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EndoVIA for quantifying A-to-I editing and mapping the subcellular localization of edited transcripts.
Methods Enzymol
January 2025
Department of Chemistry, Washington University in St. Louis, MO, United States. Electronic address:
Adenosine-to-inosine (A-to-I) editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a prevalent post-transcriptional modification that is vital for numerous biological functions. Given that this modification impacts global gene expression, RNA localization, and innate cellular immunity, dysregulation of A-to-I editing has unsurprisingly been linked to a variety of cancers and other diseases. However, our current understanding of the underpinning mechanisms that connect dysregulated A-to-I editing and disease processes remains limited.
View Article and Find Full Text PDFGenome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes.
Nat Commun
January 2025
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro-a new group-II intron-encoded RT-to map and quantify genome-wide tRNA modifications in Induro-tRNAseq.
View Article and Find Full Text PDFNucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen .
bioRxiv
January 2025
Department of Biological Sciences, University of North Carolina, Charlotte, NC, USA, United States of America.
is an obligate human parasite of the phylum Apicomplexa and is the causative agent of the most lethal form of human malaria. Although N6-methyladenosine modification is thought to be one of the major post-transcriptional regulatory mechanisms for stage-specific gene expression in apicomplexan parasites, the precise base position of m6A in mRNAs or noncoding RNAs in these parasites remains unknown. Here, we report global nucleotide-resolution mapping of m6A residues in using DART-seq technology, which quantitatively displayed a stage-specific, dynamic distribution pattern with enrichment near mRNA 3' ends.
View Article and Find Full Text PDFPredicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation.
Nat Genet
January 2025
Calico Life Sciences LLC, South San Francisco, CA, USA.
Sequence-based machine-learning models trained on genomics data improve genetic variant interpretation by providing functional predictions describing their impact on the cis-regulatory code. However, current tools do not predict RNA-seq expression profiles because of modeling challenges. Here, we introduce Borzoi, a model that learns to predict cell-type-specific and tissue-specific RNA-seq coverage from DNA sequence.
View Article and Find Full Text PDFIdentification and characterisation of temporal abundance of microRNAs in synovial fluid from an experimental equine model of osteoarthritis.
Equine Vet J
January 2025
Department of Veterinary Clinical Sciences, University of Copenhagen, Taastrup, Denmark.
Background: MicroRNAs, a class of small noncoding RNAs, serve as post-transcriptional regulators of gene expression and are present in a stable and quantifiable form in biological fluids. MicroRNAs may influence intra-articular responses and the course of disease, but very little is known about their temporal changes in osteoarthritis.
Objectives: To identify miRNAs and characterise the temporal changes in their abundance in SF from horses with experimentally induced osteoarthritis.
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