16 papers · ranked by Valyu relevance
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Isaac Adeyemi Babarinde, Andrew Paul Hutchins
Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. The heterogeneity of the assembled transcript sets might…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 5 more
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs…
Ya-Hui Lin, Jennifer E. Dodd, Luisa Cutillo, Lydia M. Castelli + 14 more
Transcriptomes and translatomes measure genome-wide levels of total and ribosome-associated RNAs. A few hundred translatomes were reported over >250,000 transcriptomes highlighting the challenges of identifying translating RNAs. Here, we used a human isogenic inducible model of TDP-43-linked amyotrophic lateral…
David Murphy, Mina Ryten, Nicholas W. Wood, Emil K. Gustavsson
Long-read RNA sequencing has expanded our understanding of the transcriptome, revealing unannotated transcripts. However, interpreting their functional relevance remains challenging. To address this, we developed TX2P, a user-friendly tool that integrates transcriptomic and proteomic data to link RNA discoveries with…
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans + 79 more
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species…
Jan Grau, Jens Keilwagen
Annotation of genes and transcripts is an important requirement for understanding the information that is encoded in newly sequenced genomes. One source of information suited for this purpose are RNA-seq data mapped to the respective genome sequence. RNA-seq-based approaches for transcript reconstruction generate…
Eleanor Elgood Hunt, Claudia Vivori, Folkert J van Werven
Transcription initiation is a highly dynamic and tightly regulated process involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently…
Joel Nunes Leite Junior, Helba Cirino, Priscila C. Antonello, Marcelo Marques Zerillo + 2 more
Transcriptome studies have contributed to the understanding of protein coding and non-coding gene expression of several organisms. They also provide knowledge into host responses to pathogen infections. Not common yet is to detect transcripts from multiple interacting organisms present in a given sample. In addition…
Vighnesh Ghatpande, Uma Paul, MacKenzie A Howard, Can Cenik
In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca^2+^ regulation in muscle, and signaling during embryonic…
Vincent Leon Gotsmann, Michael Kien Yin Ting, Nadin Haase, Sophia Rudorf + 2 more
Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Here, we established an optimized and high resolution Ribo-seq protocol for the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas). Comparing different…
Meriem Hadjer Hamadou, Laura Alunno, Tecla Venturelli, Samuel Valentini + 20 more
Relatively few studies have examined the link between SNPs and mRNA translation, despite the established importance of translational regulation in shaping cell phenotypes. We developed a pipeline analyzing the allelic imbalance in total and polysome-bound mRNAs from paired RNA-seq data of HCT116 cells and identified 40…
Rodrigo Alarcon, Daniel Köster, Stine Behrmann, Zoya Ignatova
Transfer RNAs (tRNAs) play an essential role in protein synthesis and cellular homeostasis, with their dysregulation associated with various human pathologies. Recent advances in direct RNA sequencing by the Nanopore platform have enabled simultaneous profiling of tRNA abundance, modifications, and aminoacylation…
John R. Prensner, Jennifer G. Abelin, Leron W. Kok, Karl R. Clauser + 5 more
Ribosome profiling (Ribo-seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of non-canonical sites of ribosome translation outside of the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7,000 non-canonical open…
Tom Rappol, Maria Waldl, Anastasia Chugunova, Ivo L. Hofacker + 2 more
tRNA genes exist in multiple copies in the genome of all organisms across the three domains of life. Besides the sequence differences across tRNA copies, extensive post-transcriptional modification adds a further layer to tRNA diversification. Whilst the crucial role of tRNAs as adapter molecules in protein translation…
Aaron Wacholder, Anne-Ruxandra Carvunis
Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection…