Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages.
Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages.
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DOI：
10.1186/s12864-015-1270-5
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发表时间：
2015-02-05
期刊：
影响因子：
4.4
通讯作者：
Zuo Z
中科院分区：
文献类型：
--
作者：
Mao AP;Shen J;Zuo Z
尽管长链非编码RNA（lncRNA）已成为免疫应答的重要调节因子，但它们是否参与LPS激活的TLR 4信号通路以及它们在小鼠巨噬细胞中的表达调控机制尚不清楚。通过重新利用表达微阵列探针，我们在骨髓源性巨噬细胞（BMDM）中鉴定了994种lncRNA，并根据H3 K4 me 1和H3 K4 me 3的相对水平定义的染色质特征将其分为增强子样lncRNA（elncRNA）和启动子相关lncRNA（plncRNA）。15种elncRNA和12种plncRNA在LPS刺激后差异表达。lncRNA及其邻近蛋白编码基因的表达变化显著相关。此外，elncRNA和plncRNA表达的调节与H3 K4 me 3和H3 K27 Ac相关。重要的是，许多已鉴定的LPS调节的lncRNA，如lncRNA-Nfkb 2和lncRNA-Rel，位于免疫应答蛋白编码基因附近。大多数LPS调节的lncRNA在转录因子p65、IRF 3、JunB和cJun中至少有一个结合位点。我们建立了一个整合的微阵列分析管道，用于分析lncRNA。此外，我们的研究结果表明，lncRNA可以是LPS诱导的BMDM先天免疫反应的重要调节因子。本文的在线版本（doi：10.1186/s12864-015-1270-5）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/s12864-015-1270-5) contains supplementary material, which is available to authorized users.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
14.9
作者：
Flicek P;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt S;Johnson N;Juettemann T;Kähäri AK;Keenan S;Kulesha E;Martin FJ;Maurel T;McLaren WM;Murphy DN;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ruffier M;Sheppard D;Taylor K;Thormann A;Trevanion SJ;Vullo A;Wilder SP;Wilson M;Zadissa A;Aken BL;Birney E;Cunningham F;Harrow J;Herrero J;Hubbard TJ;Kinsella R;Muffato M;Parker A;Spudich G;Yates A;Zerbino DR;Searle SM
通讯作者：
Searle SM
影响因子：
30.5
作者：
通讯作者：
--
影响因子：
14.9
作者：
Dreszer TR;Karolchik D;Zweig AS;Hinrichs AS;Raney BJ;Kuhn RM;Meyer LR;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Pohl A;Malladi VS;Li CH;Learned K;Kirkup V;Hsu F;Harte RA;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;James Kent W
通讯作者：
James Kent W
DOI：
10.1126/science.1240925
发表时间：
2013-08-16
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Carpenter S;Aiello D;Atianand MK;Ricci EP;Gandhi P;Hall LL;Byron M;Monks B;Henry-Bezy M;Lawrence JB;O'Neill LA;Moore MJ;Caffrey DR;Fitzgerald KA
通讯作者：
Fitzgerald KA