hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function

We report that mice lacking the heterogeneous nuclear ribonucleoprotein U (hnRNP U) in the heart develop lethal dilated cardiomyopathy and display numerous defects in cardiac pre-mRNA splicing. Mutant hearts have disorganized cardiomyocytes, impaired contractility, and abnormal excitation–contraction coupling activities. RNA-seq analyses of Hnrnpu mutant hearts revealed extensive defects in alternative splicing of pre-mRNAs encoding proteins known to be critical for normal heart development and function, including Titin and calcium/calmodulin-dependent protein kinase II delta (Camk2d). Loss of hnRNP U expression in cardiomyocytes also leads to aberrant splicing of the pre-mRNA encoding the excitation–contraction coupling component Junctin. We found that the protein product of an alternatively spliced Junctin isoform is N-glycosylated at a specific asparagine site that is required for interactions with specific protein partners. Our findings provide conclusive evidence for the essential role of hnRNP U in heart development and function and in the regulation of alternative splicing.The expression of more than 95% of human genes is affected by alternative pre-mRNA splicing (AS) (1, 2). Differentially spliced isoforms play distinct roles in a temporally and spatially specific manner (3), and mutations that lead to aberrant splicing are the cause of many human genetic diseases (4). RNA-binding proteins (RBPs) play a central role in the regulation of alternative splicing during development and disease. They function primarily by positively or negatively regulating splice-site recognition by the spliceosome (1). Many RBPs are expressed in specific tissues, and AS is regulated by the combinatorial activities of these factors on specific pre-mRNAs through their interactions with distinct regulatory sequences in pre-mRNA that function as splicing enhancers or silencers (5).The developing heart is one of the best studied systems where splicing changes occur during normal development, and mutations affecting specific splicing outcomes contribute to cardiomyopathy (6, 7). Although these mutations can either disrupt splicing elements or affect the expression of specific splicing factors, the latter mechanism is clearly responsible for the distinct splicing profiles at different developmental stages. For example, the dynamics of alternative splicing during postnatal heart development correlate with expression changes of many RBPs, including CUG-BP, Elav-like family member 1 (CELF1), Muscleblind-like 1 (MBNL1), and FOX proteins (8). Detailed biochemical studies have elucidated the mechanisms by which these splicing factors regulate splicing in a position- and context-dependent manner (9, 10). The function of other RBPs during heart development has also been studied. For example, two of the muscle-specific splicing factors, RBM20 and RBM24, play distinct roles in splicing regulation. RBM20 mainly acts as a splicing repressor, as its absence leads to multiple exon inclusion events in the heart. For example, the Titin gene is one of the major targets of RBM20 (11, 12). On the other hand, loss of RBM24 expression gives rise to many exon skipping events (13), implicating RBM24 as a splicing activator. Strikingly, there is little overlap between RBM20 and RBM24 splicing targets, suggesting that RBM20 and RBM24 are involved in regulating splicing of distinct groups of pre-mRNAs and there is little cross-talk between these two splicing factors.Distinct splicing activities have also been ascribed to general splicing factors (1). There are two major types of ubiquitously expressed RBPs: the heterogeneous nuclear ribonucleoproteins (hnRNPs) and serine/arginine (SR)-rich proteins. hnRNPs and SR proteins are generally believed to play opposite roles in splicing: SR proteins promote the inclusion of exons during splicing, whereas hnRNP proteins repress inclusion (1). The function of certain SR proteins has been studied in the mouse heart through the conditional knockout approach. Srsf1 deletion in the heart leads to lethal dilated cardiomyopathy (DCM) (death occurs 6–8 wk after birth) (14). SRSF1 is required for the cardiac-specific splicing of Cypher (also called Ldb3) pre-mRNA, and the regulation of alternative splicing of calcium/calmodulin-dependent protein kinase II delta (Camk2d) and cardiac Troponin T (cTnT) during heart development. In particular, the persistent splicing of a neuronal isoform of Camk2d and its ability to enhance excitation and contraction coupling (ECC) activity in Srsf1 mutant cardiomyocytes have been proposed as a possible cause of the phenotype in mutant mice (14). Ablation of another SR protein, SRSF10 (SRp38), from the mouse also leads to heart defects (15). SRSF10 has been shown to regulate the splicing of Triadin, an important component of ECC machinery (15). Interestingly, conditional deletion of Srsf2 from the heart leads to DCM with little splicing misregulation but instead affects the expression of the calcium channel Ryr2 (16). It is striking that these SR proteins affect ECC activity in the heart by directly regulating the expression/splicing of distinct players in this machinery. Because these studies were conducted before the advent of next-generation RNA sequencing, only a few splicing targets specifically regulated by these SR proteins were identified. A more comprehensive study of the effects of deleting the genes encoding these proteins from the heart on the splicing program has not been reported.In contrast to SR proteins, specific functions of hnRNP proteins in cardiac pre-mRNA splicing have not been determined. In this report, we selectively inactivated the expression of one of the most abundant hnRNP proteins—hnRNP U—in the heart. We found that Hnrnpu mutant mice develop a lethal DCM phenotype, with death occurring around 2 wk after birth. There are multiple cardiac defects in mutant hearts accompanied by many splicing alterations. Some of these splicing targets are commonly regulated by hnRNP U and other SR and RBM proteins. We also identified many hnRNP U-specific splicing targets in the heart, including an ECC component Junctin. The protein product of the alternatively spliced Junctin isoform is N-glycosylated at a specific asparagine site in Hnrnpu mutant cells and could contribute to abnormal cardiac function. Our study also enables comparisons of the roles of different splicing factors in heart development and function.     

基于转录组测序的放射性肠损伤基因动态变化

目的 探讨致死剂量的电离辐射对小鼠空肠组织转录组动态变化。方法 小鼠经14 Gy ¹³⁷Cs γ射线腹部照射后,分别于6 h,3.5和5 d提取各组小鼠空肠总RNA进行转录组测序。表达变化倍数在2倍以上即视为显著差异,对表达差异的基因进行IPA、Funrich、GO和KEGG软件分析。结果 小鼠在腹部照射后6 h和3.5 d共同激活了p53信号通路。在照射后第3.5天的差异基因中,基因相互作用网络分析结果表明,Lck、Cdk1和Fyn可能起关键作用,通路分析表明,上调了DNA损伤修复信号通路,下调了细胞黏附分子、黏着斑和IgA分泌途径信号通路。结论 p53信号通路以及Lck、Cdk1和Fyn等基因在放射性肠损伤中可能起关键作用。     

Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin

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