RNA-Seq characterization of select lincRNA knockout mouse models

It has become clear that long intergenic noncoding RNAs (lincRNAs) are an important layer of genome regulation. Thousands have been identified in mammals, yet only a few have been tested through genetic ablation in animal models. Of the few that have, many yields weak to unobservable phenotypes, raising the question of their in vivo relevance. To more broadly investigate the functional relevance of lincRNAs in physiological conditions, we developed a collection of 18 lincRNA knockout strains. We found that two knockout strains, linc-Sox2 and linc-Foxf1a (Fendrr), exhibit perinatal lethal phenotypes in addition to multiple developmental abnormalities. Notably, in depth analysis of a third mutant strain, linc-Brn1b-/-, revealed defects in brain development, with distinct abnormalities in class-specific generation of upper layer II/III-IV neurons in the neocortex. Thus far, we found at least 6 of 18 mutant strains exhibit distinct developmental or lethality phenotypes. Therefore, this study demonstrates that lincRNAs are required for life and play critical roles during mammalian development, highlighting the importance of studying them further to better understand the molecular mechanisms leading to disease. Minimum 2 replicates each of select wild type and lincRNA knockout embryonic and postnatal tissues for three distinct lincRNA knockout mouse strains.

越来越多的研究表明，基因间长链非编码RNA（long intergenic noncoding RNAs，lincRNAs）是基因组调控的重要层面。目前已在哺乳动物中鉴定出数千种lincRNAs，但仅有极少数通过动物模型的基因敲除实验完成了功能验证。在已开展验证的少数lincRNAs中，多数仅表现出微弱乃至难以观测的表型，这引发了关于其在体生物学相关性的疑问。为更广泛地探究lincRNAs在生理条件下的功能相关性，我们构建了包含18种lincRNA敲除小鼠品系的资源库。研究发现，linc-Sox2与linc-Foxf1a（Fendrr）这两种敲除品系不仅存在多种发育异常，还表现出围产期致死表型。值得注意的是，对第三种突变品系linc-Brn1b-/-的深度分析显示，该品系存在大脑发育缺陷，具体表现为新皮层上层II/III-IV神经元的类别特异性生成出现显著异常。截至目前，我们已在18种突变品系中发现至少6种存在明确的发育异常或致死表型。因此，本研究证实lincRNAs对生命活动不可或缺，并在哺乳动物发育过程中发挥关键作用，凸显了进一步研究此类RNA以阐明疾病相关分子机制的重要性。本数据集涵盖3种不同lincRNA敲除小鼠品系的野生型及对应lincRNA敲除的胚胎、产后组织样本，每个选定样本组至少设置2次生物学重复。