Genome Studies of Gene Expression and Alternative Splicing During iPSC Skeletal Muscle Induction and Differentiation

• Main Author: Wu, Yibo
• Other Authors: Zheyang Wu, Advisor
• Format: Others
• Published: Digital WPI 2019
• Subjects: differential expression; FSHD; functional analysis; iPSC; Iso-Seq; novel genes and transcripts
• Online Access: https://digitalcommons.wpi.edu/etd-theses/1319; https://digitalcommons.wpi.edu/cgi/viewcontent.cgi?article=2318&context=etd-theses

Facioscapulohumeral muscular dystrophy(FSHD) is a disorder characterized by muscle weakness and wasting (atrophy). This disease is typically inherited as autosomal dominant and has a complex genetic and epigenetic etiology. Our collaborator had differentiated healthy human pluripotent stem cells(iPSC) into skeletal muscles and exploited ISO-Seq to explore cell gene expression and transcript alternative splicing usage profile during 8 differentiation stages. Later, stage specific gene differential expression, transcript alternative splicing, gene ontology and novel gene/transcript were analysed to characterize the feature of each stage during the differentiation. In terms of expressed genes with more than or equal to 5 transcripts, each stage had shown their own stage specific features. About transcripts, iPS, S1, ADM.D0, ADM.D4 have about 30% to 40% more total transcripts than the rest 4 stages. 4 kinds of alternative splicing events are generally distributed and S2 stage has the least alternative splicing events potentially due to technical reasons. As for gene differential expressions, ADM.D4 has considerable amount of differential expressed genes with 5 other stages and it has minor difference with ISM.D4 and S3 stages(they are all myotubes cells). The gene ontology analysis is performed according to the results of previous step, stage specific GO terms are revealed.