Comprehensive discovery of non-coding RNAs in acute myeloid leukemia cell transcriptomes.
Zhang J, Griffith M, Miller CA, Griffith OL, Spencer DH, Walker JR, Magrini V, McGrath SD, Ly A, Helton NM, Trissal M, Link DC, Dang HX, Larson DE, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Klco JM, Mardis ER, Ley TJ, Wilson RK, Maher CA
Exp Hematol in press 07/28/2017
To comprehensively detect diverse and novel RNA species, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method employing broader insert size selection. We analyzed the long non-coding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample we studied, then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associate with specific AML subtypes. Our study revealed the complexity of the non-coding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA based analyses.