Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events).Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.Key words: Alternative splicing; transcript; protein; SNP
Background: To investigate the biological basis of radiosensitivity difference in lung adenocarcinoma cells, EGFR mutant or a wide variety of signal pathways?Methods: There were fourteen lung adenocarcinoma cell lines used to carry out experiments in this study. The SF2 experimental test data of fourteen cell lines used in this study are from the previous work we did. EGFR mutation in each cell line detected by Next-Generation Sequencing. Statistical difference in SF2 about fourteen cells used the Kruskal-Wallis test. Correlation between EGFR mutant or not and SF2 analyzed by Student’s t-test. The proteomes of the 14 lung adenocarcinoma organisms were identified by DIA in LC-MS/MS proteomic technology. P < 0.05 showed statistical significance. R language software was used to perform the bioinformatics analysis.Results: The SF2(Surviving fractional 2Gy ) median value is 0.351(0.122-0.825). The number of cell lines in the EGFR mutatant-type is five, wild-type is nine. We obtained a mean coverage of 5425 proteins from fourteen lung adenocarcinoma cell lines. There are thirty-nine different expression proteins in total. Significant differences of SF2 was found among fourteen cell lines (P=0.004 < 0.05). showed that there is no correlation between the EGFR mutant-type group and the EGFR wild-type group(P=0.822> 0.05). The R language analyzed based on proteomic explored that there were thirty-nine DEPs(differently expresse proteins) and four KEGG pathways: ECM-receptor interaction, Focal adhesion, Hematopoietic cell lineage, and Prion diseases. LAMC1, ITGB4/ITGA6, and CD44 participated in multiple signaling pathways. PPI examined that LAMC1, ITGB4/ITGA6, CD44, FLNB, CD59, PRNP interacted more concentratedly.Conclusion: The inherent radiosensitivity of lung adenocarcinoma cell lines is not determined by the status of EGFR mutant, maybe by other signal pathways such as LAMC1, ITGB4/ITGA6, CD44, and PRNP.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.