Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
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DOI：
10.1101/gad.1705308
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发表时间：
2008-10-15
影响因子：
10.5
通讯作者：
Blelloch, Robert
中科院分区：
文献类型：
--
作者：
Babiarz, Joshua E.;Ruby, J. Graham;Blelloch, Robert
规范的microRNA（miRNA）需要两个处理步骤：第一个处理步骤，由微处理器，DGCR8和Drosha的复合物，第二个由TRBP和DICER组成的。与DICER1 DELTA/DELTA MESC相比，DGCR8 Delta/Delta小鼠胚胎干细胞（MESC）的表型不太严重，这表明微处理器独立，dicer依赖性的小rNA具有生理作用。为了鉴定具有异常生物发生的这些小型RNA，我们从野生型，DGCR8 Delta/delta和Dicer1 Delta/delta Mesc进行了高通量测序。所得的几个独立于DICER依赖性RNA是非规范的miRNA。这些来自mirtron和新鉴定的miRNA前体的亚类，这似乎是shrnas的内源性对应物。我们的分析还揭示了由长发蛋白的迪切尔裂解引起的内源性siRNA，其中绝大多数源自一个带有串联的基因组基因座，倒置了短散布的核元素（SINES）。我们的结果扩展了哺乳动物小RNA生成途径的已知多样性，并表明哺乳动物siRNA存在于卵母细胞以外的其他细胞类型中。
Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by a complex of TRBP and Dicer. dgcr8 Delta/Delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1 Delta/Delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild-type, dgcr8 Delta/Delta, and dicer1 Delta/Delta mESCs. Several of the resulting DGCR8-independent, Dicer-dependent RNAs were noncanonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of shRNAs. Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes.