Abstract:
:Across species and tissues and especially in the mammalian brain, production of gene isoforms is widespread. While gene expression coordination has been previously described as a scale-free coexpression network, the properties of transcriptome-wide isoform production coordination have been less studied. Here we evaluate the system-level properties of cosplicing in mouse, macaque, and human brain gene expression data using a novel network inference procedure. Genes are represented as vectors/lists of exon counts and distance measures sensitive to exon inclusion rates quantifies differences across samples. For all gene pairs, distance matrices are correlated across samples, resulting in cosplicing or cotranscriptional network matrices. We show that networks including cosplicing information are scale-free and distinct from coexpression. In the networks capturing cosplicing we find a set of novel hubs with unique characteristics distinguishing them from coexpression hubs: heavy representation in neurobiological functional pathways, strong overlap with markers of neurons and neuroglia, long coding lengths, and high number of both exons and annotated transcripts. Further, the cosplicing hubs are enriched in genes associated with autism spectrum disorders. Cosplicing hub homologs across eukaryotes show dramatically increasing intronic lengths but stable coding region lengths. Shared transcription factor binding sites increase coexpression but not cosplicing; the reverse is true for splicing-factor binding sites. Genes with protein-protein interactions have strong coexpression and cosplicing. Additional factors affecting the networks include shared microRNA binding sites, spatial colocalization within the striatum, and sharing a chromosomal folding domain. Cosplicing network patterns remain relatively stable across species.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Iancu OD,Colville A,Oberbeck D,Darakjian P,McWeeney SK,Hitzemann Rdoi
10.3389/fgene.2015.00174subject
Has Abstractpub_date
2015-05-13 00:00:00pages
174issn
1664-8021journal_volume
6pub_type
杂志文章abstract::Extracellular vesicles (EVs) are abundant in most biological fluids and considered promising biomarker candidates, but the development of EV biomarker assays is hindered, in part, by their requirement for prior EV purification and the lack of standardized and reproducible EV isolation methods. We now describe a far-fi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01273
更新日期:2019-12-17 00:00:00
abstract::Neurodegenerative diseases share pathogenic mechanisms at the cellular level including protein misfolding, excitotoxicity and altered RNA homeostasis among others. Recent advances have shown that the genetic causes underlying these pathologies overlap, hinting at the existence of a genetic network for neurodegeneratio...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00085
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01200
更新日期:2019-11-22 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.586308
更新日期:2020-11-11 00:00:00
abstract::The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about the G-quadruplexes of th...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.587829
更新日期:2020-11-27 00:00:00
abstract::Post-translational methylation of H3 lysine 36 (H3K36) is an important epigenetic marker that majorly contributes to the functionality of the chromatin. This mark is interpreted by the cell in several crucial biological processes including gene transcription and DNA methylation. The homeostasis of H3K36 methylation is...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.01291
更新日期:2020-01-09 00:00:00
abstract::Alport syndrome is a hereditary progressive chronic kidney disease caused by mutations in type IV collagen genes COL4A3/4/5. X-linked Alport syndrome (XLAS) is caused by mutations in the COL4A5 gene and is the most common form of Alport syndrome. A strong correlation between the type of COL4A5 mutation and the age dev...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00036
更新日期:2020-02-10 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2013.00254
更新日期:2013-11-28 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.604336
更新日期:2020-11-24 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.578712
更新日期:2020-09-18 00:00:00
abstract::Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00496
更新日期:2019-05-22 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00254
更新日期:2018-07-17 00:00:00
abstract::Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpre...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2017.00085
更新日期:2017-06-30 00:00:00
abstract::Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00007
更新日期:2018-01-26 00:00:00
abstract::The aging brain undergoes a range of changes varying from subtle structural and physiological changes causing only minor functional decline under healthy normal aging conditions, to severe cognitive or neurological impairment associated with extensive loss of neurons and circuits due to age-associated neurodegenerativ...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00419
更新日期:2014-12-04 00:00:00
abstract::It is time to review all the available data and find the distinctive characteristics of actin that make it such an important cell molecule. The presented double-stranded organization of filamentous actin cannot explain the strong polymorphism of actin fibrils. In this work, we performed bioinformatics analysis of a se...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.617763
更新日期:2020-12-10 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00707
更新日期:2020-07-10 00:00:00
abstract::Ethylmalonic encephalopathy (EE) is a very rare autosomal recessive metabolic disorder that primarily affects children. Less than one hundred EE patients have been diagnosed worldwide. The clinical manifestations include chronic diarrhea, petechiae, orthostatic acrocyanosis, psychomotor delay and regression, seizures,...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00341
更新日期:2020-04-17 00:00:00
abstract::Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important f...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.603552
更新日期:2020-10-29 00:00:00
abstract::Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-prot...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00104
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abstract::As a conserved protein family, WRKY has been shown to be involved in multiple biological processes in plants. However, the mechanism of functional diversity for WRKYs in pepper has not been well elucidated. Here, a total of 223 WRKY members from solanaceae crops including pepper, tomato and potato, were analyzed using...
journal_title:Frontiers in genetics
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doi:10.3389/fgene.2019.00492
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00061
更新日期:2012-05-03 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01080
更新日期:2019-11-04 00:00:00
abstract::Filamentous pathogens, such as phytopathogenic oomycetes and fungi, secrete a remarkable diversity of apoplastic effector proteins to facilitate infection, many of which are able to induce cell death in plants. Over the past decades, over 177 apoplastic cell death-inducing proteins (CDIPs) have been identified in fila...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.00661
更新日期:2020-06-26 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00526
更新日期:2019-06-13 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00195
更新日期:2012-09-28 00:00:00
abstract::Background: There is a continued debate and inconsistent findings in previous literature about the relationship of catechol-O-methyltransferase (COMT) and Parkinson's disease (PD) susceptibility as well as cognitive dysfunction. To substantiate this existing gap, we comprehensively examine COMT genotype effects on the...
journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2019.00644
更新日期:2019-07-12 00:00:00
abstract::Alzheimer's disease (AD) is a neurodegenerative and progressive disease, which often causes irreversible damages to the cerebrum. The pathogenesis of AD is far from being fully understood, while there are some popular hypotheses. So far, the diagnosis of AD relies only on clinical screening in the form of imaging tech...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00157
更新日期:2019-03-12 00:00:00
abstract::Decreased expression of the fly and worm Indy genes extends longevity. The fly Indy gene and its mammalian homolog are transporters of Krebs cycle intermediates, with the highest rate of uptake for citrate. Cytosolic citrate has a role in energy regulation by affecting fatty acid synthesis and glycolysis. Fly, worm, a...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00047
更新日期:2013-04-08 00:00:00
abstract::The genetic predisposition to chronic kidney disease (CKD) has been widely evaluated especially using the genome-wide association studies, which highlighted some novel genetic susceptibility variants in many genes, and estimated glomerular filtration rate to diagnose and stage CKD. Of these variants, rs7805747 in PRKA...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00573
更新日期:2018-12-03 00:00:00