scholarly journals Correction: Hu et al. Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27. Int. J. Mol. Sci. 2019, 20, 6207

2021 ◽  
Vol 22 (10) ◽  
pp. 5129
Author(s):  
Xiaojun Hu ◽  
Suranjana Goswami ◽  
Ju Qiu ◽  
Qian Chen ◽  
Sylvain Laverdure ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Human Macrophages ◽  
Interleukin 27 ◽  
Non Coding Rnas

The authors wish to make the following corrections to this paper [...]

99 Effects of Combined TLR Stimulation on Interleukin-27 mRNA Expression in Human Monocyte-derived Dendritic Cells

Cytokine ◽  
2007 ◽  
Vol 39 (1) ◽  
pp. 27
Author(s):  
Claudius U. Meyer ◽  
Doreen Krumbiegel ◽  
Helena Markus ◽  
Michaela Fuidl ◽  
Fred Zepp
Keyword(s):  
Dendritic Cells ◽  
Mrna Expression ◽  
Human Monocyte ◽  
Interleukin 27

scholarly journals Long non-coding RNA MALAT1 regulates BLCAP mRNA expression through binding to miR-339-5p and promotes poor prognosis in breast cancer

2019 ◽  
Vol 39 (2) ◽  
Author(s):  
Liuhong Zheng ◽  
Yuhan Zhang ◽  
Yajun Fu ◽  
Hangdi Gong ◽  
Jianjun Guo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mrna Expression ◽  
Ductal Carcinoma ◽  
The Cancer Genome Atlas ◽  
Clinical Samples ◽  
Non Coding Rna ◽  
Competitive Endogenous Rnas ◽  
Tumorigenesis And Progression ◽  
Non Coding Rnas ◽  
Cancer Tissues

AbstractThe human genome transcribes a large amount of non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs. LncRNAs and microRNAs have been shown to play a critical regulatory role in tumorigenesis and progression. Competitive endogenous RNAs (ceRNAs) affect other RNAs transcription through competitively binding to common microRNAs (miRNAs). MALAT1 is a typical lncRNA that is markedly up-regulated in breast cancer. However, current understanding of the involvement of MALAT1 in breast cancer development and prognosis remains unclear. In the present study, the expression of MALAT1 in clinical samples of breast cancer tissues was found to be significantly up-regulated that was consistent with the result based on the dataset of the Cancer Genome Atlas (TCGA) at cBioportal. A negative correlation between overall survival and the expression of MALAT1 was statistically significant in the group of diagnosis age below 60 or in the group of infiltrating ductal carcinoma analyzed by TCGA database, which declared that MALAT1 might be a potentially useful prognostic factor. Furthermore, the combination of bioinformatics prediction with experimental verifications indicated that lncRNA MALAT1 can regulate BLCAP mRNA expression through binding to miR-339-5p.

scholarly journals Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

2017 ◽  
Author(s):  
Sophie R Atkinson ◽  
Samuel Marguerat ◽  
Danny A Bitton ◽  
Maria Rodríguez-López ◽  
Charalampos Rallis ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Fission Yeast ◽  
Rna Processing ◽  
Non Coding Rna ◽  
Processing Pathways ◽  
Antisense Lncrnas ◽  
Nuclear Exosome ◽  
Non Coding Rnas ◽  
Functional Analyses ◽  
Long Non Coding Rna

AbstractTranscriptomes feature pervasive, but poorly defined long non-coding RNAs (lncRNAs). We identify 5775 novel lncRNAs in Schizosaccharomyces pombe, nearly 4-times the previously annotated lncRNAs. Most lncRNAs become derepressed under genetic and physiological perturbations, especially during late meiosis. These lncRNAs are targeted by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease and RNAi, with substantial coordination and redundancy among pathways. We classify lncRNAs into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease and RNAi repress thousands of meiotically induced RNAs. Antisense lncRNA and sense mRNA expression often negatively correlate in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. This broad survey of the S. pombe lncRNA repertoire and characteristics provides a rich resource for functional analyses.

Long non-coding RNAs are differentially expressed in dysferlinopathy (Preprint)

2021 ◽  
Author(s):  
Richa Singhal ◽  
Rachel Lukose ◽  
Gwenyth Carr ◽  
Afsoon Moktar ◽  
Eric C Rouchka ◽  
...  
Keyword(s):  
Network Analysis ◽  
Mrna Expression ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Disease Process ◽  
C2c12 Cells ◽  
Differentially Expressed ◽  
Aberrant Expression ◽  
Non Coding Rnas ◽  
Go Terms

BACKGROUND Long non-coding RNAs (lncRNAs) are non-coding RNA transcripts greater than 200 nucleotides in length and are known to play a role in regulating the transcription of genes involved in vital cellular functions. We hypothesized the disease process in dysferlinopathy is linked to an aberrant expression of lncRNAs and mRNAs. OBJECTIVE In this study, we compared the lncRNA and mRNA expression profiles between the normal and dysferlin deficient murine myoblasts (C2C12 cells). METHODS LncRNA and mRNA expression profiling were performed using a microarray. Several lncRNAs with differential expression were validated using quantitative real time polymerase chain reaction (qRT-PCR). Gene Ontology analysis was performed to understand the functional role of the differentially expressed mRNAs. Further bioinformatics analysis was used to explore the potential function, lncRNA-mRNA correlation and potential targets of the differentially expressed lncRNAs. RESULTS We found 3195 lncRNAs and 1966 mRNAs that are differentially expressed. The chromosomal distribution of the differentially expressed lncRNAs and mRNAs was unequal, with the chromosome 2 having the highest number of lncRNAs and chromosome 7 having the highest number of mRNAs that were differentially expressed. Pathway analysis of the differentially expressed genes indicated the involvement of several signaling pathways including PI3K-Akt, FoxO, Wnt, cAMP and Hippo. The differentially expressed genes were also enriched for the GO terms, developmental process and muscle system process. Network analysis identified 8 statistically significant (p<0.05) network objects from the upregulated lncRNAs and 3 statistically significant network objects from the downregulated lncRNAs. CONCLUSIONS Our results thus far imply that dysferlinopathy is associated with an aberrant expression of multiple lncRNAs many of which may have a specific function in the disease process. GO terms and Network Analysis suggest a muscle specific role for these lncRNAs. To elucidate the specific roles of these abnormally expressed non-coding RNAs, further studies engineering their expression are required.

Genome-Wide Profiling of Epigenetic and Transcription Factor Regulation In Human Macrophage Differentiation

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3875-3875
Author(s):  
Thu-Hang Pham ◽  
Monika Lichtinger ◽  
Chris Benner ◽  
Sabine Pape ◽  
Lucia Schwarzfischer ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Mrna Expression ◽  
Binding Sites ◽  
Cell Types ◽  
Human Macrophage ◽  
Macrophage Differentiation ◽  
Human Macrophages ◽  
Expression Levels

Abstract Abstract 3875 The differentiation of human macrophages is accompanied by distinctive phenotypical changes and generally proceeds in the absence of proliferation. The molecular events governing this process are still poorly understood. Using ChIP-Seq technology we studied epigenetic changes as well as alterations in transcription factor occupancy during human monocyte differentiation and correlated these events with gene expression levels in hematopoietic cell types. We show that putative enhancer regions marked by histone H3 lysine4 monomethylation (H3K4me1) at different developmental stages (human progenitor cells, peripheral blood monocytes and in vitro differentiated macrophages) are enriched in distinct sets of transcription factor motifs corresponding to lineage-determining factors. Cell stage-specific histone methylation at promoter-distal sites corresponds with increased mRNA expression levels of neighboring genes. We generated global DNA-binding maps in monocytes and macrophages for two transcription factors (PU.1 and C/EBPβ) with a well established role in monocyte/macrophage differentiation. Comparison of human binding sites with corresponding mouse data revealed a surprisingly low level of conservation (∼10-15%) of PU.1-or C/EBPβ -bound sites between man and mouse, despite a highly conserved binding preference for both transcription factors. During monocytic differentiation, human macrophages primarily gained additional binding sites for both transcription factors (as well as promoter-distal H3K4me1). Interestingly, only neighboring genes with multiple binding events showed significantly increased, macrophage-specific mRNA expression as compared to monocytic as well as lymphocytic cell types. Human macrophage-specific H3K4me1-marked regions as well as macrophage-specific PU.1- and C/EBP-bound sites were characterized by overlapping sets of novel sequence motifs, suggesting that the combinatorial interaction of corresponding DNA-binding factors with PU.1 and C/EBPβ may be required for the establishment of human macrophage-specific enhancers. These data provide novel insights into PU.1 and C/EBPβ mediated gene regulation during human macrophage differentiation. Disclosures: No relevant conflicts of interest to declare.

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