Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data

Huang, Shangzhen; Dou, Junling; Li, Zhongshu; Hu, Lirong; Yu, Ying; Wang, Yachun

doi:10.3390/genes13020358

Cited by 10 publications

(3 citation statements)

References 93 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These variants could be the result of post‐transcriptional modification that produces distinct mature mRNA and subsequent proteins that are tuned to different environmental conditions or different cell lines. Alternative splicing (one of the forms of post‐transcriptional modification) has been observed in response to thermal or salinity stress in metazoan animal species including fish and rats (Huang et al., 2022; Tan et al., 2019; Tian et al., 2020). It is possible that the changes in environment that are part of the diel migration result in the preferential production of different isoforms at surface and depth.…”

Section: Discussionmentioning

confidence: 99%

Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod

Maas,

Timmins‐Schiffman,

Tarrant

et al. 2024

Molecular Ecology

View full text Add to dashboard Cite

Zooplankton undergo a diel vertical migration (DVM) which exposes them to gradients of light, temperature, oxygen, and food availability on a predictable daily schedule. Disentangling the co‐varying and potentially synergistic interactions on metabolic rates has proven difficult, despite the importance of this migration for the delivery of metabolic waste products to the distinctly different daytime (deep) and nighttime (surface) habitats. This study examines the transcriptomic and proteomic profiles of the circumglobal migratory copepod, Pleuromamma xiphias, over the diel cycle. The transcriptome showed that 96% of differentially expressed genes were upregulated during the middle of the day – the period often considered to be of lowest zooplankton activity. The changes in protein abundance were more spread out over time, peaking (42% of comparisons) in the early evening. Between 9:00 and 15:00, both the transcriptome and proteome datasets showed increased expression related to chitin synthesis and degradation. Additionally, at 09:00 and 22:00, there were increases in myosin and vitellogenin proteins, potentially linked to the stress of migration and/or reproductive investment. Based on protein abundances detected, there is an inferred switch in broad metabolic processes, shifting from electron transport system in the day to glycolysis and glycogen mobilization in the afternoon/evening. These observations provide evidence of the diel impact of DVM on transcriptomic and proteomic pathways that likely influence metabolic processes and subsequent excretion products, and clarify how this behaviour results in the direct rapid transport of waste metabolites from the surface to the deep ocean.

show abstract

Section: Discussionmentioning

confidence: 99%

Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod

Maas,

Timmins‐Schiffman,

Tarrant

et al. 2024

Molecular Ecology

View full text Add to dashboard Cite

show abstract

“…splicing, with 95% of all human genes undergoing alternatively splicing 53 . Importantly, alternative splicing has been widely recognized to constitute a critical response mechanism to stress in plants 54 , and recent reports indicate that it may also play a similar role in animals, including mammals [55][56][57] . SUMOylation has been known to affect splicing by directly modifying numerous spliceosomal components and modulating the assembly of the spliceosome on a pre-mRNA substrate 19,58 .…”

mentioning

confidence: 99%

Alternative splicing of the SUMO1/2/3 transcripts affects cellular SUMOylation and produces functionally distinct SUMO protein isoforms

Acuña

García-Morin

Orozco-Sepúlveda

et al. 2023

Sci Rep

View full text Add to dashboard Cite

Substantial increases in the conjugation of the main human SUMO paralogs, SUMO1, SUMO2, and SUMO3, are observed upon exposure to different cellular stressors, and such increases are considered important to facilitate cell survival to stress. Despite their critical cellular role, little is known about how the levels of the SUMO modifiers are regulated in the cell, particularly as it relates to the changes observed upon stress. Here we characterize the contribution of alternative splicing towards regulating the expression of the main human SUMO paralogs under normalcy and three different stress conditions, heat-shock, cold-shock, and Influenza A Virus infection. Our data reveal that the normally spliced transcript variants are the predominant mature mRNAs produced from the SUMO genes and that the transcript coding for SUMO2 is by far the most abundant of all. We also provide evidence that alternatively spliced transcripts coding for protein isoforms of the prototypical SUMO proteins, which we refer to as the SUMO alphas, are also produced, and that their abundance and nuclear export are affected by stress in a stress- and cell-specific manner. Additionally, we provide evidence that the SUMO alphas are actively synthesized in the cell as their coding mRNAs are found associated with translating ribosomes. Finally, we provide evidence that the SUMO alphas are functionally different from their prototypical counterparts, with SUMO1α and SUMO2α being non-conjugatable to protein targets, SUMO3α being conjugatable but targeting a seemingly different subset of protein from those targeted by SUMO3, and all three SUMO alphas displaying different cellular distributions from those of the prototypical SUMOs. Thus, alternative splicing appears to be an important contributor to the regulation of the expression of the SUMO proteins and the cellular functions of the SUMOylation system.

show abstract

“…Humans exhibit the largest prevalence of alternative splicing, with 95% of all human genes undergoing alternatively splicing 53 . Importantly, alternative splicing has been widely recognized to constitute a critical response mechanism to stress in plants 54 , and recent reports indicate that it may also play a similar role in animals, including mammals [55][56][57] . SUMOylation has been known to affect splicing by directly modifying numerous spliceosomal components and modulating the assembly of the spliceosome on a pre-mRNA substrate 19,58 .…”

mentioning

confidence: 99%

Alternative splicing of the SUMO transcripts contributes to the regulation of the cellular SUMOylation system and produces messages coding for protein isoforms functionally distinct from the prototypical SUMO proteins

Acuña

García-Morin

Orozco-Sepúlveda

et al. 2022

Preprint

View full text Add to dashboard Cite

Substantial increases in the conjugation of the main human SUMO paralogs, SUMO1, SUMO2, and SUMO3, are observed upon exposure to different cellular stressors, and such increases are considered important to facilitate cell survival to stress. Despite their critical cellular role, little is known about how the levels of the SUMO modifiers are regulated in the cell, particularly as it relates to the changes observed upon stress. Here we characterize the contribution of alternative splicing towards regulating the expression of the main human SUMO paralogs under normalcy and three different stress conditions, heat-shock, cold-shock, and Influenza A Virus infection. Our data reveal that the normally spliced transcript variants are the predominant mature mRNAs produced from the SUMO genes and that the transcript coding for SUMO2 is by far the most abundant of all. We also provide evidence that alternatively spliced transcripts coding for protein isoforms of the prototypical SUMO proteins, which we refer to as the SUMO alphas, are also produced, and that their abundance and nuclear export are affected by stress in a stress- and cell-specific manner. Additionally, we provide evidence that the SUMO alphas are actively synthesized in the cell as their coding mRNAs are found associated with translating ribosomes. Finally, we provide evidence that the SUMO alphas are functionally different from their prototypical counterparts, with SUMO1α and SUMO2α being non-conjugatable to protein targets, SUMO3α being conjugatable but targeting a seemingly different subset of proteins from those targeted by SUMO3, and all three SUMO alphas displaying different cellular distributions from those of the prototypical SUMOs. Thus, alternative splicing appears to be an important contributor to the regulation of the expression of the SUMO proteins and the cellular functions of the SUMOylation system.

show abstract

Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data

Cited by 10 publications

References 93 publications

Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod

Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod

Alternative splicing of the SUMO1/2/3 transcripts affects cellular SUMOylation and produces functionally distinct SUMO protein isoforms

Alternative splicing of the SUMO transcripts contributes to the regulation of the cellular SUMOylation system and produces messages coding for protein isoforms functionally distinct from the prototypical SUMO proteins

Contact Info

Product

Resources

About