18 papers · ranked by Valyu relevance
Houlin Yu, Christophe H. Georgescu, Akanksha Khorgade, Ghamdan Al-Eryani + 19 more
Recent advances in long-read transcriptome sequencing enable high-throughput profiling of full-length RNA isoforms in bulk, single-cell, and single-nucleus samples. However, long-read datasets typically contain a mixture of complete and partial transcripts, leading to pervasive ambiguity in read-to-isoform assignment…
Andrew Xue, Bo Cai, Qian Xue, Nianping Liu + 3 more
Single-cell RNA sequencing has transformed our understanding of tissue complexity and heterogeneous cell states, yet provides little information about the subcellular organization of transcriptomes - despite the central role of RNA localization in splicing, translation, and function. Here we introduce single-cell…
Xinchang Zheng, Zev Kronenberg, Sonia Garcia-Ruiz, Ryan M. Layer + 3 more
Alternative splicing generates extensive transcriptomic complexity, yet “novelty” is often inflated because of incomplete reference annotations, with 20-70% of transcripts in RNA-Seq studies labeled as novel. Isopedia provides an expandable data structure for reference-agnostic isoform annotation, which we demonstrate…
Justin T. Roberts, Viktor M. Pastukh, Grant T. Daly, Adeyeye I. Haastrup + 3 more
Hypoxia is a fundamental pathophysiological stimulus that plays important roles in multiple cardiopulmonary diseases. During hypoxic stress, cells adapt by undergoing widespread transcriptional reprogramming. The conventional approach to investigating this response has largely involved RNA-seq analysis which typically…
Shakunthala Natarajan, Claudia Sterling, Nancy Choudhary, Najnin Khatun + 3 more
Rapid developments in sequencing technologies have reduced the costs of transcriptomic experiments and resulted in a plethora of publicly available RNA-seq datasets. This is a valuable resource that can be harnessed to obtain novel biological insights through data upcycling. In this wake, we introduce XpBrew, an…
Molly Borowiak, Yun William Yu
Eukaryotic genes can encode multiple protein isoforms based on alternative splicing of their transcribed regions. Most modern novel isoform discovery methods function by identifying and assembling exon splice junctions from an RNAseq sample. However, splice junctions can only be accurately annotated with time-intensive…
Maxfield M.G. Kelsey, Radha L. Kalekar, John M. Sedivy
Cellular senescence drives aging-related tissue dysfunction through the senescence-associated secretory phenotype (SASP), an inflammatory secretome linked to retrotransposable element (RTE) derepression. Transcriptomic and proteomic approaches have extensively characterized the senescence program, but key gaps remain…
Florian Bernard, Emma Kandel, Delphine Dargere, Eric Cornes + 1 more
Single-cell RNA sequencing technology dramatically changed the way we investigate transcriptomes. However, the amount and complexity of data generated by such methods poses new challenges for biologists who are trying to extract detailed insights into the genetic programs that drive cellular functions and…
Y-H Taguchi, Turki Turki
Integrating transcriptome, translatome, and proteome data remains challenging because changes in mRNA, ribosome occupancy, and protein abundance do not always occur simultaneously. To address this, we applied tensor-decomposition-based unsupervised feature extraction to a tri-omics dataset generated under…
Mathurin Fatou, Etienne Kornobis, Thibaut Douché, Karen Druart + 4 more
Back to the 1990’ the single step method developed by Chomczynski and Sacchi for RNA isolation was extended for sequential isolation of RNA, DNA and proteins from a same sample. Although the quality of the extracted RNA turned compatible with RNA-Seq analyses, the extraction of the protein fraction from the same sample…
Cesar Arcasi Matta, Zhi Qi Ten, Simpson Joseph
Translation is a central control point of gene expression, linking nucleotide sequences to functional proteins. Dysregulated translation contributes to diverse diseases, underscoring the need for methods that can directly reveal which transcripts are actively translated. Ribosome profiling, the current gold standard…
Jingyi Ren, Seth Furniss, Chengjie Zhou, Haowen Zhou + 3 more
Spatial patterning of mRNA translation is a fundamental process in early embryogenesis. Existing RNA translation profiling methods lack subcellular spatial resolution at the single-molecule level, limiting our understanding of spatial RNA biology in embryogenesis. To address this, we profiled the spatial translatome of…
Mie Monti, Hasan Yilmaz, Alessia Del Piano, Michele Arnoldi + 7 more
During translation, transfer RNAs (tRNAs) deliver specific amino acids to the ribosome in a coordinated manner with the sequence encoded by the mRNA. Despite their central role in protein synthesis, their precise contribution to the modulation of translation remains poorly understood, primarily due to lack of methods…
Eric Malekos, Valeriy Smaliy, Susan Carpenter
Ribosome profiling has revealed thousands of noncanonical translation events across mammalian genomes, yet functional characterization has overwhelmingly focused on proliferative fitness in cancer cell lines. Here, we present a comprehensive survey of noncanonical translation in the mouse immune system and its…
Yuyang Qi, Chengkang Li, Nur Yesiltac-Tosun, Jannick Schicktanz + 4 more
RNA modifications play crucial roles in regulating cellular processes, but comprehensive mapping of the human RNome still remains limited by technological challenges. Mass spectrometry (MS) is a valuable tool to analyse RNA modifications complementing sequencing-based analysis. Current MS-based oligonucleotide…
Umut Çakır, Noujoud Gabed, Selen Kaya, Vagner A. Benedito + 3 more
Non-canonical open reading frames (ncORFs) are an emerging area of research that is quickly gaining momentum. Many peptides and proteins missed in initial annotation efforts (ncProts) were subsequently shown to be crucial for a wide range of biological processes. The discovery of ncORFs continues to improve the…
Caroline West, Lauren Dineen, Abigail Leavitt LaBella
Transfer RNAs (tRNAs) are known for delivering amino acids to the growing polypeptide chain during translation. They can also influence gene expression, especially in times of nutrient starvation, through differential tRNA expression and modification. tRNAs have a highly consistent cloverleaf structure, but relatively…
Tiziano Vignolini, Olivia Carril, Victor Tobiasson, Joe Georgeson + 8 more
Ribosome composition can vary through differences in associated proteins, post-transcriptional and post-translational modifications. Such heterogeneity enables ribosomes to respond to environmental^1^ or pathological^2,3^ conditions, and modulate localized translation^4^. A long-standing observation has also been the…