Publication

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes.

Exp Hematol. 2017 Jul 28. pii: S0301-472X(17)30701-4. doi: 10.1016/j.exphem.2017.07.008. [Epub ahead of print]

Abstract

To detect diverse and novel RNA species comprehensively, 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 using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding 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.

Authors

Zhang J1, Griffith M2, Miller CA3, Griffith OL4, Spencer DH5, Walker JR6, Magrini V7, McGrath SD7, Ly A6, Helton NM5, Trissal M5, Link DC5, Dang HX1, Larson DE8, Kulkarni S9, Cordes MG6, Fronick CC6, Fulton RS6, Klco JM10, Mardis ER7, Ley TJ4, Wilson RK7, Maher CA11.