Alternative splicing exists in most multi-exonic genes,and exploring these complex alternative splicing events and their resultant isoform expressions is essential.However,it has become conventional that RNA sequencin...Alternative splicing exists in most multi-exonic genes,and exploring these complex alternative splicing events and their resultant isoform expressions is essential.However,it has become conventional that RNA sequencing results have often been summarized into gene-level expression counts mainly due to the multiple ambiguous mapping of reads at highly similar regions.Transcript-level quantification and interpretation are often overlooked,and biological interpretations are often deduced based on combined transcript information at the gene level.Here,for the most variable tissue of alternative splicing,the brain,we estimate isoform expressions in 1,191 samples collected by the Genotype-Tissue Expression(GTEx)Consortium using a powerful method that we previously developed.We perform genome-wide association scans on the isoform ratios per gene and identify isoform-ratio quantitative trait loci(irQTL),which could not be detected by studying gene-level expressions alone.By analyzing the genetic architecture of the irQTL,we show that isoform ratios regulate edu-cational attainment via multiple tissues including the frontal cortex(BA9),cortex,cervical spinal cord,and hippocampus.These tissues are also associated with different neuro-related traits,including Alzheimer’s or dementia,mood swings,sleep duration,alcohol intake,intelligence,anxiety or depression,etc.Mendelian randomization(MR)analysis revealed 1,139 pairs of isoforms and neuro-related traits with plausible causal relationships,showing much stronger causal effects than on general diseases measured in the UK Biobank(UKB).Our results highlight essential transcript-level biomarkers in the human brain for neuro-related complex traits and diseases,which could be missed by merely investigating overall gene expressions.展开更多
基金Funding XS was in receipt of a National Natural Science Foundation of China(NSFC)grant(No.12171495)a Natural Science Foundation of Guangdong Province grant(No.2114050001435)+3 种基金a National Key Research and Development Program grant(No.2022YFF1202105)Swedish Research Council(Vetenskapsraet)grants(No.2017-02543&No.2022-01309)supported by the Swedish Research Council grant(No.2017-02543)XS The Swedish National Infrastructure for Computing(SNIC)utilized was partially funded by the Swedish Research Council through grant agreement No.2018-05973.
文摘Alternative splicing exists in most multi-exonic genes,and exploring these complex alternative splicing events and their resultant isoform expressions is essential.However,it has become conventional that RNA sequencing results have often been summarized into gene-level expression counts mainly due to the multiple ambiguous mapping of reads at highly similar regions.Transcript-level quantification and interpretation are often overlooked,and biological interpretations are often deduced based on combined transcript information at the gene level.Here,for the most variable tissue of alternative splicing,the brain,we estimate isoform expressions in 1,191 samples collected by the Genotype-Tissue Expression(GTEx)Consortium using a powerful method that we previously developed.We perform genome-wide association scans on the isoform ratios per gene and identify isoform-ratio quantitative trait loci(irQTL),which could not be detected by studying gene-level expressions alone.By analyzing the genetic architecture of the irQTL,we show that isoform ratios regulate edu-cational attainment via multiple tissues including the frontal cortex(BA9),cortex,cervical spinal cord,and hippocampus.These tissues are also associated with different neuro-related traits,including Alzheimer’s or dementia,mood swings,sleep duration,alcohol intake,intelligence,anxiety or depression,etc.Mendelian randomization(MR)analysis revealed 1,139 pairs of isoforms and neuro-related traits with plausible causal relationships,showing much stronger causal effects than on general diseases measured in the UK Biobank(UKB).Our results highlight essential transcript-level biomarkers in the human brain for neuro-related complex traits and diseases,which could be missed by merely investigating overall gene expressions.
