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A cell's transcriptome is regulated through the integration of external and internal signals that activate intracellular signal pathways, epigenetic modifications and post-translational changes. Post-transcriptional regulation through RNA methylation has emerged as an important mechanism in …
Read PDFNanopore direct RNA sequencing (DRS) offers distinct advantages for transcriptome analysis over the traditional high-throughput RNA sequencing methods by preserving native RNA modifications, eliminating polymerase chain reaction bias, and simplifying the workflow. However, its high …
Read PDFRNA modifications are essential regulators of gene expression and cellular function, modulating RNA stability, splicing, translation, and localization. Dysregulation of these modifications has been linked to cancer, neurodegenerative disorders, viral infections, and other diseases. Precise …
Read PDFIn this protocol, we detect pseudouridine using nanopore direct RNA sequencing (DRS 002/004) and analyze dynamic changes to mRNA modifications in response to perturbation. We cover RNA extraction, poly(A) selection, DRS, unmodified transcriptome (in vitro …
Read PDFRNA polymerase III (Pol III) transcribes cytosolic transfer RNAs (tRNAs) and other non-coding RNAs (ncRNAs) essential to cellular function. However, many aspects of Pol III transcription and processing, including RNA modifications, remain poorly understood, mainly …
Read PDF2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2'-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for …
Read PDFN6-methyladenosine (m6A) is the most prevalent internal mRNA modification and is enriched in the central nervous system (CNS), yet its role in glioma remains incompletely defined. Using long-read direct RNA sequencing, we mapped transcriptome-wide m6A …
Read PDFBACKGROUND: Leishmania relies on posttranscriptional control to regulate gene expression. Protein-coding genes are synthesised as polycistronic precursors that are processed into individual mRNAs by trans-splicing adding the spliced leader (SL) RNA to the 5’-end and …
Read PDFShort-read RNA sequencing (RNAseq) remains a cornerstone for transcriptome profiling, but is limited in reconstructing full-length transcripts and capturing transcript diversity. While long-read RNAseq spans entire transcripts and resolves complex structures, this technology is hindered …
Read PDFHuman T-lymphotropic virus type 1 (HTLV-1), the first human retrovirus identified, is linked to adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. However, its post-transcriptional regulation remains poorly understood. Here, we used Oxford Nanopore direct …
Read PDF<h4>Background</h4>Nanopore technology enables the direct sequencing of intact RNA molecules allowing for the detection of native chemical modifications. In 2024, Oxford Nanopore Technologies updated direct RNA sequencing from RNA002 to RNA004 platform as well as …
Read PDFCharting the eukaryotic epitranscriptome by direct RNA sequencing is promising but still very challenging, as current bioinformatics tools are based on modification-unaware software and require multiple modification-specific learning steps. Here, we introduce NanoSpeech, a modification-aware …
Read PDFGoats play a significant role in global livestock production and are highly valued for their meat, which is both nutritious and easily digestible. The longissimus dorsi and biceps femoris muscles are not only critical for …
Read PDFThe placenta is critical for fetal development and mediates effects of pregnancy complications on offspring metabolic health yet remains poorly characterized in genomic studies. Existing transcriptomic analyses rely on adult tissue reference annotations, overlooking developmentally …
Read PDFMaize (Zea mays) is one of the world's most important crops and a recognized model for biological research, with some individuals having supernumerary B chromosomes. This B chromosome has been studied for decades, yet its …
Read PDFLong-read RNA sequencing is a powerful technology for transcriptomics, but low throughput and high cost pose challenges. Adaptive sampling, a feature of Oxford Nanopore Technologies, offers real-time enrichment by selectively ejecting non-target molecules. We evaluate …
Read PDFWhile nanopore direct RNA sequencing has substantially advanced transcriptomics, its detection of RNA modifications remains primarily focused on abundant biological base modifications. However, therapeutic RNAs employ a diverse catalog of modifications, including base, sugar, and …
Read PDFOn-demand access to information encoded in nucleotides lies at the heart of DNA/RNA applications. However, contemporary methods for targeted retrieval using PCR amplification or bead-based extraction, rely on Watson-Crick base pairing and pre-defined primers, limiting …
Read PDFLeishmania spp. regulate gene expression posttranscriptionally, yet untranslated regions (UTRs) that can affect mRNA stability and translation remain poorly delineated. We generated a de novo assembled genome for Leishmania donovani strain 1S2D (Ld1S) using PacBio …
Read PDFThe placenta is a temporary organ present during pregnancy that is responsible for coordinating all aspects of pregnancy between the mother and fetus. It has a distinct epigenetic, transcriptomic, and mutational landscape with low levels …
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