A Novel Targeted Long-read Sequencing Approach Boosts Transcriptomic Profiling
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Long-read sequencing reveals novel transcript diversity in <i>Polypterus senegalus</i>
<i>Polypterus senegalus</i> is a fish species characterized by primitive traits and unique physiological-anatomical features, representing a transitional stage toward terrestrial vertebrates. Diverging from other ray-finned fishes approximately 420 million years ago, it serves as a …
Read PDFNotable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
Long-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated genomes, while developing new …
Read PDFPrecise identification of viral-host integration events in HPV-positive cervical cancers by targeted long-read sequencing
Human papillomaviral (HPV) integrations into host human genome, a frequently observed event in HPV associated cervical cancer, are currently mapped through expensive Whole Genome sequencing (WGS) or RNA sequencing (RNA-seq) methodologies. This study aims to …
Read PDFDe novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing
Acartia tonsa is a calanoid copepod with a cosmopolitan distribution. Its ecological relevance makes it a useful bioindicator organism for assessing the toxicity of various compounds. However, transcriptomic assemblies of A. tonsa using long-read technologies …
Read PDFThe additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
Long-read sequencing (LRS) is a promising technology positioned to study the significant proportion of rare diseases (RDs) that remain undiagnosed as it addresses many of the limitations of short-read sequencing, detecting and clarifying additional disease-associated …
Read PDFIsoform analysis of heterozygous putative splicing variants at the allele level using nanopore long-read sequencing
One of the challenges in clinical genetics for rare diseases and personalized medicine is evaluating isoform alterations arising from heterozygous putative splicing variants at the allele level. Our aim was to analyze these variants by …
Read PDFPolyA_DB v4: systematic polyA site identification and isoform annotation in human and mouse genomes using 3' end and long-read sequencing data
The cleavage and polyadenylation site (PAS) defines the 3' end of almost all protein-coding and long non-coding RNAs in eukaryotes. Most genes harbor multiple PAS, resulting in expression of alternative polyadenylation (APA) isoforms. Here, we …
Read PDFA bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data
<h4>Background</h4>Even though alternative RNA splicing was discovered nearly 50 years ago (1977), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their …
Read PDFUnraveling the hidden complexity of cancer through long-read sequencing
Cancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can …
Read PDFLong-read sequencing of recurrent FGF12 duplications in epilepsy: Insights into structural mechanisms and aberrant isoforms
<h4>Objective</h4>Fibroblast growth factor 12 (FGF12), a member of the fibroblast homologous factor family, plays a key role in the modulation of voltage-gated sodium (Nav) channels. Pathogenic variants in the FGF12 gene leading to a gain-of-function …
Read PDFLong-read sequencing reveals increased isoform diversity in key transcription factor effectors of intercellular signalling at the invertebrate-vertebrate transition
<h4>Background</h4>Several intercellular signalling pathways (including wingless (Wnt), hedgehog (Hh), and bone morphogenetic protein (BMP)) are used repeatedly in animals throughout development and evolution and are also frequent targets for disease-associated disruptions. We have previously shown …
Read PDFLong-read sequencing-based analyses of the adult Drosophila brain transcriptome in physiological and pathological settings
Optimal brain function requires that neurons carry out extensive post-transcriptional RNA processing to produce a vast diversity of transcripts. Accurate reconstruction and quantification of highly processed RNA using standard RNA sequencing approaches is challenging due …
Read PDFChromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies
Malcolmia littorea, a member of the family Brassicaceae, is adapted to coastal and sandy environments and has become a model in studies of reproductive barriers. However, genomic resources for the species are limited. Here, with …
Read PDFBioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution
Alternative splicing (AS) plays a key role in regulating gene expression, and its dysregulation is implicated in numerous human diseases, including cancer. While bulk RNA sequencing has advanced our understanding of AS, it cannot capture …
Read PDFLong-Read Sequencing Reveals Cell- and State-Specific Alternative Splicing in 293T and A549 Cell Transcriptomes
Alternative splicing (AS) is a fundamental mechanism governing transcriptomic diversity and cellular identity. Although 293T (human embryonic kidney) and A549 (human lung adenocarcinoma) cell lines are widely used, cell-type-specific splicing dynamics-including responses to receptor overexpression-remain …
Read PDFExpanding the genetic landscape of inherited metabolic diseases using long-read sequencing and transcriptomic profiling
Although next-generation sequencing has emerged as a powerful tool for diagnosing rare diseases (RD), many cases of inherited metabolic diseases (IMD) remain unsolved, hindering the diagnosis, clinical and therapeutic management of the patients. The primary …
Read PDFSarcomeric remodelling in human heart failure unraveled by single molecule long read sequencing
Dysregulation of alternative splicing - mediated by factors such as RBM20 or SLM2 - can affect proper gene isoform control, disrupting gene isoform homeostasis and underpins severe cardiomyopathy in both animal models and patients. Although …
Read PDFLong-read sequencing disentangles isoform complexity at allele-specific loci
In recent years, long-read sequencing technologies have detected transcript isoforms with unprecedented accuracy and resolution. However, it remains unclear whether long-read sequencing can effectively disentangle the isoform landscape of complex allele-specific loci that arise from …
Read PDFThe genome of Phlebotomus chinensis, the primary vector of visceral leishmaniasis in China: insights from chromosome-level assembly and comparative analysis
<h4>Background</h4>Phlebotomus chinensis is the primary vector of visceral leishmaniasis (VL) in China. However, the lack of a high-quality genome assembly for this species has limited research on its biology, vector-pathogen interactions, and evolutionary adaptations. To …
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