Fig. 2: MALNC is a non-coding RNA specifically expressed in bone marrow.

A In silico coding probability prediction of currently annotated lncRNA LOC105370601 and the longer MALNC RNA transcript in comparison to well-investigated coding (TNF, POLR2A, GAPDH, AKT1, TBP) and non-coding (HOTAIR, PANDAR, MEG3, XIST, NEAT1, HOTTIP, MALAT1, CRNDE, GAS5, UCA1, CCAT1) RNA transcripts. Coding probability was determined by CPAT web tool application (Coding Potential Assessment tool, coding cut-off >0.364). B Non-coding potential of MALNC was determined by its association with ribosomes. Cell lysates from HL60 cells were analyzed by 15–50% sucrose density gradient fractionation. RNA was extracted from each gradient fraction and expression of ACTB RNA, spike Luciferase RNA (Luc) and MALNC RNA was determined by RT-qPCR. (Top) Sucrose gradient absorbance profile (254 nm) from HL60 cells indicating the localization of free RNA, ribosomal subunits (40S and 60S), monosomes (80S) and polysomes along the sampled sucrose gradient fractions (1–13). One representative absorbance profile is shown. (Bottom) Bar charts presenting the distribution of co-sedimented ACTB, Luc and MALNC RNA transcripts in HL60 from each sucrose gradient fraction as percent from total RNA detected by RT-qPCR. Data is shown as mean with SEM of 3–4 fractionations and was normalized to spiked-in XENO RNA. C RNA expression of lncRNA LOC105370601 (RPKM, Total RNA-seq) in 16 different normal tissue types (Illumina bodyMap2 transcriptome data, BioProject: RJEB2445). D Level of RNA from nuclear and cytoplasmic fractions in HL60 cells. Data are shown from three biological experiments. MALNC localization was compared to ACTB RNA, which is predominantly exported to the cytoplasm, and U6 RNA, which is predominantly located in the nuclear compartment.