scholarly journals Transcriptome-Wide Analyses Identify Dominant as the Predominantly Non-Conservative Alternative Splicing Inheritance Patterns in F1 Chickens

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Qi ◽  
Hongchang Gu ◽  
Lujiang Qu
Keyword(s):  
Alternative Splicing ◽  
Broiler Chickens ◽  
Reproductive Traits ◽  
Hierarchical Cluster ◽  
Strain Specificity ◽  
Inheritance Patterns ◽  
Crossing Experiment ◽  
Post Transcriptional Regulation ◽  
The Brain ◽  
Liver Tissues

Transcriptome analysis has been used to investigate many economically traits in chickens; however, alternative splicing still lacks a systematic method of study that is able to promote proteome diversity, and fine-tune expression dynamics. Hybridization has been widely utilized in chicken breeding due to the resulting heterosis, but the dynamic changes in alternative splicing during this process are significant yet unclear. In this study, we performed a reciprocal crossing experiment involving the White Leghorn and Cornish Game chicken breeds which exhibit major differences in body size and reproductive traits, and conducted RNA sequencing of the brain, muscle, and liver tissues to identify the inheritance patterns. A total of 40 515 and 42 612 events were respectively detected in the brain and muscle tissues, with 39 843 observed in the liver; 2807, 4242, and 4538 events significantly different between two breeds were identified in the brain, muscle, and liver tissues, respectively. The hierarchical cluster of tissues from different tissues from all crosses, based on the alternative splicing profiles, suggests high tissue and strain specificity. Furthermore, a comparison between parental strains and hybrid crosses indicated that over one third of alternative splicing genes showed conserved patterns in all three tissues, while the second prevalent pattern was non-additive, which included both dominant and transgressive patterns; this meant that the dominant pattern plays a more important role than suppression. Our study provides an overview of the inheritance patterns of alternative splicing in layer and broiler chickens, to better understand post-transcriptional regulation during hybridization.

scholarly journals Alternative splicing during mammalian organ development

2021 ◽  
Author(s):  
Pavel V. Mazin ◽  
Philipp Khaitovich ◽  
Margarida Cardoso-Moreira ◽  
Henrik Kaessmann
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Regulatory Networks ◽  
Organ Development ◽  
Functional Diversification ◽  
Mammalian Genomes ◽  
Species Comparisons ◽  
Time Specific ◽  
The Brain ◽  
Gene Expression Levels

AbstractAlternative splicing (AS) is pervasive in mammalian genomes, yet cross-species comparisons have been largely restricted to adult tissues and the functionality of most AS events remains unclear. We assessed AS patterns across pre- and postnatal development of seven organs in six mammals and a bird. Our analyses revealed that developmentally dynamic AS events, which are especially prevalent in the brain, are substantially more conserved than nondynamic ones. Cassette exons with increasing inclusion frequencies during development show the strongest signals of conserved and regulated AS. Newly emerged cassette exons are typically incorporated late in testis development, but those retained during evolution are predominantly brain specific. Our work suggests that an intricate interplay of programs controlling gene expression levels and AS is fundamental to organ development, especially for the brain and heart. In these regulatory networks, AS affords substantial functional diversification of genes through the generation of tissue- and time-specific isoforms from broadly expressed genes.

Alternative splicing within the human cytochrome P450 superfamily with an emphasis on the brain: the convolution continues

2006 ◽  
Vol 2 (3) ◽  
pp. 399-418 ◽  
Author(s):  
Cheri M Turman ◽  
Jade M Hatley ◽  
Daniel J Ryder ◽  
Vijayalakshmi Ravindranath ◽  
Henry W Strobel
Keyword(s):  
Cytochrome P450 ◽  
Alternative Splicing ◽  
Human Cytochrome ◽  
The Brain

scholarly journals Neuronal cell-type-specific alternative splicing: A mechanism for specifying connections in the brain?

Neurogenesis ◽  
2015 ◽  
Vol 2 (1) ◽  
pp. e1122699 ◽  
Author(s):  
Joshua Shing Shun Li ◽  
Grace Ji-eun Shin ◽  
S Sean Millard
Keyword(s):  
Alternative Splicing ◽  
Neuronal Cell ◽  
Cell Type ◽  
Specific Alternative ◽  
Cell Type Specific ◽  
The Brain

RNA Modifications in the Central Nervous System

2020 ◽  
Author(s):  
Dan Ohtan Wang
Keyword(s):  
Gene Expression ◽  
Cell Function ◽  
Gene Expression Regulation ◽  
Spinal Injury ◽  
Regulation Of Gene Expression ◽  
Modified Nucleosides ◽  
Rna Modifications ◽  
The Central Nervous System ◽  
Post Transcriptional Regulation ◽  
The Brain

Epitranscriptomics, a recently emerged field to investigate post-transcriptional regulation of gene expression through enzyme-mediated RNA modifications, is rapidly evolving and integrating with neuroscience. Using a rich repertoire of modified nucleosides and strategically positioning them to the functionally important and evolutionarily conserved regions of the RNA, epitranscriptomics dictates RNA-mediated cell function. The new field is quickly changing our view of the genetic geography in the brain during development and plasticity, impacting major functions from cortical neurogenesis, circadian rhythm, learning and memory, to reward, addiction, stress, stroke, and spinal injury, etc. Thus understanding the molecular components and operational rules of this pathway is becoming a key for us to decipher the genetic code for brain development, function, and disease. What RNA modifications are expressed in the brain? What RNAs carry them and rely on them for function? Are they dynamically regulated? How are they regulated and how do they contribute to gene expression regulation and brain function? This chapter summarizes recent advances that are beginning to answer these questions.

scholarly journals SAT-018 Androgen Actions in Adipose Tissue and the Brain Are Key Mediators in the Development of Polycystic Ovary Syndrome

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Madeleine J Cox ◽  
Melissa C Edwards ◽  
Ali Aflatounian ◽  
Valentina Rodriguez Paris ◽  
William L Ledger ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Polycystic Ovary Syndrome ◽  
Mouse Model ◽  
Hepatic Steatosis ◽  
Polycystic Ovary ◽  
Reproductive Traits ◽  
Reproductive Age ◽  
Ovary Syndrome ◽  
Adipocyte Hypertrophy ◽  
The Brain

Abstract Polycystic ovary syndrome (PCOS) is a complex disorder characterised by endocrine, reproductive and metabolic abnormalities. Despite PCOS being the most common endocrinopathy affecting women of reproductive age, its etiology is poorly understood so there is no cure and symptom-oriented treatment is suboptimal. Elucidation of the underlying mechanisms involved in the pathogenesis of PCOS would pave the way for the development of new interventions for PCOS. Hyperandrogenism is the most consistent feature observed in PCOS patients, and recently aberrant neuroendocrine signalling and adipose tissue function have been proposed as playing a pathogenic role in the development of experimental PCOS. To investigate the role of adipose tissue and the brain as potential key sites for androgen receptor (AR)-mediated development of PCOS, we combined an adipocyte and brain-specific ARKO knockout (AdBARKO) mouse model with a dihydrotestosterone (DHT)-induced mouse model of PCOS. Wildtype (WT) and AdBARKO prepubertal mice were implanted with a blank or DHT implant and examined after 12 weeks. In WT control females, DHT exposure induced the PCOS reproductive traits of cycle irregularity, ovulatory dysfunction and reduced follicle health. In contrast, these reproductive features of PCOS were absent in DHT-treated AdBARKO females. The PCOS metabolic characteristics of increased adiposity, adipocyte hypertrophy and hepatic steatosis were induced by DHT in WT females. Despite DHT treatment, AdBARKO females displayed normal white adipose tissue weight, and adipocyte hypertrophy and hepatic steatosis were not evident. However, as with WT mice, DHT treatment induced increased fasting glucose levels in AdBARKO females. These results demonstrate that adipose tissue and the brain are key loci for androgen-mediated actions involved in the developmental origins of PCOS. These findings support targeting adipocyte and neuroendocrine AR-driven pathways in the future development of novel therapeutic strategies for PCOS.

Changes in free amino acids in the brain during embryonic development in layer and broiler chickens

Amino Acids ◽  
2008 ◽  
Vol 36 (2) ◽  
pp. 303-308 ◽  
Author(s):  
M. Sato ◽  
S. Tomonaga ◽  
D. M. Denbow ◽  
M. Furuse
Keyword(s):  
Amino Acids ◽  
Embryonic Development ◽  
Free Amino Acids ◽  
Free Amino ◽  
Broiler Chickens ◽  
The Brain

scholarly journals Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain

2012 ◽  
Vol 2 (1) ◽  
Author(s):  
Boris Rogelj ◽  
Laura E. Easton ◽  
Gireesh K. Bogu ◽  
Lawrence W. Stanton ◽  
Gregor Rot ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Nascent Rna ◽  
The Brain

scholarly journals Conserved expression of alternative splicing variants of peroxisomal acyl-CoA oxidase 1 in vertebrates and developmental and nutritional regulation in fish

2007 ◽  
Vol 28 (3) ◽  
pp. 239-252 ◽  
Author(s):  
Sofia Morais ◽  
Anja Knoll-Gellida ◽  
Michèle André ◽  
Christophe Barthe ◽  
Patrick J. Babin
Keyword(s):  
Alternative Splicing ◽  
Early Stage ◽  
Acyl Chain ◽  
Amino Acid Sequences ◽  
Fatty Acyl Chain ◽  
Nutritional Regulation ◽  
Vertebrate Lineage ◽  
Anterior Intestine ◽  
Acyl Coa Oxidase ◽  
The Brain

The acyl-coenzyme A oxidase 1 (ACOX1) catalyzes the first, rate-limiting step in peroxisomal β-oxidation of medium to very long straight-chain fatty acids. Zebrafish ( Danio rerio) acox1 was characterized and compared with homologs from other sequenced genomes, revealing a remarkable conservation of structure in the vertebrate lineage. Strictly conserved regions of the deduced proteins included acyl-CoA oxidase and FAD binding domains, as well as a COOH-terminal peroxisomal targeting signal. Whole mount in situ hybridization showed that zebrafish acox1 transcripts were diffusely distributed in early-stage embryonic cells, then discreetly expressed in the brain and widely present in the liver and intestine at later stages. An evolutionarily conserved alternative splicing of the corresponding acox1 primary transcript was identified in teleosts and tetrapods including mammals, giving rise, after exon skipping, to two splice variants, ACOX1–3I and ACOX1–3II. Real-time quantitative RT-PCR on zebrafish adult tissues indicated high levels of both variants in the liver, anterior intestine, and to a lesser extent, in the brain. However, the ACOX1–3II transcript variant was expressed seven times more in zebrafish brain than the ACOX1–3I variant. These data suggest a tissue-specific modulation of ACOX1 activity by exchanging exon 3 duplicated isoforms containing amino acid sequences that are potentially implicated in fatty acyl chain specificity. In addition, a significant pretranslational up-regulation of zebrafish and rainbow trout ( Oncorhynchus mykiss) acox1 expression was observed in the anterior intestine after feeding. Taken together, these data indicate that ACOX1 alternative splicing isoforms play a key conserved role in the vertebrate fatty acid metabolism.

Effects of the Coreopsis tinctoria extracts on anti-agingin the aging model mice

2016 ◽  
Author(s):  
Weixin Zhang ◽  
Haiyan Hao ◽  
Ailong Sha
Keyword(s):  
Hydrogen Peroxide ◽  
Aging Effects ◽  
Once Daily ◽  
Aging Model ◽  
Coreopsis Tinctoria ◽  
Kg Medium ◽  
The Brain ◽  
Liver Tissues ◽  
Brain Tissues

The effects of the Coreopsis tinctoria extracts on anti-aging were observed by investigating the cerebral index and viscera indexes, the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA) in the serums, the activities of glutathione peroxidase (GSH-Px) in the brain tissues and the ones of catalase (CAT) and superoxide dismutase (SOD) in the liver tissues of the aging model mice. The aging model mice were injected subcutaneously with D-galactose in vivo and intragastric administrated with the Coreopsis tinctoria extracts at doses of low (0.5g/kg), medium (1g/ kg) and high (2g/ kg) once daily for 6 weeks. The results showed that all the cerebral index, spleen index, thymus index, liver index and kidney index of the three groups dosed of the Coreopsis tinctoria extracts increased, the activities of GSH-Px in the brain tissues and the ones of CAT and SOD in the liver tissues increased to different degree while the contents of H2O2 and MDA in the serums decreased extremely and significantly (P<0.01) compared with the aging model mice. All of these results suggested that the Coreopsis tinctoria extracts might possess anti-aging effects by improving antioxidant capacity of the mice.

scholarly journals PSI controls tim splicing and circadian period in Drosophila

2018 ◽  
Author(s):  
Lauren Foley ◽  
Jinli Ling ◽  
Radhika Joshi ◽  
Naveh Evantal ◽  
Sebastian Kadener ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Circadian Rhythms ◽  
Translational Regulation ◽  
Transcriptional Control ◽  
Rna Binding ◽  
P Element ◽  
Peripheral Tissues ◽  
Associated Proteins ◽  
Splicing Regulator ◽  
Post Transcriptional Regulation

AbstractThe Drosophila circadian pacemaker consists of transcriptional feedback loops subjected to both post-transcriptional and post-translational regulation. While post-translational regulatory mechanisms have been studied in detail, much less is known about circadian post-transcriptional control. To have a better understanding of the role and mechanisms of circadian post-transcriptional regulation, we targeted 364 RNA binding and RNA associated proteins with RNA interference. Among the 43 genes we identified was the alternative splicing regulator P-element somatic inhibitor (PSI). PSI downregulation shortens the period of circadian rhythms both in the brain and in peripheral tissues. Interestingly, we found that PSI regulates the thermosensitive alternative splicing of timeless (tim), promoting splicing events favored at warm temperature over those increased at cold temperature. Moreover, the period of circadian behavior was insensitive to PSI downregulation when flies could produce functional TIM proteins only from a transgene that cannot form the thermosensitive splicing isoforms. Therefore, we conclude that PSI regulates the period of Drosophila circadian rhythms through its modulation of the tim splicing pattern.

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