Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Abstract

Key Points• Hundreds of lineage-specific lncRNAs are expressed during mouse and human erythropoiesis.• Most mouse erythroid lncRNAs are not expressed in human erythroblasts and vice versa, yet some appear to be functional.Mammals express thousands of long noncoding (lnc) RNAs, a few of which are known to function in tissue development. However, the entire repertoire of lncRNAs in most tissues and species is not defined. Indeed, most lncRNAs are not conserved, raising questions about function. We used RNA sequencing to identify 1109 polyadenylated lncRNAs expressed in erythroblasts, megakaryocytes, and megakaryocyte-erythroid precursors of mice, and 594 in erythroblasts of humans. More than half of these lncRNAs were unannotated, emphasizing the opportunity for new discovery through studies of specialized cell types. Analysis of the mouse erythro-megakaryocytic polyadenylated lncRNA transcriptome indicates that ∼75% arise from promoters and 25% from enhancers, many of which are regulated by key transcription factors including GATA1 and TAL1. Erythroid lncRNA expression is largely conserved among 8 different mouse strains, yet only 15% of mouse lncRNAs are expressed in humans and vice versa, reflecting dramatic speciesspecificity. RNA interference assays of 21 abundant erythroid-specific murine lncRNAs in primary mouse erythroid precursors identified 7 whose knockdown inhibited terminal erythroid maturation. At least 6 of these 7 functional lncRNAs have no detectable expression in human erythroblasts, suggesting that lack of conservation between mammalian species does not predict lack of

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

“…All samples were determined as biological replicates. RNA-seq reads were mapped using TopHat2 in a reference-assisted manner Kim et al 2013;Paralkar et al 2014). We used Cuffdiff2 ) to identify DE genes, using the following options: dispersion-method = per-condition, library-type = fr-firststrand, max-bundle-frags = 20000000, min-reps-for-js-test = 2, Àb for bias correction, and -M to mask globin transcripts.…”

“…The dynamic occupancy patterns for TAL1 and GATA1 were strongly associated with the expression response of presumptive target genes. We reexamined this issue using the RNA-seq data for G1E and G1E-ER4 + E2 cells Paralkar et al 2014) and employing EPUs for assigning presumptive gene targets. For each TAL1 OS, all genes with a TSS within the same EPU were considered as potential targets, and the fraction of those genes that were induced or repressed was computed.…”

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages

“…[18][19][20] Further, widespread IR was recently reported in cancer. 21,22 Intricate hematopoietic gene expression and alternative splicing programs exist in the related megakaryocyte (MK) and erythrocyte lineages, [23][24][25][26][27][28] and splicing-coupled NMD is observed during human erythropoiesis. 11 However, if IR occurs in the MK and erythroid lineages, whether it is distinct between these lineages, and how it is modulated during maturation is unknown.…”

Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

“…Recent evidence suggests that they are frequently cell-type specific, contribute important functions to numerous systems, [1][2][3][4][5][6][7] and may interact with known cancer genes such as EZH2. 8 Indeed, several well-described examples, such as HOTAIR 9 and ANRIL, 10 indicate that lncRNAs may be essential players in cancer biology, typically facilitating epigenetic gene repression through chromatin-modifying complexes.…”