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<h4>Motivation</h4>The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our understanding of what parts of the transcriptome are translated. Many alternative open reading …
Read PDFAnnotation of genes and transcripts is a key prerequisite for understanding the information that is encoded in newly sequenced genomes. One source of information suited for this purpose is RNA-seq data mapped to the respective …
Read PDF<h4>Background</h4>The assembly of fragmented RNA-sequencing reads into complete transcripts is error-prone, particularly for genes with complex splicing, resulting in ambiguity in transcript discovery and quantification. PacBio long-read RNA sequencing resolves transcripts with greater clarity than …
Read PDFZea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 …
Read PDF<h4>Background</h4>Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for …
Read PDFThe human cytomegalovirus (HCMV) is a ubiquitous, human pathogenic herpesvirus. The complete viral genome is transcriptionally active during infection; however, a large part of its transcriptome has yet to be annotated. In this work, we …
Read PDFCellular stresses regulate transcriptional readthrough, whereby RNA polymerase II elongates past a gene's polyadenylation cleavage site without RNA cleavage. Readthrough has been reported in several cancer types. Here, we use long-read sequencing of nascent RNA …
Read PDFHere we discuss three veterinary alphaherpesviruses-pseudorabies virus, equid alphaherpesvirus 1, and bovine alphaherpesvirus 1-that were instrumental in uncovering the true extent of transcriptome complexity through long-read RNA sequencing, which earlier short-read approaches could not resolve. …
Read PDFBACKGROUND: Crandell-Rees Feline Kidney (CRFK; kidney-derived) cells and PG-4 cells (astrocyte-derived) have been in use and have been passaged for decades in laboratories worldwide; however, no detailed information on the genetic background of the donor …
Read PDFAlthough mutations in many genes cause familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), most cases are sporadic (sALS and sFTD) with unclear etiology. Here we tested whether somatic mutations contribute to sALS and …
Read PDFAnkylosing spondylitis (AS) is a chronic immune-mediated arthritis marked by persistent inflammation and progressive structural damage. Although dysregulation of programmed cell death (PCD) is increasingly recognized in AS pathogenesis, the full spectrum of transcript-level regulation …
Read PDFBACKGROUND: Satellite DNAs (satDNAs) can arise from diverse genomic regions, but determining their precise origin remains a major challenge. A previous study reported the colocalization of the As51 satDNA and the 45S ribosomal DNA (rDNA) …
Read PDFGenome sequencing (GS) has emerged as a transformative tool in the diagnosis of rare diseases with complex phenotypes. This technology uncovers structural, intronic, non-coding, and mitochondrial variants that traditional methods might miss, thereby facilitating the …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) represents a leading cause of cancer-associated deaths worldwide, and its development is strongly associated with aberrant RNA processing and metabolic reprogramming. Splicing factor 3B subunit 4 (SF3B4), the core component of the …
Read PDFConventional genome mapping-based approaches systematically overlook genetic variation, particularly in regions that substantially differ from the reference. To explore this hidden variation, here we examine unmapped and poorly mapped reads from the genomes of 640 …
Read PDFEquine Juvenile Spinocerebellar Ataxia (EJSCA) is a novel autosomal recessive neurologic disease in Quarter Horses. Affected foals display a progressive proprioceptive ataxia by 1-5 weeks of age, leading to recumbency and necessitating euthanasia. Whole genome …
Read PDFPine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de …
Read PDFShort-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct …
Read PDFDespite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments …
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