scholarly journals The Study of Alternative Splicing Events in Human Induced Pluripotent Stem Cells From a Down's Syndrome Patient

2021 ◽  
Vol 9 ◽  
Author(s):  
Yunjie Wang ◽  
Zexu Li ◽  
Guanheng Yang ◽  
Linlin Cai ◽  
Fan Yang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Regulatory Networks ◽  
Potential Role ◽  
Down's Syndrome ◽  
Down’S Syndrome ◽  
Biological Processes ◽  
Protein Coding ◽  
Induced Pluripotent ◽  
Congenital Disabilities ◽  
Variable Penetrance

Down's syndrome (DS) is one of the most commonly known disorders with multiple congenital disabilities. Besides severe cognitive impairment and intellectual disability, individuals with DS also exhibit additional phenotypes of variable penetrance and severity, with one or more comorbid conditions, including Alzheimer's disease, congenital heart disease, or leukemia. Various vital genes and regulatory networks had been studied to reveal the pathogenesis of the disease. Nevertheless, very few studies have examined alternative splicing. Alternative splicing (AS) is a regulatory mechanism of gene expression when making one multi-exon protein-coding gene produce more than one unique mature mRNA. We employed the GeneChip Human Transcriptome Array 2.0 (HTA 2.0) for the global gene analysis with hiPSCs from DS and healthy individuals. Examining differentially expressed genes (DEGs) in these groups and focusing on specific transcripts with AS, 466 up-regulated and 722 down-regulated genes with AS events were identified. These genes were significantly enriched in biological processes, such as cell adhesion, cardiac muscle contraction, and immune response, through gene ontology (GO) analysis of DEGs. Candidate genes, such as FN1 were further explored for potentially playing a key role in DS. This study provides important insights into the potential role that AS plays in DS.

scholarly journals Role of astroglia in Down’s syndrome revealed by patient-derived human-induced pluripotent stem cells

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Chen Chen ◽  
Peng Jiang ◽  
Haipeng Xue ◽  
Suzanne E. Peterson ◽  
Ha T. Tran ◽  
...  
Keyword(s):  
Stem Cells ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
Down's Syndrome ◽  
Down’S Syndrome ◽  
Induced Pluripotent

scholarly journals Computational Evidence of NAGNAG Alternative Splicing in Human Large Intergenic Noncoding RNA

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Xiaoyong Sun ◽  
Simon M. Lin ◽  
Xiaoyan Yan
Keyword(s):  
Alternative Splicing ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Data Sets ◽  
Posttranslational Regulation ◽  
Biological Processes ◽  
Rna Seq ◽  
Splice Site Selection ◽  
Protein Coding ◽  
Sequencing Studies

NAGNAG alternative splicing plays an essential role in biological processes and represents a highly adaptable system for posttranslational regulation of gene function. NAGNAG alternative splicing impacts a myriad of biological processes. Previous studies of NAGNAG largely focused on messenger RNA. To the best of our knowledge, this is the first study testing the hypothesis that NAGNAG alternative splicing is also operative in large intergenic noncoding RNA (lincRNA). The RNA-seq data sets from recent deep sequencing studies were queried to test our hypothesis. NAGNAG alternative splicing of human lincRNA was identified while querying two independent RNA-seq data sets. Within these datasets, 31 NAGNAG alternative splicing sites were identified in lincRNA. Notably, most exons of lincRNA containing NAGNAG acceptors were longer than those from protein-coding genes. Furthermore, presence of CAG coding appeared to participate in the splice site selection. Finally, expression of the isoforms of NAGNAG lincRNA exhibited tissue specificity. Together, this study improves our understanding of the NAGNAG alternative splicing in lincRNA.

scholarly journals The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 918
Author(s):  
Dareen Almojil ◽  
Yann Bourgeois ◽  
Marcin Falis ◽  
Imtiyaz Hariyani ◽  
Justin Wilcox ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Regulatory Networks ◽  
Biological Processes ◽  
Structural Rearrangements ◽  
Protein Coding ◽  
Vast Number ◽  
Haploid Genome Size ◽  
Genomic Regions ◽  
The Impact ◽  
Host Genes

Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.

scholarly journals Transposable element expression at unique loci in single cells with CELLO-seq

2020 ◽  
Author(s):  
Rebecca V Berrens ◽  
Andrian Yang ◽  
Christopher E Laumer ◽  
Aaron TL Lun ◽  
Florian Bieberich ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Single Cells ◽  
Biological Processes ◽  
Specific Expression ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Repetitive Nature ◽  
Long Read ◽  
Induced Pluripotent

AbstractThe role of Transposable Elements (TEs) in regulating diverse biological processes, from early development to cancer, is becoming increasing appreciated. However, unlike other biological processes, next generation single-cell sequencing technologies are ill-suited for assaying TE expression: in particular, their highly repetitive nature means that short cDNA reads cannot be unambiguously mapped to a specific locus. Consequently, it is extremely challenging to understand the mechanisms by which TE expression is regulated and how they might themselves regulate other protein coding genes. To resolve this, we introduce CELLO-seq, a novel method and computational framework for performing long-read RNA sequencing at single cell resolution. CELLO-seq allows for full-length RNA sequencing and enables measurement of allelic, isoform and TE expression at unique loci. We use CELLO-seq to assess the widespread expression of TEs in 2-cell mouse blastomeres as well as human induced pluripotent stem cells (hiPSCs). Across both species, old and young TEs showed evidence of locus-specific expression, with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed surprising heterogeneity, with TEs within a class showing different patterns of correlation, suggesting distinct regulatory mechanisms.

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