Introduction: The Long-ncRNAs (LncRNAs) exert an important role in several biological functions by regulating gene expression at the transcriptional and post transcriptional levels. The role of LncRNAs in cancer and, more recently, in the immune response has been identified. Our study aims to characterize the LncRNAs modulated in LPS-activated human neutrophils (PMN) and monocytes and to discover their role in PMN and monocyte functions. Methods: RNA-seq analysis was performed on RNA from human CD14+ monocytes and high-pure PMN stimulated or not with LPS for 90min and 4h. Data were aligned on reference genome using TopHat and differential gene expression analysis was performed using DESeq2. Results and Conclusion: LPS modulates the expression of 1960 and 1136 LncRNAs in monocytes and PMN respectively, among which 180 LncRNAs in monocytes and 36 LncRNAs in PMN were de novo induced. Kinetic analysis of LncRNA transcriptome led to the identification of the following three classes: (i) Early, which includes LncRNAs whose expression rapidly increased by 90min following LPS stimulation; (ii) Early and transient, which includes those early LncRNAs whose expression returns to the basal level by 4h; (iii) Late, which includes LncRNAs whose expression is detectable after 4h of LPS stimulation. Additionally, enhancer-derived and canonical LncRNAs were identified based on H3K4me3 and H3K4me1 ChIP-seq analysis. Finally, all protein coding genes in cis to LPS-modulated LncRNAs were grouped based on GO Term Enrichment. This analysis shows a strong enrichment of GO terms related to inflammation, immune cell activation and regulation of signal transduction in both cell types. RNA-seq-based transcriptome analysis of resting and LPS-stimulated PMNs and monocytes allowed us to recognise classes of LncRNAs on the basis of different kinetic behaviour and/or their predicted genome localization and on their GO term-based functional role.
Identification and characterization of long noncoding RNAs in primary human monocytes and neutrophils.
Barbara Mariotti;Francisco Bianchetto;Nicola Tamassia;Marco A. Cassatella;Flavia Bazzoni.
2015-01-01
Abstract
Introduction: The Long-ncRNAs (LncRNAs) exert an important role in several biological functions by regulating gene expression at the transcriptional and post transcriptional levels. The role of LncRNAs in cancer and, more recently, in the immune response has been identified. Our study aims to characterize the LncRNAs modulated in LPS-activated human neutrophils (PMN) and monocytes and to discover their role in PMN and monocyte functions. Methods: RNA-seq analysis was performed on RNA from human CD14+ monocytes and high-pure PMN stimulated or not with LPS for 90min and 4h. Data were aligned on reference genome using TopHat and differential gene expression analysis was performed using DESeq2. Results and Conclusion: LPS modulates the expression of 1960 and 1136 LncRNAs in monocytes and PMN respectively, among which 180 LncRNAs in monocytes and 36 LncRNAs in PMN were de novo induced. Kinetic analysis of LncRNA transcriptome led to the identification of the following three classes: (i) Early, which includes LncRNAs whose expression rapidly increased by 90min following LPS stimulation; (ii) Early and transient, which includes those early LncRNAs whose expression returns to the basal level by 4h; (iii) Late, which includes LncRNAs whose expression is detectable after 4h of LPS stimulation. Additionally, enhancer-derived and canonical LncRNAs were identified based on H3K4me3 and H3K4me1 ChIP-seq analysis. Finally, all protein coding genes in cis to LPS-modulated LncRNAs were grouped based on GO Term Enrichment. This analysis shows a strong enrichment of GO terms related to inflammation, immune cell activation and regulation of signal transduction in both cell types. RNA-seq-based transcriptome analysis of resting and LPS-stimulated PMNs and monocytes allowed us to recognise classes of LncRNAs on the basis of different kinetic behaviour and/or their predicted genome localization and on their GO term-based functional role.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
