Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations

Hematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by...

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Bibliographic Details
Published in:Genes 2019-03, Vol.10 (4), p.253
Main Authors: Deslattes Mays, Anne, Schmidt, Marcel, Graham, Garrett, Tseng, Elizabeth, Baybayan, Primo, Sebra, Robert, Sanda, Miloslav, Mazarati, Jean-Baptiste, Riegel, Anna, Wellstein, Anton
Format: Article
Language:English
Subjects:
Alternative Splicing - genetics
Bone composition
Bone marrow
Bone Marrow Cells - metabolism
Cell differentiation
Cell Lineage - genetics
Chromatography
Gene regulation
Genes
Genomes
Genomics - methods
Hemopoiesis
High-Throughput Nucleotide Sequencing
Humans
Isoforms
Mass spectrometry
Mass spectroscopy
Population
Progenitor cells
Proteins
RNA, Messenger - genetics
Scientific imaging
Single Molecule Imaging - methods
SMRT protein
Stem cells
Transcription
Transcriptome - genetics
Transcriptomes
Whole Exome Sequencing - methods
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Summary:Hematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single-molecule real-time (SMRT) full-length RNA-sequencing. This analysis revealed a ~5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of messenger RNA (mRNA) isoforms transcribed from the and loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was evaluated by mass spectrometry and validated previously unknown protein isoforms predicted e.g., for . These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g., , , , , and ) also distinguished cell subpopulations but were only detectable by full-length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes10040253