NDLI: Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages

Content Provider	Springer Nature : BioMed Central
Author	Mao, Ai-Ping Shen, Jun Zuo, Zhixiang
Abstract	Background Though long non-coding RNAs (lncRNAs) are emerging as critical regulators of immune responses, whether they are involved in LPS-activated TLR4 signaling pathway and how is their expression regulated in mouse macrophages are still unexplored. Results By repurposing expression microarray probes, we identified 994 lncRNAs in bone marrow-derived macrophages (BMDMs) and classified them to enhancer-like lncRNAs (elncRNAs) and promoter-associated lncRNAs (plncRNAs) according to chromatin signatures defined by relative levels of H3K4me1 and H3K4me3. Fifteen elncRNAs and 12 plncRNAs are differentially expressed upon LPS stimulation. The expression change of lncRNAs and their neighboring protein-coding genes are significantly correlated. Also, the regulation of both elncRNAs and plncRNAs expression is associated with H3K4me3 and H3K27Ac. Crucially, many identified LPS-regulated lncRNAs, such as lncRNA-Nfkb2 and lncRNA-Rel, locate near to immune response protein-coding genes. The majority of LPS-regulated lncRNAs had at least one binding site among the transcription factors p65, IRF3, JunB and cJun. Conclusions We established an integrative microarray analysis pipeline for profiling lncRNAs. Also, our results suggest that lncRNAs can be important regulators of LPS-induced innate immune response in BMDMs.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-015-1270-5.pdf
Ending Page	14
Page Count	14
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-015-1270-5
Journal	BMC Genomics
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-02-05
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics TLR4 LPS elncRNA plncRNA Histone modification
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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