2025
Sultanova, Zahida; Shen, Aykut; Hencel, Katarzyna; Carlsson, Hanne; Crighton, Zoe; Clifton, Daniel; Akay, Alper; Maklakov, Alexei A.
Optimising Age-Specific Insulin Signalling to Slow Down Reproductive Ageing Increases Fitness in Different Nutritional Environments Journal Article
In: Aging Cell, vol. n/a, no. n/a, pp. e14481, 2025, ISSN: 1474-9726, (_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acel.14481).
Abstract | Links | BibTeX | Tags: ageing, developmental theory of ageing, life-history evolution, trade-offs
@article{sultanova_optimising_2025,
title = {Optimising Age-Specific Insulin Signalling to Slow Down Reproductive Ageing Increases Fitness in Different Nutritional Environments},
author = {Zahida Sultanova and Aykut Shen and Katarzyna Hencel and Hanne Carlsson and Zoe Crighton and Daniel Clifton and Alper Akay and Alexei A. Maklakov},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acel.14481},
doi = {10.1111/acel.14481},
issn = {1474-9726},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-30},
journal = {Aging Cell},
volume = {n/a},
number = {n/a},
pages = {e14481},
abstract = {The developmental theory of ageing proposes that age-specific decline in the force of natural selection results in suboptimal levels of gene expression in adulthood, leading to functional senescence. This theory explicitly predicts that optimising gene expression in adulthood can ameliorate functional senescence and improve fitness. Reduced insulin/IGF-1 signalling (rIIS) extends the reproductive lifespan of Caenorhabditis elegans at the cost of reduced reproduction. Here, we show that adulthood-only rIIS improves late-life reproduction without any detrimental effects on other life-history traits in both benign and stressful conditions. Remarkably, we show that rIIS additively extends late-life reproduction and lifespan when animals are exposed to a fluctuating food environment—intermittent fasting (IF)—resulting in reduced food intake in early adulthood. Full factorial genome-wide RNA-Seq across the life course demonstrated that IF and rIIS modulate the age-specific expression of pro-longevity genes. IF, rIIS and combined IF + rIIS treatment downregulated genes involved in biosynthesis in early life and differentially regulated immunity genes in later life. Importantly, combined IF + rIIS treatment uniquely regulated a large cluster of genes in mid-life that are associated with immune response. These results suggest that optimising gene expression in adulthood can decelerate reproductive ageing and increase fitness.},
note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acel.14481},
keywords = {ageing, developmental theory of ageing, life-history evolution, trade-offs},
pubstate = {published},
tppubtype = {article}
}
2024
Shen, Aykut; Hencel, Katarzyna; Parker, Matthew T; Scott, Robyn; Skukan, Roberta; Adesina, Aduragbemi S; Metheringham, Carey L; Miska, Eric A; Nam, Yunsun; Haerty, Wilfried; Simpson, Gordon G; Akay, Alper
U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs Journal Article
In: Nucleic Acids Research, pp. gkae447, 2024, ISSN: 0305-1048.
Abstract | Links | BibTeX | Tags:
@article{shen_u6_2024,
title = {U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs},
author = {Aykut Shen and Katarzyna Hencel and Matthew T Parker and Robyn Scott and Roberta Skukan and Aduragbemi S Adesina and Carey L Metheringham and Eric A Miska and Yunsun Nam and Wilfried Haerty and Gordon G Simpson and Alper Akay},
url = {https://doi.org/10.1093/nar/gkae447},
doi = {10.1093/nar/gkae447},
issn = {0305-1048},
year = {2024},
date = {2024-05-01},
urldate = {2024-05-29},
journal = {Nucleic Acids Research},
pages = {gkae447},
abstract = {pre-mRNA splicing is a critical feature of eukaryotic gene expression. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that the conserved U6 snRNA m6A methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of METT-10 in C. elegans and METTL16 in humans primarily leads to alternative splicing at 5′ splice sites with an adenosine at +4 position. In addition, METT-10 is required for splicing of weak 3′ cis- and trans-splice sites. We identified a significant overlap between METT-10 and the conserved splicing factor SNRNP27K in regulating 5′ splice sites with +4A. Finally, we show that editing endogenous 5′ splice site +4A positions to +4U restores splicing to wild-type positions in a mett-10 mutant background, supporting a direct role for U6 snRNA m6A modification in 5′ splice site recognition. We conclude that the U6 snRNA m6A modification is important for accurate and efficient pre-mRNA splicing.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2023
Sultanova, Zahida; Shen, Aykut; Hencel, Katarzyna; Carlsson, Hanne; Crighton, Zoe; Clifton, Daniel; Akay, Alper; Maklakov, Alexei A
2023, (Publication Title: bioRxiv).
Abstract | Links | BibTeX | Tags:
@unpublished{sultanova_early-adulthood_2023,
title = {Early-adulthood intermittent fasting and reduced insulin/IGF-1 signalling additively increase lifespan and slow down reproductive ageing},
author = {Zahida Sultanova and Aykut Shen and Katarzyna Hencel and Hanne Carlsson and Zoe Crighton and Daniel Clifton and Alper Akay and Alexei A Maklakov},
url = {https://www.biorxiv.org/content/10.1101/2023.12.22.573079v1},
doi = {10.1101/2023.12.22.573079},
year = {2023},
date = {2023-12-01},
urldate = {2024-02-20},
abstract = {Intermittent fasting (IF) and reduced insulin/IGF-1 nutrient-sensing
signalling (rIIS) increase lifespan via partially shared downstream
genetic pathways. The relationship between IF and rIIS is unclear because
IF reduces reproduction, while adulthood-only rIIS does not. Here, we show
that early-adulthood (but not late-adulthood) IF and adulthood-only rIIS
additively increase lifespan and slow reproductive ageing in C. elegans .
Mechanistically, we show that in the combined IF + rIIS treatment, nuclear
localisation of DAF-16 transcription factor is primarily driven by IF in
early-life, and primarily driven by rIIS in late-life. Full factorial
genome-wide RNA-seq across the life course demonstrates that
early-adulthood IF and rIIS modulate the age-specific expression of
pro-longevity genes. Early-adulthood IF, rIIS and combined IF + rIIS
treatment downregulated genes involved in peptide metabolism in early life
and differentially regulated immunity genes in later life. Importantly.
combined IF + rIIS treatment uniquely regulated a large cluster of genes
in mid-life that are associated with immune response. These results
suggest that the combined impact of different treatments aimed at healthy
ageing can achieve better outcomes by targeting different ages. ###
Competing Interest Statement The authors have declared no competing
interest.},
note = {Publication Title: bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
signalling (rIIS) increase lifespan via partially shared downstream
genetic pathways. The relationship between IF and rIIS is unclear because
IF reduces reproduction, while adulthood-only rIIS does not. Here, we show
that early-adulthood (but not late-adulthood) IF and adulthood-only rIIS
additively increase lifespan and slow reproductive ageing in C. elegans .
Mechanistically, we show that in the combined IF + rIIS treatment, nuclear
localisation of DAF-16 transcription factor is primarily driven by IF in
early-life, and primarily driven by rIIS in late-life. Full factorial
genome-wide RNA-seq across the life course demonstrates that
early-adulthood IF and rIIS modulate the age-specific expression of
pro-longevity genes. Early-adulthood IF, rIIS and combined IF + rIIS
treatment downregulated genes involved in peptide metabolism in early life
and differentially regulated immunity genes in later life. Importantly.
combined IF + rIIS treatment uniquely regulated a large cluster of genes
in mid-life that are associated with immune response. These results
suggest that the combined impact of different treatments aimed at healthy
ageing can achieve better outcomes by targeting different ages. ###
Competing Interest Statement The authors have declared no competing
interest.
2021
Navarro, Isabela Cunha; Tuorto, Francesca; Jordan, David; Legrand, Carine; Price, Jonathan; Braukmann, Fabian; Hendrick, Alan G; Akay, Alper; Kotter, Annika; Helm, Mark; Lyko, Frank; Miska, Eric A
Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans Journal Article
In: EMBO J., vol. 40, no. 6, pp. e105496, 2021, ISSN: 0261-4189, (Publisher: John Wiley & Sons, Ltd).
Abstract | Links | BibTeX | Tags: 5-methylcytosine, Caenorhabditis elegans, NSUN, RNA modifications, translation efficiency
@article{navarro_translational_2021,
title = {Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans},
author = {Isabela Cunha Navarro and Francesca Tuorto and David Jordan and Carine Legrand and Jonathan Price and Fabian Braukmann and Alan G Hendrick and Alper Akay and Annika Kotter and Mark Helm and Frank Lyko and Eric A Miska},
url = {http://dx.doi.org/10.15252/embj.2020105496},
doi = {10.15252/embj.2020105496},
issn = {0261-4189},
year = {2021},
date = {2021-03-01},
journal = {EMBO J.},
volume = {40},
number = {6},
pages = {e105496},
abstract = {Methylation of carbon-5 of cytosines (m5 C) is a post-transcriptional
nucleotide modification of RNA found in all kingdoms of life. While
individual m5 C-methyltransferases have been studied, the impact of the
global cytosine-5 methylome on development, homeostasis and stress remains
unknown. Here, using Caenorhabditis elegans, we generated the first
organism devoid of m5 C in RNA, demonstrating that this modification is
non-essential. Using this genetic tool, we determine the localisation and
enzymatic specificity of m5 C sites in the RNome in vivo. We find that
NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans
mitochondria. In agreement with leucine and proline being the most
frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding
of some triplets of these two amino acids, leading to reduced translation
efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG
triplets, the only codon translated by an m5 C34-modified tRNA. This leads
to reduced translation efficiency of UUG-rich transcripts and impaired
fertility, suggesting a role of m5 C tRNA wobble methylation in the
adaptation to higher temperatures.},
note = {Publisher: John Wiley & Sons, Ltd},
keywords = {5-methylcytosine, Caenorhabditis elegans, NSUN, RNA modifications, translation efficiency},
pubstate = {published},
tppubtype = {article}
}
nucleotide modification of RNA found in all kingdoms of life. While
individual m5 C-methyltransferases have been studied, the impact of the
global cytosine-5 methylome on development, homeostasis and stress remains
unknown. Here, using Caenorhabditis elegans, we generated the first
organism devoid of m5 C in RNA, demonstrating that this modification is
non-essential. Using this genetic tool, we determine the localisation and
enzymatic specificity of m5 C sites in the RNome in vivo. We find that
NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans
mitochondria. In agreement with leucine and proline being the most
frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding
of some triplets of these two amino acids, leading to reduced translation
efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG
triplets, the only codon translated by an m5 C34-modified tRNA. This leads
to reduced translation efficiency of UUG-rich transcripts and impaired
fertility, suggesting a role of m5 C tRNA wobble methylation in the
adaptation to higher temperatures.
Berkyurek, Ahmet C; Furlan, Giulia; Lampersberger, Lisa; Beltran, Toni; Weick, Eva-Maria; Nischwitz, Emily; Navarro, Isabela Cunha; Braukmann, Fabian; Akay, Alper; Price, Jonathan; Butter, Falk; Sarkies, Peter; Miska, Eric A
The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription Journal Article
In: EMBO J., vol. 40, no. 5, pp. e105565, 2021, ISSN: 0261-4189, (Publisher: EMBO).
Abstract | Links | BibTeX | Tags: integrator, piRNAs, RNA polymerase II, rpb-9, transcription termination
@article{berkyurek_rna_2021,
title = {The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription},
author = {Ahmet C Berkyurek and Giulia Furlan and Lisa Lampersberger and Toni Beltran and Eva-Maria Weick and Emily Nischwitz and Isabela Cunha Navarro and Fabian Braukmann and Alper Akay and Jonathan Price and Falk Butter and Peter Sarkies and Eric A Miska},
url = {http://dx.doi.org/10.15252/embj.2020105565},
doi = {10.15252/embj.2020105565},
issn = {0261-4189},
year = {2021},
date = {2021-03-01},
journal = {EMBO J.},
volume = {40},
number = {5},
pages = {e105565},
abstract = {PIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate
germ cell development and maintain germline integrity in many animals.
Mature piRNAs engage Piwi Argonaute proteins to silence complementary
transcripts, including transposable elements and endogenous genes. piRNA
biogenesis mechanisms are diverse and remain poorly understood. Here, we
identify the RNA polymerase II (RNA Pol II) core subunit RPB-9 as required
for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We
show that rpb-9 initiates heritable piRNA-mediated gene silencing at two
DNA transposon families and at a subset of somatic genes in the germline.
We provide genetic and biochemical evidence that RPB-9 is required for
piRNA biogenesis by recruiting the Integrator complex at piRNA genes,
hence promoting transcriptional termination. We conclude that, as a part
of its rapid evolution, the piRNA pathway has co-opted an ancient
machinery for high-fidelity transcription.},
note = {Publisher: EMBO},
keywords = {integrator, piRNAs, RNA polymerase II, rpb-9, transcription termination},
pubstate = {published},
tppubtype = {article}
}
germ cell development and maintain germline integrity in many animals.
Mature piRNAs engage Piwi Argonaute proteins to silence complementary
transcripts, including transposable elements and endogenous genes. piRNA
biogenesis mechanisms are diverse and remain poorly understood. Here, we
identify the RNA polymerase II (RNA Pol II) core subunit RPB-9 as required
for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We
show that rpb-9 initiates heritable piRNA-mediated gene silencing at two
DNA transposon families and at a subset of somatic genes in the germline.
We provide genetic and biochemical evidence that RPB-9 is required for
piRNA biogenesis by recruiting the Integrator complex at piRNA genes,
hence promoting transcriptional termination. We conclude that, as a part
of its rapid evolution, the piRNA pathway has co-opted an ancient
machinery for high-fidelity transcription.
Kranse, Olaf; Beasley, Helen; Adams, Sally; Pires-daSilva, Andre; Bell, Christopher; Lilley, Catherine J; Urwin, Peter E; Bird, David; Miska, Eric; Smant, Geert; Gheysen, Godelieve; Jones, John; Viney, Mark; Abad, Pierre; Maier, Thomas R; Baum, Thomas J; Siddique, Shahid; Williamson, Valerie; Akay, Alper; den Akker, Sebastian Eves-van
In: G3, vol. 11, no. 2, 2021, ISSN: 2160-1836.
Abstract | Links | BibTeX | Tags: genetic modification, germline, lipofection, plant-parasitic nematodes, transformation, transient expression
@article{kranse_toward_2021,
title = {Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles},
author = {Olaf Kranse and Helen Beasley and Sally Adams and Andre Pires-daSilva and Christopher Bell and Catherine J Lilley and Peter E Urwin and David Bird and Eric Miska and Geert Smant and Godelieve Gheysen and John Jones and Mark Viney and Pierre Abad and Thomas R Maier and Thomas J Baum and Shahid Siddique and Valerie Williamson and Alper Akay and Sebastian Eves-van den Akker},
url = {http://dx.doi.org/10.1093/g3journal/jkaa058},
doi = {10.1093/g3journal/jkaa058},
issn = {2160-1836},
year = {2021},
date = {2021-02-01},
journal = {G3},
volume = {11},
number = {2},
abstract = {Plant-parasitic nematodes are a continuing threat to food security,
causing an estimated 100 billion USD in crop losses each year. The most
problematic are the obligate sedentary endoparasites (primarily root knot
nematodes and cyst nematodes). Progress in understanding their biology is
held back by a lack of tools for functional genetics: forward genetics is
largely restricted to studies of natural variation in populations and
reverse genetics is entirely reliant on RNA interference. There is an
expectation that the development of functional genetic tools would
accelerate the progress of research on plant-parasitic nematodes, and
hence the development of novel control solutions. Here, we develop some of
the foundational biology required to deliver a functional genetic tool kit
in plant-parasitic nematodes. We characterize the gonads of male
Heterodera schachtii and Meloidogyne hapla in the context of
spermatogenesis. We test and optimize various methods for the delivery,
expression, and/or detection of exogenous nucleic acids in plant-parasitic
nematodes. We demonstrate that delivery of macromolecules to cyst and root
knot nematode male germlines is difficult, but possible. Similarly, we
demonstrate the delivery of oligonucleotides to root knot nematode
gametes. Finally, we develop a transient expression system in
plant-parasitic nematodes by demonstrating the delivery and expression of
exogenous mRNA encoding various reporter genes throughout the body of H.
schachtii juveniles using lipofectamine-based transfection. We anticipate
these developments to be independently useful, will expedite the
development of genetic modification tools for plant-parasitic nematodes,
and ultimately catalyze research on a group of nematodes that threaten
global food security.},
keywords = {genetic modification, germline, lipofection, plant-parasitic nematodes, transformation, transient expression},
pubstate = {published},
tppubtype = {article}
}
causing an estimated 100 billion USD in crop losses each year. The most
problematic are the obligate sedentary endoparasites (primarily root knot
nematodes and cyst nematodes). Progress in understanding their biology is
held back by a lack of tools for functional genetics: forward genetics is
largely restricted to studies of natural variation in populations and
reverse genetics is entirely reliant on RNA interference. There is an
expectation that the development of functional genetic tools would
accelerate the progress of research on plant-parasitic nematodes, and
hence the development of novel control solutions. Here, we develop some of
the foundational biology required to deliver a functional genetic tool kit
in plant-parasitic nematodes. We characterize the gonads of male
Heterodera schachtii and Meloidogyne hapla in the context of
spermatogenesis. We test and optimize various methods for the delivery,
expression, and/or detection of exogenous nucleic acids in plant-parasitic
nematodes. We demonstrate that delivery of macromolecules to cyst and root
knot nematode male germlines is difficult, but possible. Similarly, we
demonstrate the delivery of oligonucleotides to root knot nematode
gametes. Finally, we develop a transient expression system in
plant-parasitic nematodes by demonstrating the delivery and expression of
exogenous mRNA encoding various reporter genes throughout the body of H.
schachtii juveniles using lipofectamine-based transfection. We anticipate
these developments to be independently useful, will expedite the
development of genetic modification tools for plant-parasitic nematodes,
and ultimately catalyze research on a group of nematodes that threaten
global food security.
2020
Suen, Kin Man; Braukmann, Fabian; Butler, Richard; Bensaddek, Dalila; Akay, Alper; Lin, Chi-Chuan; Milonaitytė, Dovilė; Doshi, Neel; Sapetschnig, Alexandra; Lamond, Angus; Ladbury, John Edward; Miska, Eric Alexander
DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans Journal Article
In: Nat. Commun., vol. 11, no. 1, pp. 4242, 2020, ISSN: 2041-1723.
Abstract | Links | BibTeX | Tags:
@article{suen_deps-1_2020,
title = {DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans},
author = {Kin Man Suen and Fabian Braukmann and Richard Butler and Dalila Bensaddek and Alper Akay and Chi-Chuan Lin and Dovilė Milonaitytė and Neel Doshi and Alexandra Sapetschnig and Angus Lamond and John Edward Ladbury and Eric Alexander Miska},
url = {http://dx.doi.org/10.1038/s41467-020-18089-1},
doi = {10.1038/s41467-020-18089-1},
issn = {2041-1723},
year = {2020},
date = {2020-08-01},
journal = {Nat. Commun.},
volume = {11},
number = {1},
pages = {4242},
abstract = {Membraneless organelles are sites for RNA biology including small
non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise
phase separated environments for their function is unclear. We
investigated how the PIWI-interacting RNA (piRNA) pathway engages with the
membraneless organelle P granule in Caenorhabditis elegans. Proteomic
analysis of the PIWI protein PRG-1 reveals an interaction with the
constitutive P granule protein DEPS-1. DEPS-1 is not required for piRNA
biogenesis but piRNA-dependent silencing: deps-1 mutants fail to produce
the secondary endo-siRNAs required for the silencing of piRNA targets. We
identify a motif on DEPS-1 which mediates a direct interaction with PRG-1.
DEPS-1 and PRG-1 form intertwining clusters to build elongated condensates
in vivo which are dependent on the Piwi-interacting motif of DEPS-1.
Additionally, we identify EDG-1 as an interactor of DEPS-1 and PRG-1. Our
study reveals how specific protein-protein interactions drive the spatial
organisation and piRNA-dependent silencing within membraneless organelles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise
phase separated environments for their function is unclear. We
investigated how the PIWI-interacting RNA (piRNA) pathway engages with the
membraneless organelle P granule in Caenorhabditis elegans. Proteomic
analysis of the PIWI protein PRG-1 reveals an interaction with the
constitutive P granule protein DEPS-1. DEPS-1 is not required for piRNA
biogenesis but piRNA-dependent silencing: deps-1 mutants fail to produce
the secondary endo-siRNAs required for the silencing of piRNA targets. We
identify a motif on DEPS-1 which mediates a direct interaction with PRG-1.
DEPS-1 and PRG-1 form intertwining clusters to build elongated condensates
in vivo which are dependent on the Piwi-interacting motif of DEPS-1.
Additionally, we identify EDG-1 as an interactor of DEPS-1 and PRG-1. Our
study reveals how specific protein-protein interactions drive the spatial
organisation and piRNA-dependent silencing within membraneless organelles.
2019
Akay, Alper; Jordan, David; Navarro, Isabela Cunha; Wrzesinski, Tomasz; Ponting, Chris P; Miska, Eric A; Haerty, Wilfried
Identification of functional long non-coding RNAs in C. elegans Journal Article
In: BMC Biol., vol. 17, no. 1, pp. 14, 2019, ISSN: 1741-7007.
Abstract | Links | BibTeX | Tags: Akay_Lab/lncRNA, C. elegans, CRISPR, lincRNA, lncRNA, Long non-coding RNA, Non-coding
@article{akay_identification_2019,
title = {Identification of functional long non-coding RNAs in C. elegans},
author = {Alper Akay and David Jordan and Isabela Cunha Navarro and Tomasz Wrzesinski and Chris P Ponting and Eric A Miska and Wilfried Haerty},
url = {http://dx.doi.org/10.1186/s12915-019-0635-7},
doi = {10.1186/s12915-019-0635-7},
issn = {1741-7007},
year = {2019},
date = {2019-02-01},
journal = {BMC Biol.},
volume = {17},
number = {1},
pages = {14},
abstract = {BACKGROUND: Functional characterisation of the compact genome of the model
organism Caenorhabditis elegans remains incomplete despite its sequencing
20 years ago. The last decade of research has seen a tremendous increase
in the number of non-coding RNAs identified in various organisms. While we
have mechanistic understandings of small non-coding RNA pathways, long
non-coding RNAs represent a diverse class of active transcripts whose
function remains less well characterised. RESULTS: By analysing hundreds
of published transcriptome datasets, we annotated 3392 potential lncRNAs
including 143 multi-exonic loci that showed increased nucleotide
conservation and GC content relative to other non-coding regions. Using
CRISPR/Cas9 genome editing, we generated deletion mutants for ten long
non-coding RNA loci. Using automated microscopy for in-depth phenotyping,
we show that six of the long non-coding RNA loci are required for normal
development and fertility. Using RNA interference-mediated gene
knock-down, we provide evidence that for two of the long non-coding RNA
loci, the observed phenotypes are dependent on the corresponding RNA
transcripts. CONCLUSIONS: Our results highlight that a large section of
the non-coding regions of the C. elegans genome remains unexplored. Based
on our in vivo analysis of a selection of high-confidence lncRNA loci, we
expect that a significant proportion of these high-confidence regions is
likely to have a biological function at either the genomic or the
transcript level.},
keywords = {Akay_Lab/lncRNA, C. elegans, CRISPR, lincRNA, lncRNA, Long non-coding RNA, Non-coding},
pubstate = {published},
tppubtype = {article}
}
organism Caenorhabditis elegans remains incomplete despite its sequencing
20 years ago. The last decade of research has seen a tremendous increase
in the number of non-coding RNAs identified in various organisms. While we
have mechanistic understandings of small non-coding RNA pathways, long
non-coding RNAs represent a diverse class of active transcripts whose
function remains less well characterised. RESULTS: By analysing hundreds
of published transcriptome datasets, we annotated 3392 potential lncRNAs
including 143 multi-exonic loci that showed increased nucleotide
conservation and GC content relative to other non-coding regions. Using
CRISPR/Cas9 genome editing, we generated deletion mutants for ten long
non-coding RNA loci. Using automated microscopy for in-depth phenotyping,
we show that six of the long non-coding RNA loci are required for normal
development and fertility. Using RNA interference-mediated gene
knock-down, we provide evidence that for two of the long non-coding RNA
loci, the observed phenotypes are dependent on the corresponding RNA
transcripts. CONCLUSIONS: Our results highlight that a large section of
the non-coding regions of the C. elegans genome remains unexplored. Based
on our in vivo analysis of a selection of high-confidence lncRNA loci, we
expect that a significant proportion of these high-confidence regions is
likely to have a biological function at either the genomic or the
transcript level.
2018
Sarabipour, Sarvenaz; Wissink, Erin M.; Burgess, Steven J.; Hensel, Zach; Debat, Humberto; Emmott, Edward; Akay, Alper; Akdemir, Kadir; Schwessinger, Benjamin
Maintaining confidence in the reporting of scientific outputs Technical Report
PeerJ Preprints no. e27098v1, 2018, (ISSN: 2167-9843).
Abstract | Links | BibTeX | Tags: academic publishing, Open science, Peer review, Preprints, science communication, science journalism
@techreport{sarabipour_maintaining_2018,
title = {Maintaining confidence in the reporting of scientific outputs},
author = {Sarvenaz Sarabipour and Erin M. Wissink and Steven J. Burgess and Zach Hensel and Humberto Debat and Edward Emmott and Alper Akay and Kadir Akdemir and Benjamin Schwessinger},
url = {https://peerj.com/preprints/27098},
doi = {10.7287/peerj.preprints.27098v1},
year = {2018},
date = {2018-08-01},
urldate = {2024-05-30},
number = {e27098v1},
institution = {PeerJ Preprints},
abstract = {The timely and accurate dissemination of scientific discoveries is of utmost importance so that scientific knowledge can be advanced and applied to benefit the public. Scientists communicate amongst themselves at conferences, via journal articles, and, increasingly in the life sciences, in preprint manuscripts which have not been subject to peer review. Journalists translate new research into a language the public can understand, relying on both work presented in scientific forums and interviews with experts. Critically, scientists and journalists both share the ethical principle that publications should be rigorously sourced and fact-checked, with errors subject to publicized corrections. Here we respond to concerns raised about the impact of reporting on results that have not passed through peer review, calling for improved dialogue between scientists and journalists to maintain public trust in research and arguing that imposing limits is against the public interest.},
note = {ISSN: 2167-9843},
keywords = {academic publishing, Open science, Peer review, Preprints, science communication, science journalism},
pubstate = {published},
tppubtype = {techreport}
}
Sarabipour, Sarvenaz
Preprints are good for science and good for the public Journal Article
In: Nature, vol. 560, no. 7720, pp. 553, 2018, ISSN: 0028-0836, (Publisher: Nature Publishing Group).
Abstract | Links | BibTeX | Tags: Communication, Media, Publishing
@article{sarabipour_preprints_2018,
title = {Preprints are good for science and good for the public},
author = {Sarvenaz Sarabipour},
url = {http://www.nature.com/articles/d41586-018-06054-4},
doi = {10.1038/d41586-018-06054-4},
issn = {0028-0836},
year = {2018},
date = {2018-08-01},
urldate = {2018-08-29},
journal = {Nature},
volume = {560},
number = {7720},
pages = {553},
abstract = {Discover the world’s best science and medicine textbar Nature.com},
note = {Publisher: Nature Publishing Group},
keywords = {Communication, Media, Publishing},
pubstate = {published},
tppubtype = {article}
}
2017
Akay, Alper; Domenico, Tomas Di; Suen, Kin M; Nabih, Amena; Parada, Guillermo E; Larance, Mark; Medhi, Ragini; Berkyurek, Ahmet C; Zhang, Xinlian; Wedeles, Christopher J; Rudolph, Konrad L M; Engelhardt, Jan; Hemberg, Martin; Ma, Ping; Lamond, Angus I; Claycomb, Julie M; Miska, Eric A
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription Journal Article
In: Dev. Cell, vol. 42, no. 3, pp. 241–255.e6, 2017, ISSN: 1534-5807.
Abstract | Links | BibTeX | Tags: C. elegans, epigenetic inheritance, nuclear RNAi, piRNA, Piwi, RNA processing, RNAi, splicing, transcription, transposable elements
@article{akay_helicase_2017,
title = {The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription},
author = {Alper Akay and Tomas Di Domenico and Kin M Suen and Amena Nabih and Guillermo E Parada and Mark Larance and Ragini Medhi and Ahmet C Berkyurek and Xinlian Zhang and Christopher J Wedeles and Konrad L M Rudolph and Jan Engelhardt and Martin Hemberg and Ping Ma and Angus I Lamond and Julie M Claycomb and Eric A Miska},
url = {http://dx.doi.org/10.1016/j.devcel.2017.07.002},
doi = {10.1016/j.devcel.2017.07.002},
issn = {1534-5807},
year = {2017},
date = {2017-08-01},
journal = {Dev. Cell},
volume = {42},
number = {3},
pages = {241–255.e6},
abstract = {Small RNAs play a crucial role in genome defense against transposable
elements and guide Argonaute proteins to nascent RNA transcripts to induce
co-transcriptional gene silencing. However, the molecular basis of this
process remains unknown. Here, we identify the conserved RNA helicase
Aquarius/EMB-4 as a direct and essential link between small RNA pathways
and the transcriptional machinery in Caenorhabditis elegans. Aquarius
physically interacts with the germline Argonaute HRDE-1. Aquarius is
required to initiate small-RNA-induced heritable gene silencing. HRDE-1
and Aquarius silence overlapping sets of genes and transposable elements.
Surprisingly, removal of introns from a target gene abolishes the
requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene
silencing. We conclude that Aquarius allows small RNA pathways to compete
for access to nascent transcripts undergoing co-transcriptional splicing
in order to detect and silence transposable elements. Thus, Aquarius and
HRDE-1 act as gatekeepers coordinating gene expression and genome defense.},
keywords = {C. elegans, epigenetic inheritance, nuclear RNAi, piRNA, Piwi, RNA processing, RNAi, splicing, transcription, transposable elements},
pubstate = {published},
tppubtype = {article}
}
elements and guide Argonaute proteins to nascent RNA transcripts to induce
co-transcriptional gene silencing. However, the molecular basis of this
process remains unknown. Here, we identify the conserved RNA helicase
Aquarius/EMB-4 as a direct and essential link between small RNA pathways
and the transcriptional machinery in Caenorhabditis elegans. Aquarius
physically interacts with the germline Argonaute HRDE-1. Aquarius is
required to initiate small-RNA-induced heritable gene silencing. HRDE-1
and Aquarius silence overlapping sets of genes and transposable elements.
Surprisingly, removal of introns from a target gene abolishes the
requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene
silencing. We conclude that Aquarius allows small RNA pathways to compete
for access to nascent transcripts undergoing co-transcriptional splicing
in order to detect and silence transposable elements. Thus, Aquarius and
HRDE-1 act as gatekeepers coordinating gene expression and genome defense.
Delft, Pieter; Akay, Alper; Huber, Sabrina M; Bueschl, Christoph; Rudolph, Konrad L M; Domenico, Tomás Di; Schuhmacher, Rainer; Miska, Eric A; Balasubramanian, Shankar
The Profile and Dynamics of RNA Modifications in Animals Journal Article
In: Chembiochem, vol. 18, no. 11, pp. 979–984, 2017, ISSN: 1439-4227.
Abstract | Links | BibTeX | Tags: Caenorhabditis elegans, isotopic labeling, mass spectrometry, RNA modifications, stress response, tRNA
@article{van_delft_profile_2017,
title = {The Profile and Dynamics of RNA Modifications in Animals},
author = {Pieter Delft and Alper Akay and Sabrina M Huber and Christoph Bueschl and Konrad L M Rudolph and Tomás Di Domenico and Rainer Schuhmacher and Eric A Miska and Shankar Balasubramanian},
url = {http://dx.doi.org/10.1002/cbic.201700093},
doi = {10.1002/cbic.201700093},
issn = {1439-4227},
year = {2017},
date = {2017-06-01},
journal = {Chembiochem},
volume = {18},
number = {11},
pages = {979–984},
abstract = {More than a hundred distinct modified nucleosides have been identified in
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.},
keywords = {Caenorhabditis elegans, isotopic labeling, mass spectrometry, RNA modifications, stress response, tRNA},
pubstate = {published},
tppubtype = {article}
}
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.
2015
Akay, Alper; Sarkies, Peter; Miska, Eric A
E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans Journal Article
In: Sci. Rep., vol. 5, pp. 9597, 2015, ISSN: 2045-2322.
Abstract | Links | BibTeX | Tags:
@article{akay_e_2015,
title = {E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans},
author = {Alper Akay and Peter Sarkies and Eric A Miska},
url = {http://dx.doi.org/10.1038/srep09597},
doi = {10.1038/srep09597},
issn = {2045-2322},
year = {2015},
date = {2015-04-01},
journal = {Sci. Rep.},
volume = {5},
pages = {9597},
abstract = {The discovery of RNA interference (RNAi) in C. elegans has had a major
impact on scientific research, led to the rapid development of RNAi tools
and has inspired RNA-based therapeutics. Astonishingly, nematodes,
planaria and many insects take up double-stranded RNA (dsRNA) from their
environment to elicit RNAi; the biological function of this mechanism is
unclear. Recently, the E. coli OxyS non-coding RNA was shown to regulate
gene expression in C. elegans when E. coli is offered as food. This was
surprising given that C. elegans is unlikely to encounter E. coli in
nature. To directly test the hypothesis that the E. coli OxyS non-coding
RNA triggers the C. elegans RNAi pathway, we sequenced small RNAs from C.
elegans after feeding with bacteria. We clearly demonstrate that the OxyS
non-coding RNA does not trigger an RNAi response in C. elegans. We
conclude that the biology of environmental RNAi remains to be discovered.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
impact on scientific research, led to the rapid development of RNAi tools
and has inspired RNA-based therapeutics. Astonishingly, nematodes,
planaria and many insects take up double-stranded RNA (dsRNA) from their
environment to elicit RNAi; the biological function of this mechanism is
unclear. Recently, the E. coli OxyS non-coding RNA was shown to regulate
gene expression in C. elegans when E. coli is offered as food. This was
surprising given that C. elegans is unlikely to encounter E. coli in
nature. To directly test the hypothesis that the E. coli OxyS non-coding
RNA triggers the C. elegans RNAi pathway, we sequenced small RNAs from C.
elegans after feeding with bacteria. We clearly demonstrate that the OxyS
non-coding RNA does not trigger an RNAi response in C. elegans. We
conclude that the biology of environmental RNAi remains to be discovered.
2013
Akay, Alper; Craig, Ashley; Lehrbach, Nicolas; Larance, Mark; Pourkarimi, Ehsan; Wright, Jane E; Lamond, Angus; Miska, Eric; Gartner, Anton
RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans Journal Article
In: Open Biol., vol. 3, no. 11, pp. 130151, 2013, ISSN: 2046-2441.
Abstract | Links | BibTeX | Tags: Caenorhabditis elegans, gld-1, let-7, miRNA, SILAC
@article{akay_rna-binding_2013,
title = {RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans},
author = {Alper Akay and Ashley Craig and Nicolas Lehrbach and Mark Larance and Ehsan Pourkarimi and Jane E Wright and Angus Lamond and Eric Miska and Anton Gartner},
url = {http://dx.doi.org/10.1098/rsob.130151},
doi = {10.1098/rsob.130151},
issn = {2046-2441},
year = {2013},
date = {2013-11-01},
journal = {Open Biol.},
volume = {3},
number = {11},
pages = {130151},
abstract = {Messenger RNA translation is regulated by RNA-binding proteins and small
non-coding RNAs called microRNAs. Even though we know the majority of
RNA-binding proteins and microRNAs that regulate messenger RNA expression,
evidence of interactions between the two remain elusive. The role of the
RNA-binding protein GLD-1 as a translational repressor is well studied
during Caenorhabditis elegans germline development and maintenance.
Possible functions of GLD-1 during somatic development and the mechanism
of how GLD-1 acts as a translational repressor are not known. Its human
homologue, quaking (QKI), is essential for embryonic development. Here, we
report that the RNA-binding protein GLD-1 in C. elegans affects multiple
microRNA pathways and interacts with proteins required for microRNA
function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1,
two known modulators of miRNA function, genetically interact with GLD-1.
gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7
family mutants during somatic development. We used stable isotope
labelling with amino acids in cell culture to globally analyse the changes
in the proteome conferred by let-7 and gld-1 during animal development. We
identified the histone mRNA-binding protein CDL-1 to be, in part,
responsible for the phenotypes observed in let-7 and gld-1 mutants. The
link between GLD-1 and miRNA-mediated gene regulation is further supported
by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins
implicated in miRNA regulation. Overall, we have uncovered genetic and
biochemical interactions between GLD-1 and miRNA pathways.},
keywords = {Caenorhabditis elegans, gld-1, let-7, miRNA, SILAC},
pubstate = {published},
tppubtype = {article}
}
non-coding RNAs called microRNAs. Even though we know the majority of
RNA-binding proteins and microRNAs that regulate messenger RNA expression,
evidence of interactions between the two remain elusive. The role of the
RNA-binding protein GLD-1 as a translational repressor is well studied
during Caenorhabditis elegans germline development and maintenance.
Possible functions of GLD-1 during somatic development and the mechanism
of how GLD-1 acts as a translational repressor are not known. Its human
homologue, quaking (QKI), is essential for embryonic development. Here, we
report that the RNA-binding protein GLD-1 in C. elegans affects multiple
microRNA pathways and interacts with proteins required for microRNA
function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1,
two known modulators of miRNA function, genetically interact with GLD-1.
gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7
family mutants during somatic development. We used stable isotope
labelling with amino acids in cell culture to globally analyse the changes
in the proteome conferred by let-7 and gld-1 during animal development. We
identified the histone mRNA-binding protein CDL-1 to be, in part,
responsible for the phenotypes observed in let-7 and gld-1 mutants. The
link between GLD-1 and miRNA-mediated gene regulation is further supported
by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins
implicated in miRNA regulation. Overall, we have uncovered genetic and
biochemical interactions between GLD-1 and miRNA pathways.
Gartner, A; Akay, A
Stress response: anything that doesn't kill you makes you stronger Journal Article
In: Curr. Biol., 2013, ISSN: 0960-9822, (Publisher: Elsevier).
Abstract | Links | BibTeX | Tags:
@article{gartner_stress_2013,
title = {Stress response: anything that doesn't kill you makes you stronger},
author = {A Gartner and A Akay},
url = {https://www.sciencedirect.com/science/article/pii/S0960982213011834},
issn = {0960-9822},
year = {2013},
date = {2013-01-01},
journal = {Curr. Biol.},
abstract = {Hormesis occurs when a low-level stress elicits responses that protect
against subsequent exposure to severe stress. Such protection often
affects a variety of stress conditions. For instance, oxidative and
thermal stress can extend lifespan by hormetic mechanisms [1]. By analogy,
surviving continuous …},
note = {Publisher: Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
against subsequent exposure to severe stress. Such protection often
affects a variety of stress conditions. For instance, oxidative and
thermal stress can extend lifespan by hormetic mechanisms [1]. By analogy,
surviving continuous …
2008
Feitsma, Harma; Akay, Alper; Cuppen, Edwin
Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos Journal Article
In: Nucleic Acids Res., vol. 36, no. 12, pp. 4047–4056, 2008, ISSN: 0305-1048.
Abstract | Links | BibTeX | Tags:
@article{feitsma_alkylation_2008,
title = {Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos},
author = {Harma Feitsma and Alper Akay and Edwin Cuppen},
url = {http://dx.doi.org/10.1093/nar/gkn341},
doi = {10.1093/nar/gkn341},
issn = {0305-1048},
year = {2008},
date = {2008-07-01},
journal = {Nucleic Acids Res.},
volume = {36},
number = {12},
pages = {4047–4056},
abstract = {S(N)1-type alkylating agents, like N-methyl-N-nitrosourea (MNU) and
N-ethyl-N-nitrosourea (ENU), are potent mutagens. Exposure to alkylating
agents gives rise to O(6)-alkylguanine, a modified base that is recognized
by DNA mismatch repair (MMR) proteins but is not repairable, resulting in
replication fork stalling and cell death. We used a somatic mutation
detection assay to study the in vivo effects of alkylation damage on
lethality and mutation frequency in developing zebrafish embryos.
Consistent with the damage-sensing role of the MMR system, mutant embryos
lacking the MMR enzyme MSH6 displayed lower lethality than wild-type
embryos after exposure to ENU and MNU. In line with this,
alkylation-induced somatic mutation frequencies were found to be higher in
wild-type embryos than in the msh6 loss-of-function mutants. These
mutations were found to be chromosomal aberrations that may be caused by
chromosomal breaks that arise from stalled replication forks. As these
chromosomal breaks arise at replication, they are not expected to be
repaired by non-homologous end joining. Indeed, Ku70 loss-of-function
mutants were found to be equally sensitive to ENU as wild-type embryos.
Taken together, our results suggest that in vivo alkylation damage results
in chromosomal instability and cell death due to aberrantly processed
MMR-induced stalled replication forks.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
N-ethyl-N-nitrosourea (ENU), are potent mutagens. Exposure to alkylating
agents gives rise to O(6)-alkylguanine, a modified base that is recognized
by DNA mismatch repair (MMR) proteins but is not repairable, resulting in
replication fork stalling and cell death. We used a somatic mutation
detection assay to study the in vivo effects of alkylation damage on
lethality and mutation frequency in developing zebrafish embryos.
Consistent with the damage-sensing role of the MMR system, mutant embryos
lacking the MMR enzyme MSH6 displayed lower lethality than wild-type
embryos after exposure to ENU and MNU. In line with this,
alkylation-induced somatic mutation frequencies were found to be higher in
wild-type embryos than in the msh6 loss-of-function mutants. These
mutations were found to be chromosomal aberrations that may be caused by
chromosomal breaks that arise from stalled replication forks. As these
chromosomal breaks arise at replication, they are not expected to be
repaired by non-homologous end joining. Indeed, Ku70 loss-of-function
mutants were found to be equally sensitive to ENU as wild-type embryos.
Taken together, our results suggest that in vivo alkylation damage results
in chromosomal instability and cell death due to aberrantly processed
MMR-induced stalled replication forks.