ArticlePublisher preview availableLiterature Review

Alternative splicing in aging and longevity

March 2020
Human Genetics 139(3):1-13

March 2020
139(3):1-13

DOI:10.1007/s00439-019-02094-6

Authors:

Caroline Heintz

Harvard University

Show all 5 authorsHide

Alternative pre-mRNA splicing increases the complexity of the proteome that can be generated from the available genomic coding sequences. Dysregulation of the splicing process has been implicated in a vast repertoire of diseases. However, splicing has recently been linked to both the aging process itself and pro-longevity interventions. This review focuses on recent research towards defining RNA splicing as a new hallmark of aging. We highlight dysfunctional alternative splicing events that contribute to the aging phenotype across multiple species, along with recent efforts toward deciphering mechanistic roles for RNA splicing in the regulation of aging and longevity. Further, we discuss recent research demonstrating a direct requirement for specific splicing factors in pro-longevity interventions, and specifically how nutrient signaling pathways interface to splicing factor regulation and downstream splicing targets. Finally, we review the emerging potential of using splicing profiles as a predictor of biological age and life expectancy. Understanding the role of RNA splicing components and downstream targets altered in aging may provide opportunities to develop therapeutics and ultimately extend healthy lifespan in humans.

Regulation of RNA processing and disruption with age and disease. RNA processing fidelity is maintained at multiple points between transcription and translation in normal physiology. With advanced age, disruption of RNA homeostasis can compromise cellular/tissue function and contribute to development of age-related diseases. Depicted are some of the points of dysregulation in RNA homeostasis including splicing factor expression changes and modifications affecting splicing factor localization, spliceosome dysfunction, aberrant splicing, defective RNA surveillance and aberrant mRNA translation

…

Constitutive and alternative splicing events. Seven types of alternative splicing are cassette exon, alternative 5′ splice site, alternative 3′ splice site, mutually exclusive exons, intron retention, alternative promoter and alternative polyadenylation. Boxes represent exons and lines represent introns

…

Regulation of alternative splicing by nutrient sensing signaling pathways. Examples of nutrient sensing factors, implicated in the mechanisms of aging and longevity, impacting splicing factor regulatory protein phosphorylation, localization and levels. Extracellular signals including insulin/IGF activate growth factor receptors and impact signaling to a number of different pathways. Activated Ras causes a signaling cascade that involves MAPK/ERK signaling to increase SRSF1 expression and subsequent increase in exon inclusion of the insulin receptor (INSR) transcript to form insulin receptor beta (INSR-B). PI3K signaling downstream of insulin increases AKT mediated phosphorylation of SR protein kinases (SRPKs) or SR proteins directly. Phosphorylation induces nuclear localization and can alter splicing of transcripts including PKC exon inclusion to form PKC beta isoform. Also, mTORC1 signaling increases phosphorylation of S6K which phosphorylates SRPK2 and leads to nuclear translocation. SRPK2 then phosphorylates SR proteins. The impact of these splicing regulatory factor-mediated changes in alternative splicing is alterations in isoform expression and cellular functions including lipogenesis and glucose uptake. Finally, nutrient sensing and alternative splicing are important for survival in yeast as nutrient depletion leads to an accumulation of stable introns in a TORC1-dependent manner that protect cells from starvation by downregulating ribosomal biogenesis

…

Core and regulatory splicing factors are implicated in longevity. Longevity associated splicing factors participating at different stages of the splicing process are depicted in red. Expression of Hnrnpk, Hnrnpul2, Hnrnpm, Hnrnpd, Hnrnpa0, Hnrnpul1, Sf3b1, Srsf3 and Tra2β are associated with strain longevity in mice (Lee et al. 2016). Hnrnpa1 and Hnrnpa2b1 levels are associated with strain longevity in mice as well as parental longevity in humans (Lee et al. 2016) while expression of PRP-38 is required for mediating longevity in C. elegans (Curran and Ruvkun 2007). Notably, splicing factors SF1/SFA-1, SF3A2/REPO-1 (Heintz et al. 2017) and HNRNPUL1/HRPU-1 (Tabrez et al. 2017) are required for DR-mediated longevity in C. elegans

…

Figures - available from: Human Genetics

This content is subject to copyright. Terms and conditions apply.

A preview of this full-text is provided by Springer Nature.

Learn more

Content available from Human Genetics

This content is subject to copyright. Terms and conditions apply.

Vol.:(0123456789)

1 3

Human Genetics (2020) 139:357–369

https://doi.org/10.1007/s00439-019-02094-6

REVIEW

Alternative splicing inaging andlongevity

MaliniBhadra1· PorshaHowell1· SnehaDutta1· CarolineHeintz1· WilliamB.Mair1

Received: 28 September 2019 / Accepted: 24 November 2019 / Published online: 13 December 2019

Abstract

Alternative pre-mRNA splicing increases the complexity of the proteome that can be generated from the available genomic

coding sequences. Dysregulation of the splicing process has been implicated in a vast repertoire of diseases. However, splic-

ing has recently been linked to both the aging process itself and pro-longevity interventions. This review focuses on recent

research towards deﬁning RNA splicing as a new hallmark of aging. We highlight dysfunctional alternative splicing events

that contribute to the aging phenotype across multiple species, along with recent eﬀorts toward deciphering mechanistic

roles for RNA splicing in the regulation of aging and longevity. Further, we discuss recent research demonstrating a direct

requirement for speciﬁc splicing factors in pro-longevity interventions, and speciﬁcally how nutrient signaling pathways

interface to splicing factor regulation and downstream splicing targets. Finally, we review the emerging potential of using

splicing proﬁles as a predictor of biological age and life expectancy. Understanding the role of RNA splicing components

and downstream targets altered in aging may provide opportunities to develop therapeutics and ultimately extend healthy

lifespan in humans.

Introduction

Aging andRNA homeostasis

Aging is characterized by the progressive decline in physi-

ological function leading to an increased risk of mortality.

Advances in public health have increased the proportion of

the population that lives into old age, resulting in an increase

in the incidence of many chronic age-related diseases includ-

ing cardiovascular disease, neurodegenerative diseases and

cancers (Christensen etal. 2009). Aging is now considered

a key risk factor for these chronic diseases and as a result,

individuals who reach advanced age are likely to suﬀer from

multiple chronic diseases concurrently (Hung etal. 2011).

The current strategy is to treat these co-morbidities in isola-

tion. However, a limit of this approach is that even complete

removal of the symptoms of one isolated age-related disease

has little impact on remaining conditions. As a result, pro-

gress towards increasing the overall disease-free years of

life (healthspan) has been marginal (Goldman etal. 2017).

A new approach to tackling health and human disease is that

of ‘Geroscience’ (Kennedy etal. 2014) which is focused on

understanding and then targeting the underlying biology of

aging that leads to chronic disease burden, in order to pro-

long the healthspan of the population. Dietary restriction

(DR), a regimen with reduced food intake without malnutri-

tion delays aging and increases healthspan in multiple spe-

cies. Along with the increase in longevity, DR in organisms

from yeast to mammals modulates similar genetic pathways,

suggesting that the mechanism of increased lifespan is con-

served throughout evolution (Mair and Dillin 2008). There-

fore, research has focused on understanding the mechanisms

of how DR inﬂuences lifespan in order to develop thera-

peutics that would mimic DR without nutrient restriction

in humans.

Research into the mechanisms of aging and longevity to

date has largely focused on deterioration of DNA and protein

quality control. However, a key intermediary step between

transcription and translation in the central dogma is RNA

processing, which involves 5′-capping, pre-mRNA splicing,

3′-polyadenylation and RNA editing (Fig.1). Recently, RNA

processing, especially pre-mRNA splicing is increasingly

recognized as both an important contributor to the aging

process and a causal mediator of pro-longevity interventions.

Malini Bhadra and Porsha Howell contributed equally to this work.

* William B. Mair

wmair@hsph.harvard.edu

1 Department ofMolecular Metabolism, Harvard T.H. Chan

School ofPublic Health, Boston, MA02115, USA

Content courtesy of Springer Nature, terms of use apply. Rights reserved.

Single-cell transcriptome profiling highlights the importance of telocyte, kallikrein genes, and alternative splicing in mouse testes aging

Article

Full-text available

Jun 2024

Advancing healthcare for elderly men requires a deeper understanding of testicular aging processes. In this study, we conducted transcriptomic profiling of 43,323 testicular single cells from young and old mice, shedding light on 1032 telocytes—an underexplored testicular cell type in previous research. Our study unveiled 916 age-related differentially expressed genes (age-DEGs), with telocytes emerging as the cell type harboring the highest count of age-DEGs. Of particular interest, four genes (Klk1b21, Klk1b22, Klk1b24, Klk1b27) from the Kallikrein family, specifically expressed in Leydig cells, displayed down-regulation in aged testes. Moreover, cell-type-level splicing analyses unveiled 1838 age-related alternative splicing (AS) events. While we confirmed the presence of more age-DEGs in somatic cells compared to germ cells, unexpectedly, more age-related AS events were identified in germ cells. Further experimental validation highlighted 4930555F03Rik, a non-coding RNA gene exhibiting significant age-related AS changes. Our study represents the first age-related single-cell transcriptomic investigation of testicular telocytes and Kallikrein genes in Leydig cells, as well as the first delineation of cell-type-level AS dynamics during testicular aging in mice.

Molecular Regulation of Fetal Brain Development in Inbred and Congenic Mouse Strains Differing in Longevity

Article

Full-text available

May 2024

The objective of this study was to investigate gene regulation of the developing fetal brain from congenic or inbred mice strains that differed in longevity. Gene expression and alternative splice variants were analyzed in a genome-wide manner in the fetal brain of C57BL/6J mice (long-lived) in comparison to B6.Cg-Cav1tm1Mls/J (congenic, short-lived) and AKR/J (inbred, short-lived) mice on day(d) 12, 15, and 17 of gestation. The analysis showed a contrasting gene expression pattern during fetal brain development in these mice. Genes related to brain development, aging, and the regulation of alternative splicing were significantly differentially regulated in the fetal brain of the short-lived compared to long-lived mice during development from d15 and d17. A significantly reduced number of splice variants was observed on d15 compared to d12 or d17 in a strain-dependent manner. An epigenetic clock analysis of d15 fetal brain identified DNA methylations that were significantly associated with single-nucleotide polymorphic sites between AKR/J and C57BL/6J strains. These methylations were associated with genes that show epigenetic changes in an age-correlated manner in mice. Together, the finding of this study suggest that fetal brain development and longevity are epigenetically linked, supporting the emerging concept of the early-life origin of longevity.

Why do we age? The main signs of aging

Article

Feb 2024

Aging is a gradual and irreversible pathophysiological process. This is manifested in the decline of tissue and cell functions and a significant variety of pathologies associated with aging, including neurodegenerative diseases, cardiovascular diseases, metabolic disorders, increased risk of diseases of the skeleton and the immune system. Although modern medical advances have made a certain contribution to human health and greatly extended life expectancy, along with the aging of society, various chronic diseases are gradually emerging, which are the most important causes of disability and death of the elderly. Aim. The aim of the work is to analyze modern ideas in the field of causes and manifestations of aging processes for the possibility of developing a strategy to slow down its course. At the molecular and cellular level, aging is a complex biological process involving the gradual deterioration of various cellular and molecular processes in the body over time. The length of a person’s life is closely related to the decrease in the possibilities of repair and regeneration of tissues and organs. In response to stress at the molecular, cellular, and systemic levels, genetic, epigenetic, and environmental regulatory factors cause a decrease in the body’s physiological capabilities. They use complex molecular mechanisms that together contribute to aging. Molecular mechanisms (such as telomere shortening, accumulation of DNA damage, metabolic changes, and excessive free radical generation) strongly link various factors to the rate of aging. Collectively, these mechanisms inhibit cell proliferation, alter metabolism and gene expression, and induce high levels of free radicals, maintaining a senescent cell phenotype. Although the number of early senescent cells is low, they can limit the regenerative capacity of tissue stem cells and lead to the accumulation of cellular damage, thereby contributing to age-related diseases. Conclusions. Current advances in high-throughput genomics, transcriptomics, proteomics, and metabolomics enable the characterization and quantification of thousands of epigenetic markers, transcripts, proteins, metabolites, and can reveal general changes that occur with age in complex organisms at the molecular level. Thus, the integration of these molecular markers and related molecular mechanisms into a comprehensive assessment of biological age to prevent age-related functional decline and morbidity is becoming an increasingly pressing issue in medical science and should be implemented in practice as soon as possible.

A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training

Article

Full-text available

Apr 2024

The skeletal muscle proteome alterations to aging and resistance training have been reported in prior studies. However, conventional proteomics in skeletal muscle typically yields wide protein abundance ranges that mask the detection of lowly expressed proteins. Thus, we adopted a novel deep proteomics approach whereby myofibril (MyoF) and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS). Specifically, we investigated MyoF and non-MyoF proteomic profiles of the vastus lateralis muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6). Additionally, MA muscle was analyzed following eight weeks of resistance training (RT, 2d/week). Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteomes were evident between age cohorts, and most differentially expressed non-MyoF proteins (447/543) were more enriched in MA versus Y. Biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. RT in MA participants only altered ~0.3% of MyoF and ~1.0% of non-MyoF proteomes. In summary, aging and RT predominantly affect non-contractile proteins in skeletal muscle. Additionally, marginal proteome adaptations with RT suggest more rigorous training may stimulate more robust effects or that RT, regardless of age, subtly alters basal state skeletal muscle protein abundances.

Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin

Article

Full-text available

Apr 2024

The number of Y chromosomes is positively associated with transposable element expression in humans, in line with the toxic Y hypothesis

Article

Full-text available

Jun 2024

Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies

Article

Full-text available

Apr 2024

Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients’ outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.

Role of Alternative Splicing in Fish Immunity

Article

May 2024
FISH SHELLFISH IMMUN

Identification of differentially expressed genes and splicing events in early-onset colorectal cancer

Article

Full-text available

Apr 2024

Background The incidence of colorectal cancer (CRC) has been steadily increasing in younger individuals over the past several decades for reasons that are incompletely defined. Identifying differences in gene expression profiles, or transcriptomes, in early-onset colorectal cancer (EOCRC, < 50 years old) patients versus later-onset colorectal cancer (LOCRC, > 50 years old) patients is one approach to understanding molecular and genetic features that distinguish EOCRC. Methods We performed RNA-sequencing (RNA-seq) to characterize the transcriptomes of patient-matched tumors and adjacent, uninvolved (normal) colonic segments from EOCRC (n=21) and LOCRC (n=22) patients. The EOCRC and LOCRC cohorts were matched for demographic and clinical characteristics. We used The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) database for validation. We used a series of computational and bioinformatic tools to identify EOCRC-specific differentially expressed genes, molecular pathways, predicted cell populations, differential gene splicing events, and predicted neoantigens. Results We identified an eight-gene signature in EOCRC comprised of ALDOB, FBXL16, IL1RN, MSLN, RAC3, SLC38A11, WBSCR27 and WNT11, from which we developed a score predictive of overall CRC patient survival. On the entire set of genes identified in normal tissues and tumors, cell type deconvolution analysis predicted a differential abundance of immune and non-immune populations in EOCRC versus LOCRC. Gene set enrichment analysis identified increased expression of splicing machinery in EOCRC. We further found differences in alternative splicing (AS) events, including one within the long non-coding RNA, HOTAIRM1. Additional analysis of AS found seven events specific to EOCRC that encode potential neoantigens. Conclusion Our transcriptome analyses identified genetic and molecular features specific to EOCRC which may inform future screening, development of prognostic indicators, and novel drug targets.

Single-cell multiplex chromatin and RNA interactions in ageing human brain

Article

Full-text available

Mar 2024
NATURE

Dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA1–3. Chromatin complex compositions change during cellular differentiation and ageing, and are expected to be highly heterogeneous among terminally differentiated single cells4–7. Here we introduce the multinucleic acid interaction mapping in single cells (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression and RNA–chromatin associations within individual nuclei. When applied to 14 human frontal cortex samples from older donors, MUSIC delineated diverse cortical cell types and states. We observed that nuclei exhibiting fewer short-range chromatin interactions were correlated with both an ‘older’ transcriptomic signature and Alzheimer’s disease pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci and a promoter tends to be that in which these cis expression quantitative trait loci specifically affect the expression of their target gene. In addition, female cortical cells exhibit highly heterogeneous interactions between XIST non-coding RNA and chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploration of chromatin architecture and transcription at cellular resolution in complex tissues.

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control

Article

Full-text available

Sep 2019
NUCLEIC ACIDS RES

U2 auxiliary factor 1 (U2AF1) functions in 3'-splice site selection during pre-mRNA processing. Alternative usage of duplicated tandem exons in U2AF1 produces two isoforms, U2AF1a and U2AF1b, but their functional differences are unappreciated due to their homology. Through integrative approaches of genome editing, customized-transcriptome profiling and crosslinking-mediated interactome analyses, we discovered that the expression of U2AF1 isoforms is controlled by mTOR and they exhibit a distinctive molecular profile for the splice site and protein interactomes. Mechanistic dissection of mutually exclusive alternative splicing events revealed that U2AF1 isoforms' inherent differential preferences of nucleotide sequences and their stoichiometry determine the 3'-splice site. Importantly, U2AF1a-driven transcriptomes feature alternative splicing events in the 5'-untranslated region (5'-UTR) that are favorable for translation. These findings unveil distinct roles of duplicated tandem exon-derived U2AF1 isoforms in the regulation of the transcriptome and suggest U2AF1a-driven 5'-UTR alternative splicing as a molecular mechanism of mTOR-regulated translational control.

The transcript expression levels of HNRNPM, HNRNPA0 and AKAP17A splicing factors may be predictively associated with ageing phenotypes in human peripheral blood

Article

Full-text available

Oct 2019
BIOGERONTOLOGY

Dysregulation of splicing factor expression is emerging as a driver of human ageing; levels of transcripts encoding splicing regulators have previously been implicated in ageing and cellular senescence both in vitro and in vivo. We measured the expression levels of an a priori panel of 20 age- or senescence-associated splicing factors by qRT-PCR in peripheral blood samples from the InCHIANTI Study of Aging, and assessed longitudinal relationships with human ageing phenotypes (cognitive decline and physical ability) using multivariate linear regression. AKAP17A, HNRNPA0 and HNRNPM transcript levels were all predictively associated with severe decline in MMSE score (p = 0.007, 0.001 and 0.008 respectively). Further analyses also found expression of these genes was associated with a performance decline in two other cognitive measures; the Trail Making Test and the Purdue Pegboard Test. AKAP17A was nominally associated with a decline in mean hand-grip strength (p = 0.023), and further analyses found nominal associations with two other physical ability measures; the Epidemiologic Studies of the Elderly-Short Physical Performance Battery and calculated speed (m/s) during a timed 400 m fast walking test. These data add weight to the hypothesis that splicing dyregulation may contribute to the development of some ageing phenotypes in the human population.

Dietary restriction induces posttranscriptional regulation of longevity genes

Article

Full-text available

Aug 2019

Dietary restriction (DR) increases life span through adaptive changes in gene expression. To understand more about these changes, we analyzed the transcriptome and translatome of Caenorhabditis elegans subjected to DR. Transcription of muscle regulatory and structural genes increased, whereas increased expression of amino acid metabolism and neuropeptide signaling genes was controlled at the level of translation. Evaluation of posttranscriptional regulation identified putative roles for RNA-binding proteins, RNA editing, miRNA, alternative splicing, and nonsense-mediated decay in response to nutrient limitation. Using RNA interference, we discovered several differentially expressed genes that regulate life span. We also found a compensatory role for translational regulation, which offsets dampened expression of a large subset of transcriptionally down-regulated genes. Furthermore, 3′ UTR editing and intron retention increase under DR and correlate with diminished translation, whereas trans-spliced genes are refractory to reduced translation efficiency compared with messages with the native 5′ UTR. Finally, we find that smg-6 and smg-7 , which are genes governing selection and turnover of nonsense-mediated decay targets, are required for increased life span under DR.

Increased intron retention is a post‐transcriptional signature associated with progressive aging and Alzheimer’s disease

Article

Full-text available

Mar 2019
AGING CELL

Intron retention (IR) by alternative splicing is a conserved regulatory mechanism that can affect gene expression and protein function during adult development and age‐onset diseases. However, it remains unclear whether IR undergoes spatial or temporal changes during different stages of aging or neurodegeneration like Alzheimer's disease (AD). By profiling the transcriptome of Drosophila head cells at different ages, we observed a significant increase in IR events for many genes during aging. Differential IR affects distinct biological functions at different ages and occurs at several AD‐associated genes in older adults. The increased nucleosome occupancy at the differentially retained introns in young animals suggests that it may regulate the level of IR during aging. Notably, an increase in the number of IR events was also observed in healthy older mouse and human brain tissues, as well as in the cerebellum and frontal cortex from independent AD cohorts. Genes with differential IR shared many common features, including shorter intron length, no perturbation in their mRNA level, and enrichment for biological functions that are associated with mRNA processing and proteostasis. The differentially retained introns identified in AD frontal cortex have higher GC content, with many of their mRNA transcripts showing an altered level of protein expression compared to control samples. Taken together, our results suggest that an increased IR is an conserved signature that is associated with aging. By affecting pathways involved in mRNA and protein homeostasis, changes of IR pattern during aging may regulate the transition from healthy to pathological state in late‐onset sporadic AD.

Excised linear introns regulate growth in yeast

Article

Full-text available

Jan 2019
NATURE

Spliceosomal introns are ubiquitous non-coding RNAs that are typically destined for rapid debranching and degradation. Here we describe 34 excised introns in Saccharomyces cerevisiae that—despite being rapidly degraded in log-phase growth—accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, which is a key integrator of growth signalling. Introns that become stabilized remain associated with components of the spliceosome and differ from other spliceosomal introns in having a short distance between their lariat branch point and 3′ splice site, which is necessary and sufficient for their stabilization. Deletion of these unusual introns is disadvantageous in saturated conditions and causes aberrantly high growth rates in yeast that are chronically challenged with the TORC1 inhibitor rapamycin. The reintroduction of native or engineered stable introns suppresses this aberrant rapamycin response. Thus, excised introns function within the TOR growth-signalling network of S. cerevisiae and, more generally, excised spliceosomal introns can have biological functions.

Introns are mediators of cell response to starvation

Article

Full-text available

Jan 2019
NATURE

Introns are ubiquitous features of all eukaryotic cells. Introns need to be removed from nascent messenger RNA through the process of splicing to produce functional proteins. Here we show that the physical presence of introns in the genome promotes cell survival under starvation conditions. A systematic deletion set of all known introns in budding yeast genes indicates that, in most cases, cells with an intron deletion are impaired when nutrients are depleted. This effect of introns on growth is not linked to the expression of the host gene, and was reproduced even when translation of the host mRNA was blocked. Transcriptomic and genetic analyses indicate that introns promote resistance to starvation by enhancing the repression of ribosomal protein genes that are downstream of the nutrient-sensing TORC1 and PKA pathways. Our results reveal functions of introns that may help to explain their evolutionary preservation in genes, and uncover regulatory mechanisms of cell adaptations to starvation.

NOVA1 directs PTBP1 to hTERT pre-mRNA and promotes telomerase activity in cancer cells

Article

Full-text available

Apr 2019

Alternative splicing is dysregulated in cancer cells, driving the production of isoforms that allow tumor cells to survive and continuously proliferate. Part of the reactivation of telomerase involves the splicing of hTERT transcripts to produce full-length (FL) TERT. Very few splicing factors to date have been described to interact with hTERT and promote the production of FL TERT. We recently described one such splicing factor, NOVA1, that acts as an enhancer of FL hTERT splicing, increases telomerase activity, and promotes telomere maintenance in cancer cells. NOVA1 is expressed primarily in neurons and is involved in neurogenesis. In the present studies, we describe that polypyrimidine-tract binding proteins (PTBPs), which are also typically involved in neurogenesis, are also participating in the splicing of hTERT to FL in cancer. Knockdown experiments of PTBP1 in cancer cells indicate that PTBP1 reduces hTERT FL splicing and telomerase activity. Stable knockdown of PTBP1 results in progressively shortened telomere length in H1299 and H920 lung cancer cells. RNA pulldown experiments reveal that PTBP1 interacts with hTERT pre-mRNA in a NOVA1 dependent fashion. Knockdown of PTBP1 increases the expression of PTBP2 which also interacts with NOVA1, potentially preventing the association of NOVA1 with hTERT pre-mRNA. These new data highlight that splicing in cancer cells is regulated by competition for splice sites and that combinations of splicing factors interact at cis regulatory sites on pre-mRNA transcripts. By employing hTERT as a model gene, we show the coordination of the splicing factors NOVA1 and PTBP1 in cancer by regulating telomerase that is expressed in the vast majority of cancer cell types.

FOXO1 and ETV6 genes may represent novel regulators of splicing factor expression in cellular senescence

Article

Full-text available

Aug 2018
FASEB J

Cellular plasticity is a key facet of cellular homeostasis requiring correct temporal and spatial patterns of alternative splicing. Splicing factors, which orchestrate this process, demonstrate age‐related dysregulation of expression; they are emerging as potential influences on aging and longevity. The upstream drivers of these alterations are still unclear but may involve aberrant cellular signaling. We compared the phosphorylation status of proteins in multiple signaling pathways in early and late passage human primary fibroblasts. We then assessed the impact of chemical inhibition or targeted knockdown of direct downstream targets of the ERK and AKT pathways on splicing factor expression, cellular senescence, and proliferation kinetics in senescent primary human fibroblasts. Components of the ERK and AKT signaling pathways demonstrated altered activation during cellular aging. Inhibition of AKT and ERK pathways led to up‐regulation of splicing factor expression, reduction in senescent cell load, and partial reversal of multiple cellular senescence phenotypes in a dose‐dependent manner. Furthermore, targeted knockdown of the genes encoding the downstream targets FOXO1 or ETV6 was sufficient to mimic these observations. Our results suggest that age‐associated dysregulation of splicing factor expression and cellular senescence may derive in part from altered activity of ERK and AKT signaling and may act in part through the ETV6 and FOXO1 transcription factors. Targeting the activity of downstream effectors of ERK and AKT may therefore represent promising targets for future therapeutic intervention.—Latorre, E., Ostler, E. L., Faragher, R. G. A., Harries, L. W. FOXO1 and ETV6 genes may represent novel regulators of splicing factor expression in cellular senescence. FASEB J. 33, 1086–1097 (2019). www.fasebj.org

Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases

Article

Full-text available

Jul 2018

Alternative splicing contributes to phenotypic diversity at multiple biological scales, and its dysregulation is implicated in both ageing and age-associated diseases in human. Cross-tissue variability in splicing further complicates its links to age-associated phenotypes and elucidating these links requires a comprehensive map of age-associated splicing changes across multiple tissues. Here, we generate such a map by analyzing ~8500 RNA-seq samples across 48 tissues in 544 individuals. Employing a stringent model controlling for multiple confounders, we identify 49,869 tissue-specific age-associated splicing events of 7 distinct types. We find that genome-wide splicing profile is a better predictor of biological age than the gene and transcript expression profiles, and furthermore, age-associated splicing provides additional independent contribution to age-associated complex diseases. We show that the age-associated splicing changes may be explained, in part, by concomitant age-associated changes of the upstream splicing factors. Finally, we show that our splicing-based model of age can successfully predict the relative ages of cells in 8 of the 10 paired longitudinal data as well as in 2 sets of cell passage data. Our study presents the first systematic investigation of age-associated splicing changes across tissues, and further strengthening the links between age-associated splicing and age-associated diseases.

Dietary restriction in ILSXISS mice is associated with widespread changes in splicing regulatory factor expression levels

Article

Sep 2019
EXP GERONTOL

Dietary restriction (DR) represents one of the most reproducible interventions to extend lifespan and improve health outcomes in a wide range of species, but substantial variability in DR response has been observed, both between and within species. The mechanisms underlying this variation in effect are still not well characterised. Splicing regulatory factors have been implicated in the pathways linked with DR-induced longevity in C. elegans and are associated with lifespan itself in mice and humans. We used qRT-PCR to measure the expression levels of a panel of 16 age- and lifespan-associated splicing regulatory factors in brain, heart and kidney derived from three recombinant inbred strains of mice with variable lifespan responses to short-term (2 months) or long-term (10 months) 40% DR to determine their relationship to DR-induced longevity. We identified 3 patterns of association; i) splicing factors associated with DR alone, ii) splicing factors associated with strain alone or iii) splicing factors associated with both DR and strain. Tissue specific variation was noted in response to short-term or long-term DR, with the majority of effects noted in brain following long-term DR in the positive responder strain TejJ89. Association in heart and kidney were less evident, and occurred following short-term DR. Splicing factors associated with both DR and strain may be mechanistically involved in strain-specific differences in response to DR. We provide here evidence concordant with a role for some splicing factors in the lifespan modulatory effects of DR across different mouse strains and in different tissues.

Alternative splicing in aging and longevity

Abstract and Figures

Recommended publications

Splicing Factor 1 Modulates Dietary Restriction and TORC1 Pathway Longevity in C. elegans

Proper splicing contributes to visual function in the aging Drosophila eye

Corrigendum: Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in C. elega...

RNA and aging