Search

Background: Protein-coding genes have been considered the functional part of the genome, although they represent only 2% of the genome. In contrast, more than 90% of the genome produces non-coding RNA (ncRNA), including antisense (AS) genes, a type of long non-coding genes (encoding transcripts > 200 nucleotides) located on the opposite strand of coding genes. Therefore, antisense RNA (asRNA) can be complementary to the counterpart sense RNA, supporting a regulatory role with potential pathogenic consequences, as their deregulation has been associated with cardiovascular disease, cancer, and diabetes. Results: We performed an in-depth review of AS genes in Ensembl and evaluated the expression of AS genes in human liver by third-generation RNA sequencing methods. Currently, 1656 AS genes overlapping with 1556 sense genes have been identified in the human genome. Coding genes with antisense counterparts were significantly larger and had higher transcriptional activity than genes without antisense counterparts. RNA nanopore sequencing of 15 human livers identified 185 transcripts (55 novel) from 150 known AS genes, and 1316 transcripts from 807 sense genes, with 111 sense-antisense pairs. Sense transcripts showed higher expression than antisense transcripts. Remarkably, RNA nanopore sequencing of human livers identified 146 transcripts (67 novel) corresponding to 118 possible novel AS genes. Conclusion: This study reveals the landscape of AS genes in the human genome and demonstrates the power of long-read RNA sequencing to identify novel transcripts and even novel AS genes, exploring the relationship between sense and AS gene expression as well. [ABSTRACT FROM AUTHOR]

Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neurooncology patients. [ABSTRACT FROM AUTHOR]