Generation of an isoform-level transcriptome atlas of macrophage activation
| Autor: | Apple Cortez Vollmers, Christopher Vollmers, Sophia Campos, Susan Carpenter, Honey E. Mekonen |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Biochemistry Genome Medical and Health Sciences Transcriptome transcriptome analysis Gene expression NNC novel not in catalog Protein Isoforms Cells Cultured Toll-like receptor Cultured CDS full coding sequence ONT Oxford Nanopore Technologies Biological Sciences NIC novel in catalog LPS lipopolysaccharide Research Article Gene isoform Biochemistry & Molecular Biology full-length cDNA sequencing Cells Computational biology Biology DE differential expression 03 medical and health sciences Genetics Humans TLR toll-like receptor Molecular Biology Gene Innate immune system 030102 biochemistry & molecular biology Inflammatory and immune system Gene Expression Profiling Macrophages Human Genome RNA Cell Biology Macrophage Activation 030104 developmental biology FSM full-splice matches Chemical Sciences ISM incomplete splice-matches TSS transcription start site lncRNA long noncoding RNA MDM monocyte-derived macrophage PAM Pam3CSK4 RPM reads per million |
| Zdroj: | The Journal of Biological Chemistry |
| ISSN: | 1083-351X 0021-9258 |
| Popis: | RNA-seq is routinely used to measure gene expression changes in response to cell perturbation. Genes upregulated or downregulated following some perturbation are designated as genes of interest, and their most expressed isoform(s) would then be selected for follow-up experimentation. However, because of its need to fragment RNA molecules, RNA-seq is limited in its ability to capture gene isoforms and their expression patterns. This lack of isoform-specific data means that isoforms would be selected based on annotation databases that are incomplete, not tissue specific, or do not provide key information on expression levels. As a result, minority or nonexistent isoforms might be selected for follow-up, leading to loss in valuable resources and time. There is therefore a great need to comprehensively identify gene isoforms along with their corresponding levels of expression. Using the long-read nanopore-based R2C2 method, which does not fragment RNA molecules, we generated an Isoform-level transcriptome Atlas of Macrophage Activation that identifies full-length isoforms in primary human monocyte-derived macrophages. Macrophages are critical innate immune cells important for recognizing pathogens through binding of pathogen-associated molecular patterns to toll-like receptors, culminating in the initiation of host defense pathways. We characterized isoforms for most moderately-to-highly expressed genes in resting and toll-like receptor–activated monocyte-derived macrophages, identified isoforms differentially expressed between conditions, and validated these isoforms by RT-qPCR. We compiled these data into a user-friendly data portal within the UCSC Genome Browser (https://genome.ucsc.edu/s/vollmers/IAMA). Our atlas represents a valuable resource for innate immune research, providing unprecedented isoform information for primary human macrophages. |
| Databáze: | OpenAIRE |
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