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Single cell transcriptomics of noncoding RNAs and their cell-specificity.

ABSTRACT: Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA (ncRNA) are thought to be key parts of gene regulatory processes and their single cell expression patterns may help to dissect the biological function of single cell variability. Technology for measuring ncRNA in single cell is still in development and most of the current single cell datasets have reliable measurements for only long noncoding RNA (lncRNA). Most works report that lncRNAs show lineage-specific restricted expression patterns, which suggest that they might determine, at least in part, lineage fates and cell subtypes. However, evidence is still inconclusive as to whether lncRNAs and other ncRNAs are more lineage-specific than protein-coding genes. Nevertheless, measurement of ncRNAs in single cells will be important for studies of cell types and single cell function. WIREs RNA 2017, 8:e1433. doi: 10.1002/wrna.1433 For further resources related to this article, please visit the WIREs website.

SUBMITTER: Gawronski KAB

PROVIDER: S-EPMC5675046 | biostudies-other | 2017 Nov

REPOSITORIES: biostudies-other

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Single cell transcriptomics of noncoding RNAs and their cell-specificity.

Gawronski Katerina A B KAB Kim Junhyong J

Wiley interdisciplinary reviews. RNA 20170801 6

Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA (ncRNA) are thought to be key parts of gene regulatory pro ...[more]

PMID: 28762653

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Project description:In Epstein-Barr virus (EBV) latent infection, the EBV-encoded RNAs EBER1 and EBER2 accumulate in the host cell nucleus to ~10(6) copies. While the expression of EBERs in cell lines is associated with transformation, a mechanistic explanation of their roles in EBV latency remains elusive. To identify EBER-specific gene expression features, we compared the proteome and mRNA transcriptome from BJAB cells (an EBV-negative B lymphoma cell line) stably transfected with an empty plasmid or with one carrying both EBER genes. We identified ~1800 proteins with at least 2 SILAC pair measurements, of which only 8 and 12 were up- and downregulated ≥ 2-fold, respectively. One upregulated protein was PIK3AP1, a B-cell specific protein adapter known to activate the PI3K-AKT signaling pathway, which regulates alternative splicing and translation in addition to its pro-survival effects. In the mRNA-seq data, the mRNA levels for some of the proteins changing in the SILAC data did not change. We instead observed isoform switch events. We validated the most relevant findings with biochemical assays. These corroborated the upregulation of PIK3AP1 and AKT activation in BJAB cells expressing high levels of both EBERs and EBNA1 (a surrogate of Burkitt's lymphoma EBV latency I) relative to those expressing only EBNA1. The mRNA-seq data in these cells showed multiple upregulated oncogenes whose mRNAs are enriched for 3´-UTR AU-rich elements (AREs), such as ccl3, ccr7, il10, vegfa and zeb1. The CCL3, CCR7, IL10 and VEGFA proteins promote cell proliferation and are associated with EBV-mediated lymphomas. In EBV latency, ZEB1 represses the transcription of ZEBRA, an EBV lytic phase activation factor. We previously found that EBER1 interacts with AUF1 in vivo and proposed stabilization of ARE-containing mRNAs. Thus, the ~10(6) copies of EBER1 may promote not only cell proliferation due to an increase in the levels of ARE-containing genes like ccl3, ccr7, il10, and vegfa, but also the maintenance of latency, through higher levels of zeb1.

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Single cell transcriptomics of noncoding RNAs and their cell-specificity.

Publications

Single cell transcriptomics of noncoding RNAs and their cell-specificity.

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