Degner, J. F. et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390–394 (2012).
Article
PubMed
PubMed Central
CAS
Google Scholar
Farh, K. K.-H. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337–343 (2015).
Article
PubMed
CAS
Google Scholar
Gaffney, D. J. et al. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 13, R7 (2012).
Article
PubMed
PubMed Central
CAS
Google Scholar
Liebhaber, S. A. mRNA stability and the control of gene expression. Nucleic Acids Symp. Ser. 36, 29–32 (1997).
CAS
Google Scholar
Hollams, E. M., Giles, K. M., Thomson, A. M. & Leedman, P. J. MRNA stability and the control of gene expression: implications for human disease. Neurochem. Res. 27, 957–980 (2002).
Article
PubMed
CAS
Google Scholar
Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011).
Article
PubMed
Google Scholar
Tani, H. et al. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res. 22, 947–956 (2012).
Article
PubMed
PubMed Central
CAS
Google Scholar
Courel, M. et al. GC content shapes mRNA storage and decay in human cells. eLife 8, e49708 (2019).
Article
PubMed
PubMed Central
Google Scholar
LaMarre, J., Gingerich, T. J., Feige, J.-J. & LaMarre, J. AU-rich elements and the control of gene expression through regulated mRNA stability. Anim. Health Res. Rev. 5, 49–63 (2004).
Article
PubMed
Google Scholar
Agarwal, V., Bell, G. W., Nam, J.-W. & Bartel, D. P. Predicting effective microRNA target sites in mammalian mRNAs. eLife 4, e05005 (2015).
Article
PubMed
PubMed Central
Google Scholar
Wu, Q. et al. Translation affects mRNA stability in a codon-dependent manner in human cells. eLife 8, e45396 (2019).
Article
PubMed
PubMed Central
Google Scholar
Pai, A. A. et al. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 8, e1003000 (2012).
Article
PubMed
PubMed Central
CAS
Google Scholar
Alkallas, R., Fish, L., Goodarzi, H. & Najafabadi, H. S. Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease. Nat. Commun. 8, 909 (2017).
Article
PubMed
PubMed Central
Google Scholar
Li, J.-R., Tang, M., Li, Y., Amos, C. I. & Cheng, C. Genetic variants associated mRNA stability in lung. BMC Genomics 23, 196 (2022).
Article
PubMed
PubMed Central
CAS
Google Scholar
Paulsen, M. T. et al. Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc. Natl Acad. Sci. USA 110, 2240–2245 (2013).
Article
PubMed
PubMed Central
CAS
Google Scholar
Bedi, K. et al. Co-transcriptional splicing efficiencies differ within genes and between cell types. RNA 27, 829–840 (2021).
Article
PubMed
PubMed Central
CAS
Google Scholar
The GTEx Consortium et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318–1330 (2020).
Article
PubMed Central
Google Scholar
Salton, M. et al. Matrin 3 binds and stabilizes mRNA. PLoS ONE 6, e23882 (2011).
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang, G. et al. Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay. Nat. Commun. 13, 859 (2022).
Article
PubMed
PubMed Central
CAS
Google Scholar
Meyer, C. et al. The TIA1 RNA-binding protein family regulates EIF2AK2-mediated stress response and cell cycle progression. Mol. Cell 69, 622–635 (2018).
Article
PubMed
PubMed Central
CAS
Google Scholar
Kim, Y. K. & Maquat, L. E. UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond. RNA 25, 407–422 (2019).
Article
PubMed
PubMed Central
CAS
Google Scholar
Yang, E.-W. et al. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat. Commun. 10, 1338 (2019).
Article
PubMed
PubMed Central
Google Scholar
Zhang, J. et al. An integrative ENCODE resource for cancer genomics. Nat. Commun. 11, 3696 (2020).
Article
PubMed
PubMed Central
CAS
Google Scholar
Fabian, M. R., Sonenberg, N. & Filipowicz, W. Regulation of mRNA translation and stability by microRNAs. Annu. Rev. Biochem. 79, 351–379 (2010).
Article
PubMed
CAS
Google Scholar
Liu, C.-J. et al. miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. Nucleic Acids Res. 49, D1276–D1281 (2021).
Article
PubMed
CAS
Google Scholar
Fu, T. et al. Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes. Nat. Commun. 15, 3335 (2024).
Article
PubMed
PubMed Central
CAS
Google Scholar
Griesemer, D. et al. Genome-wide functional screen of 3′ UTR variants uncovers causal variants for human disease and evolution. Cell 184, 5247–5260 (2021).
Article
PubMed
PubMed Central
CAS
Google Scholar
Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652 (2021).
Article
PubMed
PubMed Central
CAS
Google Scholar
Bresson, S. & Tollervey, D. Tailing off: PABP and CNOT generate cycles of mRNA deadenylation. Mol. Cell 70, 987–988 (2018).
Article
PubMed
CAS
Google Scholar
Springer, T. A. Adhesion receptors of the immune system. Nature 346, 425–434 (1990).
Article
PubMed
CAS
Google Scholar
González-Amaro, R., Diaz-González, F. & Sánchez-Madrid, F. Adhesion molecules in inflammatory diseases. Drugs 56, 977–988 (1998).
Article
PubMed
Google Scholar
Ryter, S. W., Cloonan, S. M. & Choi, A. M. K. Autophagy: a critical regulator of cellular metabolism and homeostasis. Mol. Cells 36, 7–16 (2013).
Article
PubMed
PubMed Central
CAS
Google Scholar
Uffelmann, E. et al. Genome-wide association studies. Nat. Rev. Methods Prim. 1, 37–49 (2021).
Google Scholar
Sollis, E. et al. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51, D977–D985 (2023).
Article
PubMed
CAS
Google Scholar
Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245–252 (2016).
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhou, M. et al. Inhibition of Fam114A1 protects melanocytes from apoptosis through higher RACK1 expression. Aging 13, 24740–24752 (2021).
Article
PubMed
PubMed Central
CAS
Google Scholar
Subbaiah, K. C. V., Wu, J., Tang, W. H. W. & Yao, P. FAM114A1 influences cardiac pathological remodeling by regulating angiotensin II signaling. JCI Insight 7, e152783 (2022).
Article
PubMed
PubMed Central
Google Scholar
Imamachi, N. et al. BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells. Methods 67, 55–63 (2014).
Article
PubMed
CAS
Google Scholar
Ghandi, M. et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).
Article
PubMed
PubMed Central
CAS
Google Scholar
Carter, S. L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).
Article
PubMed
PubMed Central
CAS
Google Scholar
Suvakov, M., Panda, A., Diesh, C., Holmes, I. & Abyzov, A. CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. Gigascience 10, giab074 (2021).
Article
PubMed
PubMed Central
Google Scholar
Abdennur, N. & Mirny, L. A. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36, 311–316 (2020).
Article
PubMed
CAS
Google Scholar
Wang, X. et al. Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes. Nat. Methods 18, 661–668 (2021).
Article
PubMed
PubMed Central
CAS
Google Scholar
Yan, J. et al. Improving prime editing with an endogenous small RNA-binding protein. Nature 628, 639–647 (2024).
Article
PubMed
PubMed Central
CAS
Google Scholar
Chow, R. D., Chen, J. S., Shen, J. & Chen, S. A web tool for the design of prime-editing guide RNAs. Nat. Biomed. Eng. 5, 190–194 (2021).
Article
PubMed
CAS
Google Scholar
Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402–410 (2022).
Article
PubMed
CAS
Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Article
PubMed
CAS
Google Scholar
Ashuach, T. et al. MPRAnalyze: statistical framework for massively parallel reporter assays. Genome Biol. 20, 183 (2019).
Article
PubMed
PubMed Central
Google Scholar
Ormond, C., Ryan, N. M., Corvin, A. & Heron, E. A. Converting single nucleotide variants between genome builds: from cautionary tale to solution. Brief. Bioinform. 22, bbab069 (2021).
Article
PubMed
PubMed Central
Google Scholar
Van Nostrand, E. L. et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 583, 711–719 (2020).
Article
PubMed
PubMed Central
Google Scholar
Smedley, D. et al. BioMart–biological queries made easy. BMC Genomics 10, 22 (2009).
Article
PubMed
PubMed Central
Google Scholar
Sayols, S. rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPubl. Biol. https://doi.org/10.17912/micropub.biology.000811 (2023).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Article
PubMed
PubMed Central
CAS
Google Scholar
Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228–1235 (2015).
Article
PubMed
PubMed Central
CAS
Google Scholar
gxiaolab. Gxiaolab/RNAtracker: for publication. Zenodo https://doi.org/10.5281/zenodo.15528784 (2025).
Purcell, S. et al. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Human Genet. 81, 559–575 (2007).
Article
CAS
Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Article
PubMed
PubMed Central
CAS
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Article
PubMed
PubMed Central
CAS
Google Scholar
Yee, T. W. The VGAM package for categorical data analysis. J. Stat. Softw. 32, 1–34 (2010).
Article
Google Scholar
Lex, A., Gehlenborg, N., Strobelt, H., Vuillemot, R. & Pfister, H. UpSet: visualization of intersecting sets. IEEE Trans. Vis. Comput. Graph. 20, 1983–1992 (2014).
Article
PubMed
PubMed Central
Google Scholar
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).
Article
PubMed
CAS
Google Scholar
Gådin, J. R., van’t Hooft, F. M., Eriksson, P. & Folkersen, L. AllelicImbalance: an R/bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. BMC Bioinformatics 16, 194 (2015).
Article
PubMed
PubMed Central
Google Scholar