Discovering miRNA Regulatory Networks in Holt-Oram Syndrome Using a Zebrafish Model.
Discovering miRNA Regulatory Networks in Holt-Oram Syndrome Using a Zebrafish Model.
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DOI：
10.3389/fbioe.2016.00060
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发表时间：
2016
影响因子：
5.7
通讯作者：
Pellegrini M
中科院分区：
文献类型：
--
作者：
D'Aurizio R;Russo F;Chiavacci E;Baumgart M;Groth M;D'Onofrio M;Arisi I;Rainaldi G;Pitto L;Pellegrini M
MicroRNA（miRNAs）是一类在基因表达的转录后调控中起重要作用的非编码小RNA。miRNAs参与了许多生物学过程的调节，如分化、凋亡和细胞增殖。miRNAs在胚胎、出生后和成人心脏中表达，并且它们在心血管发育和疾病期间的基因表达调控中具有关键作用。miRNAs的异常表达与心肌细胞分化异常和功能障碍有关。Tbx 5是T-box基因家族的一员，作为转录因子参与脊椎动物心脏的发育。Tbx 5水平的改变影响数百个基因的表达。Tbx 5的单倍不足和基因重复是与Holt-Oram综合征（HOS）相关的心脏异常的基础。最近的数据表明，miRNA可能是Tbx 5控制心脏发育的调节回路的重要组成部分。使用高通量技术，我们的特点是基因组广泛的miRNA和mRNA表达谱在WT和Tbx 5耗尽斑马鱼胚胎在两个关键的发育时间点，24和48小时后受精（hpf）。我们发现，几种作为Tbx 5潜在效应物的miRNA差异表达;其中一些已知参与心脏发育和功能，如miR-30，miR-34，miR-190和miR-21。我们对miRNA表达数据与基因表达谱进行了综合分析，以通过miRNA-mRNA表达的负相关来改进计算靶点预测方法，我们强调了在心肌收缩力，心肌细胞增殖/凋亡和形态发生中起作用的靶点，这些都是由Tbx 5调节的关键功能。这种方法允许发现复杂的调控回路，涉及新的miRNA和蛋白质编码基因，如miR-34 a和miR-30及其靶标，这些基因在HOS中以前没有考虑过。
MicroRNAs (miRNAs) are small non-coding RNAs that play an important role in the post-transcriptional regulation of gene expression. miRNAs are involved in the regulation of many biological processes such as differentiation, apoptosis, and cell proliferation. miRNAs are expressed in embryonic, postnatal, and adult hearts, and they have a key role in the regulation of gene expression during cardiovascular development and disease. Aberrant expression of miRNAs is associated with abnormal cardiac cell differentiation and dysfunction. Tbx5 is a member of the T-box gene family, which acts as transcription factor involved in the vertebrate heart development. Alteration of Tbx5 level affects the expression of hundreds of genes. Haploinsufficiency and gene duplication of Tbx5 are at the basis of the cardiac abnormalities associated with Holt–Oram syndrome (HOS). Recent data indicate that miRNAs might be an important part of the regulatory circuit through which Tbx5 controls heart development. Using high-throughput technologies, we characterized genome-widely the miRNA and mRNA expression profiles in WT- and Tbx5-depleted zebrafish embryos at two crucial developmental time points, 24 and 48 h post fertilization (hpf). We found that several miRNAs, which are potential effectors of Tbx5, are differentially expressed; some of them are already known to be involved in cardiac development and functions, such as miR-30, miR-34, miR-190, and miR-21. We performed an integrated analysis of miRNA expression data with gene expression profiles to refine computational target prediction approaches by means of the inversely correlation of miRNA–mRNA expressions, and we highlighted targets, which have roles in cardiac contractility, cardiomyocyte proliferation/apoptosis, and morphogenesis, crucial functions regulated by Tbx5. This approach allowed to discover complex regulatory circuits involving novel miRNAs and protein coding genes not considered before in the HOS such as miR-34a and miR-30 and their targets.