1 (5′ sequence “5HOTAIRM1” and 3′ sequence “3HOTAIRM1”) in experiments presented in Figure 3. (C) Northern blot analysis shows HOTAIRM1 as a 0.5-kb RNA in NB4 and HL-60 myeloid leukemia cells and in human peripheral blood neutrophils.
