scholarly journals Comprehensive identification of alternative back-splicing in human tissue transcriptomes

2020 ◽  
Vol 48 (4) ◽  
pp. 1779-1789 ◽  
Author(s):  
Peng Zhang ◽  
Xiao-Ou Zhang ◽  
Tingting Jiang ◽  
Lingling Cai ◽  
Xiao Huang ◽  
...  
Keyword(s):  
Splice Site ◽  
Human Tissue ◽  
Single Gene ◽  
Brain Regions ◽  
Intron Length ◽  
Circular Rnas ◽  
Human Tissues ◽  
Alu Elements ◽  
Depth Analysis ◽  
Brain Tissues

Abstract Circular RNAs (circRNAs) are covalently closed RNAs derived from back-splicing of genes across eukaryotes. Through alternative back-splicing (ABS), a single gene produces multiple circRNAs sharing the same back-splice site. Although many ABS events have recently been discovered, to what extent ABS involves in circRNA biogenesis and how it is regulated in different human tissues still remain elusive. Here, we reported an in-depth analysis of ABS events in 90 human tissue transcriptomes. We observed that ABS occurred for about 84% circRNAs. Interestingly, alternative 5′ back-splicing occurs more prevalently than alternative 3′ back-splicing, and both of them are tissue-specific, especially enriched in brain tissues. In addition, the patterns of ABS events in different brain regions are similar to each other and are more complex than the patterns in non-brain tissues. Finally, the intron length and abundance of Alu elements positively correlated with ABS event complexity, and the predominant circRNAs had longer flanking introns and more Alu elements than other circRNAs in the same ABS event. Together, our results represent a resource for circRNA research—we expanded the repertoire of ABS events of circRNAs in human tissue transcriptomes and provided insights into the complexity of circRNA biogenesis, expression, and regulation.

scholarly journals Functional human genes typically exhibit epigenetic conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0253250
Author(s):  
Daniel Rud ◽  
Paul Marjoram ◽  
Kimberly Siegmund ◽  
Darryl Shibata
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Single Gene ◽  
Functional Genes ◽  
Human Tissues ◽  
Gene Conservation ◽  
Individual Culture ◽  
Human Genes

Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.

scholarly journals Linking the association between circRNAs and Alzheimer’s disease progression by multi-tissue circular RNA characterization

2020 ◽  
Author(s):  
IJu Lo ◽  
Jamie Hill ◽  
Bjarni J. Vilhjálmsson ◽  
Jørgen Kjems
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Inferior Frontal Gyrus ◽  
Circular Rna ◽  
Brain Regions ◽  
Parahippocampal Gyrus ◽  
Circular Rnas ◽  
Cognitive Disability ◽  
Anterior Prefrontal Cortex ◽  
Progressive Course

AbstractAlzheimer’s Disease (AD) has devastating consequences for patients during its slow, progressive course. It is important to understand the pathology of AD onset. Recently, circular RNAs (circRNAs) have been found to participate in many human diseases including cancers and neurodegenerative conditions. In this study, we mined the published dataset on the AMP-AD Knowledge Portal from the Mount Sinai Brain Bank (MSBB) to describe the circRNA profiles at different AD stage in brain samples from four AD patients brain regions, anterior prefrontal cortex, superior temporal lobe, parahippocampal gyrus, and inferior frontal gyrus. We found in total 147 circRNAs to be differentially expressed (DE) during AD progression in the four regions. We also characterized the mRNA-circRNA co-expression network and annotated the potential function of circRNAs based on the co-expressed modules. Based on our results, we propose that parahippocampal gyrus is the most circRNA-regulated region during the AD progression. The strongest negatively AD stage-correlated module in parahippocampal gyrus were enriched in cognitive disability and pathological-associated pathways such as synapse organization and regulation of membrane potential. Finally, the regression model based on the expression pattern of DE circRNAs in the module could help to distinguish the disease severity of patients, further supported the importance of circRNAs in AD pathology. In conclusion, our finding indicates that circRNAs in parahippocampal gyrus are possible regulators of AD progression and potentially be a therapeutic target or of AD.

scholarly journals Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs

BMC Genomics ◽  
2018 ◽  
Vol 19 (S1) ◽  
Author(s):  
Yu-Chen Liu ◽  
Yu-Jung Chiu ◽  
Jian-Rong Li ◽  
Chuan-Hu Sun ◽  
Chun-Chi Liu ◽  
...  
Keyword(s):  
Human Tissue ◽  
Transcriptome Sequencing ◽  
Circular Rnas ◽  
Sequencing Data ◽  
Tissue Specific

scholarly journals Assessing Autophagy in Archived Tissue or How to Capture Autophagic Flux from a Tissue Snapshot

Biology ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 59 ◽  
Author(s):  
Magali Humbert ◽  
María Morán ◽  
Patricia de la Cruz-Ojeda ◽  
Jordi Muntané ◽  
Tabea Wiedmer ◽  
...  
Keyword(s):  
Human Tissue ◽  
Degradation Mechanism ◽  
Autophagic Flux ◽  
Human Tissues ◽  
Tissue Analysis ◽  
Therapeutic Approaches ◽  
Tissue Samples ◽  
Clear Cut ◽  
Autophagic Activity ◽  
Made In

Autophagy is a highly conserved degradation mechanism that is essential for maintaining cellular homeostasis. In human disease, autophagy pathways are frequently deregulated and there is immense interest in targeting autophagy for therapeutic approaches. Accordingly, there is a need to determine autophagic activity in human tissues, an endeavor that is hampered by the fact that autophagy is characterized by the flux of substrates whereas histology informs only about amounts and localization of substrates and regulators at a single timepoint. Despite this challenging task, considerable progress in establishing markers of autophagy has been made in recent years. The importance of establishing clear-cut autophagy markers that can be used for tissue analysis cannot be underestimated. In this review, we attempt to summarize known techniques to quantify autophagy in human tissue and their drawbacks. Furthermore, we provide some recommendations that should be taken into consideration to improve the reliability and the interpretation of autophagy biomarkers in human tissue samples.

scholarly journals Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue

Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1616
Author(s):  
Tobias Jakobi ◽  
Dominik Siede ◽  
Jessica Eschenbach ◽  
Andreas W. Heumüller ◽  
Martin Busch ◽  
...  
Keyword(s):  
Cardiac Tissue ◽  
Umbilical Vein ◽  
Expression Profiles ◽  
Developed Countries ◽  
Model Systems ◽  
Start Codon ◽  
Circular Rnas ◽  
Specific Expression ◽  
Cardiac Model ◽  
Depth Analysis

For decades, cardiovascular disease (CVD) has been the leading cause of death throughout most developed countries. Several studies relate RNA splicing, and more recently also circular RNAs (circRNAs), to CVD. CircRNAs originate from linear transcripts and have been shown to exhibit tissue-specific expression profiles. Here, we present an in-depth analysis of sequence, structure, modification, and cardiac circRNA interactions. We used human induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs), human healthy and diseased (ischemic cardiomyopathy, dilated cardiomyopathy) cardiac tissue, and human umbilical vein endothelial cells (HUVECs) to profile circRNAs. We identified shared circRNAs across all samples, as well as model-specific circRNA signatures. Based on these circRNAs, we identified 63 positionally conserved and expressed circRNAs in human, pig, and mouse hearts. Furthermore, we found that the sequence of circRNAs can deviate from the sequence derived from the genome sequence, an important factor in assessing potential functions. Integration of additional data yielded evidence for m6A-methylation of circRNAs, potentially linked to translation, as well as, circRNAs overlapping with potential Argonaute 2 binding sites, indicating potential association with the RISC complex. Moreover, we describe, for the first time in cardiac model systems, a sub class of circRNAs containing the start codon of their primary transcript (AUG circRNAs) and observe an enrichment for m6A-methylation for AUG circRNAs.

scholarly journals Influence of Intron Length on Alternative Splicing of CD44

1998 ◽  
Vol 18 (10) ◽  
pp. 5930-5941 ◽  
Author(s):  
Martyn V. Bell ◽  
Alison E. Cowper ◽  
Marie-Paule Lefranc ◽  
John I. Bell ◽  
Gavin R. Screaton
Keyword(s):  
Alternative Splicing ◽  
Genomic Structure ◽  
Single Gene ◽  
Intron Length ◽  
Protein Isoforms ◽  
Major Influence ◽  
Eukaryotic Genes ◽  
Alternatively Spliced ◽  
Alternatively Spliced Exons

ABSTRACT Although the splicing of transcripts from most eukaryotic genes occurs in a constitutive fashion, some genes can undergo a process of alternative splicing. This is a genetically economical process which allows a single gene to give rise to several protein isoforms by the inclusion or exclusion of sequences into or from the mature mRNA. CD44 provides a unique example; more than 1,000 possible isoforms can be produced by the inclusion or exclusion of a central tandem array of 10 alternatively spliced exons. Certain alternatively spliced exons have been ascribed specific functions; however, independent regulation of the inclusion or skipping of each of these exons would clearly demand an extremely complex regulatory network. Such a network would involve the interaction of many exon-specific trans-acting factors with the pre-mRNA. Therefore, to assess whether the exons are indeed independently regulated, we have examined the alternative exon content of a large number of individual CD44 cDNA isoforms. This analysis shows that the downstream alternatively spliced exons are favored over those lying upstream and that alternative exons are often included in blocks rather than singly. Using a novel in vivo alternative splicing assay, we show that intron length has a major influence upon the alternative splicing of CD44. We propose a kinetic model in which short introns may overcome the poor recognition of alternatively spliced exons. These observations suggest that for CD44, intron length has been exploited in the evolution of the genomic structure to enable tissue-specific patterns of splicing to be maintained.

scholarly journals Functional Dissection of an Alternatively Spliced Herpesvirus Gene by Splice Site Mutagenesis

2016 ◽  
Vol 90 (9) ◽  
pp. 4626-4636 ◽  
Author(s):  
Tim Schommartz ◽  
Stefan Loroch ◽  
Malik Alawi ◽  
Adam Grundhoff ◽  
Albert Sickmann ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Viral Replication ◽  
Splice Site ◽  
Gene Knockout ◽  
Single Gene ◽  
Viral Gene ◽  
Gene Products ◽  
Knockout Mutants ◽  
Alternatively Spliced ◽  
Site Mutagenesis

ABSTRACTHerpesviruses have large and complex DNA genomes. The largest among the herpesviruses, those of the cytomegaloviruses, include over 170 genes. Although most herpesvirus gene products are expressed from unspliced transcripts, a substantial number of viral transcripts are spliced. Some viral transcripts are subject to alternative splicing, which leads to the expression of several proteins from a single gene. Functional analysis of individual proteins derived from an alternatively spliced gene is difficult, as deletion and nonsense mutagenesis, both common methods used in the generation of viral gene knockout mutants, affect several or all gene products at the same time. Here, we show that individual gene products of an alternatively spliced herpesvirus gene can be inactivated selectively by mutagenesis of the splice donor or acceptor site and by intron deletion or substitution mutagenesis. We used this strategy to dissect the essential M112/113 gene of murine cytomegalovirus (MCMV), which encodes the MCMV Early 1 (E1) proteins. The expression of each of the four E1 protein isoforms was inactivated individually, and the requirement for each isoform in MCMV replication was analyzed in fibroblasts, endothelial cells, and macrophages. We show that the E1 p87 isoform, but not the p33, p36, and p38 isoforms, is essential for viral replication in cell culture. Moreover, the presence of one of the two medium-size isoforms (p36 or p38) and the presence of intron 1, but not its specific sequence, are required for viral replication. This study demonstrates the usefulness of splice site mutagenesis for the functional analysis of alternatively spliced herpesvirus genes.IMPORTANCEHerpesviruses include up to 170 genes in their DNA genomes. The functions of most viral gene products remain poorly defined. The construction of viral gene knockout mutants has thus been an important tool for functional analysis of viral proteins. However, this strategy is of limited use when viral gene transcripts are alternatively spliced, leading to the expression of several proteins from a single gene. In this study, we showed, as a proof of principle, that each protein product of an alternatively spliced gene can be eliminated individually by splice site mutagenesis. Mutant viruses lacking individual protein products displayed different phenotypes, demonstrating that the products of alternatively spliced genes have nonredundant functions.

scholarly journals Truncated IRAG variants modulate cGMP-mediated inhibition of human colonic smooth muscle cell contraction

2011 ◽  
Vol 301 (6) ◽  
pp. C1445-C1457 ◽  
Author(s):  
Alexander von Werder ◽  
Martina Mayr ◽  
Günter Schneider ◽  
Daniela Oesterle ◽  
Ralph M. Fritsch ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Smooth Muscle ◽  
Alternative Splicing ◽  
Smooth Muscle Cells ◽  
Single Gene ◽  
Muscle Cells ◽  
Acceptor Site ◽  
Human Tissues ◽  
Mrna Isoforms ◽  
Donor And Acceptor

Nitric oxide (NO) induces relaxation of colonic smooth muscle cells predominantly by cGMP/cGMP-dependent protein kinase I (cGKI)-induced phosphorylation of the inositol 1,4,5-trisphosphate receptor (IP3R)-associated cGMP kinase substrate (IRAG), to block store-dependent calcium signaling. In the present study we analyzed the structure and function of the human IRAG/MRVI1 gene. We describe four unique first exon variants transcribed from individual promoters in diverse human tissues. Tissue-specific alternative splicing with exon skipping and alternative splice donor and acceptor site usage further increases diversity of IRAG mRNA variants that encode for NH2- and COOH-terminally truncated proteins. At the functional level, COOH-terminally truncated IRAG variants lacking both the cGKI phosphorylation and the IP3RI interaction site counteract cGMP-mediated inhibition of calcium transients and relaxation of human colonic smooth muscle cells. Since COOH-terminally truncated IRAG mRNA isoforms are widely expressed in human tissues, our results point to an important role of IRAG variants as negative modulators of nitric oxide/cGKI-dependent signaling. The complexity of alternative splicing of the IRAG gene impressively demonstrates how posttranscriptional processing generates functionally distinct proteins from a single gene.

scholarly journals Circular RNA Expression for Dilated Cardiomyopathy in Hearts and Pluripotent Stem Cell–Derived Cardiomyocytes

2021 ◽  
Vol 9 ◽  
Author(s):  
Yiyu Zhang ◽  
Guoqing Huang ◽  
Zhaohu Yuan ◽  
Yonggang Zhang ◽  
Rong Chang
Keyword(s):  
Heart Failure ◽  
Stem Cell ◽  
Dilated Cardiomyopathy ◽  
Pluripotent Stem Cell ◽  
Single Gene ◽  
Scientific Progress ◽  
Left Ventricular ◽  
Left Ventricular Ejection ◽  
Circular Rnas ◽  
Ventricular Ejection Fraction

Dilated cardiomyopathy (DCM) is a type of heart disease delimited by enlargement and dilation of one or both of the ventricles along with damaged contractility, which is often accompanied by the left ventricular ejection fraction (LVEF) less than 40%. DCM is progressive and always leads to heart failure. Circular RNAs (circRNAs) are unique species of noncoding RNAs featuring high cell-type specificity and long-lasting conservation, which normally are involved in the regulation of heart failure and DCM recently. So far, a landscape of various single gene or polygene mutations, which can cause complex human cardiac disorders, has been investigated by human-induced pluripotent stem cell (hiPSC) technology. Furthermore, DCM has been modeled as well, providing new perspectives on the disease study at a cellular level. In addition, current genome editing methods can not only repair defects of some genes, but also rescue the disease phenotype in patient-derived iPSCs, even introduce pathological-related mutations into wild-type strains. In this review, we gather up the aspects of the circRNA expression and mechanism in the DCM disease scenario, facilitating understanding in DCM development and pathophysiology in the molecular level. Also, we offer an update on the most relevant scientific progress in iPSC modeling of gene mutation–induced DCM.

scholarly journals Quantification of Huntington’s Disease Related Markers in the R6/2 Mouse Model

2021 ◽  
Vol 13 ◽  
Author(s):  
Estibaliz Etxeberria-Rekalde ◽  
Saioa Alzola-Aldamizetxebarria ◽  
Stefanie Flunkert ◽  
Isabella Hable ◽  
Magdalena Daurer ◽  
...  
Keyword(s):  
Mouse Model ◽  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Motor System ◽  
Biological Marker ◽  
Brain Regions ◽  
Translocator Protein ◽  
Acetyl Choline ◽  
Human Pathology ◽  
Depth Analysis

Huntington’s disease (HD) is caused by an expansion of CAG triplets in the huntingtin gene, leading to severe neuropathological changes that result in a devasting and lethal phenotype. Neurodegeneration in HD begins in the striatum and spreads to other brain regions such as cortex and hippocampus, causing motor and cognitive dysfunctions. To understand the signaling pathways involved in HD, animal models that mimic the human pathology are used. The R6/2 mouse as model of HD was already shown to present major neuropathological changes in the caudate putamen and other brain regions, but recently established biomarkers in HD patients were yet not analyzed in these mice. We therefore performed an in-depth analysis of R6/2 mice to establish new and highly translational readouts focusing on Ctip2 as biological marker for motor system-related neurons and translocator protein (TSPO) as a promising readout for early neuroinflammation. Our results validate already shown pathologies like mutant huntingtin aggregates, ubiquitination, and brain atrophy, but also provide evidence for decreased tyrosine hydroxylase and Ctip2 levels as indicators of a disturbed motor system, while vesicular acetyl choline transporter levels as marker for the cholinergic system barely change. Additionally, increased astrocytosis and activated microglia were observed by GFAP, Iba1 and TSPO labeling, illustrating, that TSPO is a more sensitive marker for early neuroinflammation compared to GFAP and Iba1. Our results thus demonstrate a high sensitivity and translational value of Ctip2 and TSPO as new marker for the preclinical evaluation of new compounds in the R6/2 mouse model of HD.

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