ABSTRACT
Genes in coronaviruses are preceded by transcription regulatory sequences (TRSs), which play a critical role in gene expression mediated by the viral RNA-dependent RNA-polymerase via the process of discontinuous transcription. In addition to being crucial for our understanding of the regulation and expression of coronavirus genes, we demonstrate for the first time how TRSs can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS AND GO_SCPLOWENEC_SCPLOW IO_SCPLOWDENTIFICATIONC_SCPLOW (TRS-GO_SCPLOWENEC_SCPLOW-ID) problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID (CORe Sequence IDentifier), a computational tool to solve this problem. We also present CORSID-A, which solves a constrained version of the TRS-GO_SCPLOWENEC_SCPLOW-ID problem, the TRS IO_SCPLOWDENTIFICATIONC_SCPLOW (TRS-ID) problem, identifying TRS sites in a coronavirus genome with specified gene annotations. We show that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses and that CORSID outperforms state-of-the-art gene finding methods in finding genes in coronavirus genomes. We demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronaviruses. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.
ABSTRACT
Genes in SARS-CoV-2 and, more generally, in viruses in the order of Nidovirales are expressed by a process of discontinuous transcription mediated by the viral RNA-dependent RNA polymerase. This process is distinct from alternative splicing in eukaryotes, rendering current transcript assembly methods unsuitable to Nidovirales sequencing samples. Here, we introduce the DO_SCPLOWISCONTINUOUSC_SCPLOW TO_SCPLOWRANSCRIPTC_SCPLOW AO_SCPLOWSSEMBLYC_SCPLOW problem of finding transcripts [Formula] and their abundances c given an alignment [Formula] under a maximum likelihood model that accounts for varying transcript lengths. Underpinning our approach is the concept of a segment graph, a directed acyclic graph that, distinct from the splice graph used to characterize alternative splicing, has a unique Hamiltonian path. We provide a compact characterization of solutions as subsets of non-overlapping edges in this graph, enabling the formulation of an efficient mixed integer linear program. We show using simulations that our method, JO_SCPLOWUMPERC_SCPLOW, drastically outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1 and SARS-CoV-2 samples, we find that JO_SCPLOWUMPERC_SCPLOW not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are well supported by direct evidence from long-read data, presence in multiple, independent samples or a conserved core sequence. JO_SCPLOWUMPERC_SCPLOW enables detailed analyses of Nidovirales transcriptomes. Code availabilitySoftware is available at https://github.com/elkebir-group/Jumper
ABSTRACT
Objective: To compare the effects of invigorating the kidney and strengthening yang on four kinds of Semen Custutae. Methods: Sexual organs of juvenile rat and shen yang deficiency rat were weighed to analyze its contents of SOD and MDA. Results: Alcohol extracts of four kinds of Semen Custutae have conspicuous effects on increasing weight of sexual organs. Water extracts of Semen Custutae have better effects on raising the contents of SOD and MDA and increasing weight of immune organs of shen yang deficiency rat. Conclusion: The effects of Cuscuta chinensis Lam. and C.australis R. Br. have better than that of C. japonica Choisy and C.lupuliformis Krockr in invigorating the kidney and strengthening yang.
