MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus.
MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus.
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DOI：
10.1371/journal.pone.0021495
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Hovatta I
中科院分区：
文献类型：
--
作者：
Juhila J;Sipilä T;Icay K;Nicorici D;Ellonen P;Kallio A;Korpelainen E;Greco D;Hovatta I
microRNA（miRNAs）是一类能引起转录后基因沉默的小分子调控分子。虽然已知一些miRNA在成人脑中具有区域特异性表达模式，但区域特异性对脑核团基因调控网络的功能后果尚不清楚。因此，我们通过miRNA-Seq和微阵列研究了两个大脑区域，额叶皮层（FCx）和海马（HP）中的miRNA表达模式，这两个区域具有不同的生物学功能。我们使用miRNA-Seq从FCx中鉴定了354个miRNAs，从HP中鉴定了408个miRNAs，使用微阵列从FCx中鉴定了245个miRNAs，从HP中鉴定了238个miRNAs。几个miRNA家族和簇在FCx和HP之间差异表达，包括miR-8家族、miR-182家族、miR-183家族和miR-184家族。|miR-96| miR-183簇和miR-212|在FCx中过表达的miR-312簇和在HP中过表达的miR-34家族。为了可视化聚类，我们开发了在Chipster基因组浏览器中查看miRNA-Seq读取的基因组比对的支持。我们对差异表达的miRNA家族和簇的预测靶基因进行了通路分析，以评估其推定的生物学功能。有趣的是，来自同一家族/簇的几种miRNA被预测调节特定的生物学途径。我们开发了一种具有生物信息学分析工作流程的miRNA-Seq方法，该方法适用于研究特定脑核团的miRNA表达模式。FCx和HP显示具有不同的miRNA表达模式，其反映在预测的基因调控途径中。该方法可用于鉴定成年和发育中啮齿动物脑的脑区域特异性和表型特异性miRNA-mRNA调控网络。
MicroRNAs (miRNAs) are small regulatory molecules that cause post-transcriptional gene silencing. Although some miRNAs are known to have region-specific expression patterns in the adult brain, the functional consequences of the region-specificity to the gene regulatory networks of the brain nuclei are not clear. Therefore, we studied miRNA expression patterns by miRNA-Seq and microarrays in two brain regions, frontal cortex (FCx) and hippocampus (HP), which have separate biological functions. We identified 354 miRNAs from FCx and 408 from HP using miRNA-Seq, and 245 from FCx and 238 from HP with microarrays. Several miRNA families and clusters were differentially expressed between FCx and HP, including the miR-8 family, miR-182|miR-96|miR-183 cluster, and miR-212|miR-312 cluster overexpressed in FCx and miR-34 family overexpressed in HP. To visualize the clusters, we developed support for viewing genomic alignments of miRNA-Seq reads in the Chipster genome browser. We carried out pathway analysis of the predicted target genes of differentially expressed miRNA families and clusters to assess their putative biological functions. Interestingly, several miRNAs from the same family/cluster were predicted to regulate specific biological pathways. We have developed a miRNA-Seq approach with a bioinformatic analysis workflow that is suitable for studying miRNA expression patterns from specific brain nuclei. FCx and HP were shown to have distinct miRNA expression patterns which were reflected in the predicted gene regulatory pathways. This methodology can be applied for the identification of brain region-specific and phenotype-specific miRNA-mRNA-regulatory networks from the adult and developing rodent brain.
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影响因子：
12.3
作者：
Hovatta, Iiris;Zapala, Matthew A.;Broide, Ron S.;Schadt, Eric E.;Libiger, Ondrej;Schork, Nicholas J.;Lockhart, David J.;Barlow, Carrolee
通讯作者：
Barlow, Carrolee
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
影响因子：
64.8
作者：
Hovatta, I;Tennant, RS;Barlow, C
通讯作者：
Barlow, C
影响因子：
14.9
作者：
Altuvia Y;Landgraf P;Lithwick G;Elefant N;Pfeffer S;Aravin A;Brownstein MJ;Tuschl T;Margalit H
通讯作者：
Margalit H