RESUMEN
Bombyx mori nucleopolyhedrovirus (BmNPV) significantly impacts silkworm sericulture, causing substantial economic losses. The GP64 protein, a primary envelope protein of BmNPV budded virus (BV), retains its signal peptide (SP) in the mature form, crucial for its translocation to the plasma membrane (PM) and viral infectivity. This study investigates the role of the uncleaved SP of GP64 in activating the expression of BmSpz7, a novel Spätzle family member identified through RNA-seq analysis. We cloned and characterized BmSpz7, demonstrating its upregulated expression in BmN cells and silkworm larvae infected with BmNPV containing GP64 with an uncleaved SP. Additionally, transient expression of GP64's SP significantly enhanced BmSpz7 expression and protein secretion. These findings suggest that the uncleaved SP of GP64 plays a pivotal role in activating BmSpz7, providing new insights into the molecular interactions between BmNPV and its host, and revealing potential targets for antiviral strategies in sericulture.
RESUMEN
In their expression process, different genes can generate diverse functional products, including various protein-coding or noncoding RNAs. Here, we investigated the protein-coding capacities and the expression levels of their isoforms for human known genes, the conservation and disease association of long noncoding RNAs (ncRNAs) with two transcriptome sequencing datasets from human brain tissues and 10 mixed cell lines. Comparative analysis revealed that about two-thirds of the genes expressed between brain and cell lines are the same, but less than one-third of their isoforms are identical. Besides those genes specially expressed in brain and cell lines, about 66% of genes expressed in common encoded different isoforms. Moreover, most genes dominantly expressed one isoform and some genes only generated protein-coding (or noncoding) RNAs in one sample but not in another. We found 282 human genes could encode both protein-coding and noncoding RNAs through alternative splicing in the two samples. We also identified more than 1,000 long ncRNAs, and most of those long ncRNAs contain conserved elements across either 46 vertebrates or 33 placental mammals or 10 primates. Further analysis showed that some long ncRNAs differentially expressed in human breast cancer or lung cancer, several of those differentially expressed long ncRNAs were validated by RT-PCR. In addition, those validated differentially expressed long ncRNAs were found significantly correlated with certain breast cancer or lung cancer related genes, indicating the important biological relevance between long ncRNAs and human cancers. Our findings reveal that the differences of gene expression profile between samples mainly result from the expressed gene isoforms, and highlight the importance of studying genes at the isoform level for completely illustrating the intricate transcriptome.
Asunto(s)
Encéfalo/metabolismo , Sistemas de Lectura Abierta/genética , ARN no Traducido/genética , Análisis de Secuencia de ARN/métodos , Adulto , Secuencia de Bases , Línea Celular , Secuencia Conservada , Enfermedad/genética , Exones/genética , Femenino , Regulación de la Expresión Génica , Humanos , Masculino , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Reproducibilidad de los Resultados , Reacción en Cadena de la Polimerasa de Transcriptasa InversaRESUMEN
De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences. We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line, respectively. We then determined an efficient way to yield an optimal overall assembly using three different strategies. We first assembled brain and cell line transcriptome using a single k-mer length. Next we tested a range of values of k-mer length and coverage cutoff in assembling. Lastly, we combined the assembled contigs from a range of k values to generate a final assembly. By comparing these assembly results, we found that using only one k-mer value for assembly is not enough to generate good assembly results, but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.