Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload. So far, no connections between the function of the host genes and the function of their payloads have been reported. Here we investigate whether there is evidence for an association of host gene function or mechanisms with the type of payload. To assess this hypothesis we test whether the miRNA host genes (MIRHGs), snoRNA host genes (SNHGs), and other lncRNA host genes can be distinguished based on sequence and/or structure features unrelated to their payload. A positive answer would imply a functional and mechanistic correlation between host genes and their payload, provided the classification does not depend on the presence and type of the payload. A negative answer would indicate that to the extent that secondary functions are acquired, they are not strongly constrained by the prior, primary function of the payload. We find that the three classes can be distinguished reliably when the classifier is allowed to extract features from the payloads. They become virtually indistinguishable, however, as soon as only sequence and structure of parts of the host gene distal from the snoRNAs or miRNA payload is used for classification. This indicates that the functions of MIRHGs and SNHGs are largely independent of the functions of their payloads. Furthermore, there is no evidence that the MIRHGs and SNHGs form coherent classes of long non-coding RNAs distinguished by features other than their payloads.

许多小的核仁 RNA 和许多 miRNA 的发夹前体是从长的非蛋白质编码宿主基因加工而来的。与其高度保守和结构严密的有效载荷相比，宿主基因的序列保守性较差。然而，越来越多的证据表明，宿主基因具有超出其携带 ncRNA 作为有效载荷的主要任务的生物学功能。到目前为止，尚未报道宿主基因的功能与其有效载荷的功能之间的联系。在这里，我们调查是否有证据表明宿主基因功能或机制与有效载荷类型有关。为了评估这一假设，我们测试了 miRNA 宿主基因 (MIRHG)、snoRNA 宿主基因 (SNHG) 和其他 lncRNA 宿主基因是否可以根据与其有效载荷无关的序列和/或结构特征进行区分。如果分类不依赖于有效载荷的存在和类型，则肯定的答案将意味着宿主基因与其有效载荷之间存在功能和机制相关性。否定答案表明，在获得次要功能的范围内，它们不受有效载荷的先前主要功能的强烈约束。我们发现，当允许分类器从有效载荷中提取特征时，可以可靠地区分这三个类。然而，一旦仅使用远离 snoRNA 或 miRNA 有效载荷的宿主基因部分的序列和结构进行分类，它们就变得几乎无法区分。这表明 MIRHG 和 SNHG 的功能在很大程度上独立于其有效载荷的功能。此外，