The role of Nuclear phosphoinositides in epigenetic signalling
Lead Research Organisation:
University of Southampton
Department Name: Sch of Biological Sciences
Abstract
If genetics is represented by a book containing the sequence of DNA encoding humans then epigenetics can be considered as the notes written in the margins by a previous reader. They do not alter the code itself but remind and instruct the next reader how they might interpret the written code. Epigenetics provides the means for environmental signals, such as how much food has been eaten or how warm it is, to be written on top of the genetic code to help instruct how cells and organisms might respond. Like the DNA code the notes can also be inherited. In essence epigenetics provides a rational model for the nature versus nurture hypothesis.
DNA is complexed with proteins to form a structure called chromatin that enables the large amount of DNA to be packed into the very small volume of the cell. Problematically this packing prevents the DNA from being used easily. The epigenetic notes which are deposited on to the components of chromatin help to pack and un-pack the chromatin. The notes are deposited, removed and interpreted by a series of enzyme complexes. Exactly how these complexes are regulated in response to environmental signals is not very well understood.
We have found that one of these enzyme complexes is regulated by an enzyme called PIP5K1A. In response to environmental signals PIP5K1A produces a small molecule called PIP2. Our studies suggest that PIP2 sticks to the enzyme complex and controls how well it works. This leads to changes in the epigenetic notes that are deposited and eventually to how the cell behaves. In this way we think that PIP2 acts a messenger informing and controlling the enzyme complex in response to changes in the environment.
In this proposal we intend to understand how PIP2 sticks to and changes how well the enzyme complex works. The enzyme complex is made up of many different protein components and we have found that one of these proteins can stick to PIP2. By using different molecular technologies we want to find out exactly how PIP2 sticks to this protein and if this alters how well the enzyme complex deposits the epigenetic notes. Understanding the molecular details of this process is important as it increases our basic understanding of how cells respond to their environment. Furthermore the enzyme complexes that deposit epigenetic notes often do not work properly which can change how organisms age. It can also lead to the development of different human diseases such as cancer and diabetes. Understanding how the enzyme complexes are controlled will help us to design medicines that alter how well these complexes work which could be useful in modulating how well we age and how we combat diseases.
DNA is complexed with proteins to form a structure called chromatin that enables the large amount of DNA to be packed into the very small volume of the cell. Problematically this packing prevents the DNA from being used easily. The epigenetic notes which are deposited on to the components of chromatin help to pack and un-pack the chromatin. The notes are deposited, removed and interpreted by a series of enzyme complexes. Exactly how these complexes are regulated in response to environmental signals is not very well understood.
We have found that one of these enzyme complexes is regulated by an enzyme called PIP5K1A. In response to environmental signals PIP5K1A produces a small molecule called PIP2. Our studies suggest that PIP2 sticks to the enzyme complex and controls how well it works. This leads to changes in the epigenetic notes that are deposited and eventually to how the cell behaves. In this way we think that PIP2 acts a messenger informing and controlling the enzyme complex in response to changes in the environment.
In this proposal we intend to understand how PIP2 sticks to and changes how well the enzyme complex works. The enzyme complex is made up of many different protein components and we have found that one of these proteins can stick to PIP2. By using different molecular technologies we want to find out exactly how PIP2 sticks to this protein and if this alters how well the enzyme complex deposits the epigenetic notes. Understanding the molecular details of this process is important as it increases our basic understanding of how cells respond to their environment. Furthermore the enzyme complexes that deposit epigenetic notes often do not work properly which can change how organisms age. It can also lead to the development of different human diseases such as cancer and diabetes. Understanding how the enzyme complexes are controlled will help us to design medicines that alter how well these complexes work which could be useful in modulating how well we age and how we combat diseases.
Technical Summary
DNA and histones are packaged into chromatin. Epigenetic signaling enzymes that modify chromatin alter the packaging and consequently transcriptional output. For example histoneH3 lysine 4 (H3K4) tri-methylation is associated with enhanced transcription. H3K4 methylation is controlled by six different methylation complexes (MLL-SET) and impacts on differentiation, development, aging and transgenerational epigenetic memory. While much is known about H3K4 signalling and its relationship to transcription much less is known about how MLL-SET complexes are regulated.
Nuclear Phosphoinositides (PI), such as Phosphatidylinositol(4,5)bisphosphate (PIP2), are lipid messengers that change during cell cycle progression, differentiation and adaptive stress responses. Nuclear PI operate by interacting with and regulating proteins often involved in chromatin regulation.
We have identified a direct functional interaction between PIP5K1A, which synthesises PIP2, and an essential core component of all MLL-SET complexes. We suggest that nuclear PIP2 regulates H3K4 methylation by interacting with this core component. We will use an array of molecular and structural technologies to identify: A. components that constitute the nuclear PIP2/H3K4 methylation pathway; B. how PIP5K1A and PIP2 interact with the MLL-SET core component and C. how these interactions might regulate MLL-SET activity in vitro and in cells. Next generation sequencing will investigate how nuclear PIP2 influences global transcriptional output and H3K4 methylation. Finally, we will develop novel technologies to investigate how different sub-nuclear pools of PIP2 impact on H3K4 methylation and transcription.
Epigenetics will provide novel targets to impact on healthy ageing and diseases. Defining how small molecule such as PIP2 might allosterically regulate MLL-SET activity will likely provide highly selective, less toxic approaches to intervene in H3K4 methylation signalling.
Nuclear Phosphoinositides (PI), such as Phosphatidylinositol(4,5)bisphosphate (PIP2), are lipid messengers that change during cell cycle progression, differentiation and adaptive stress responses. Nuclear PI operate by interacting with and regulating proteins often involved in chromatin regulation.
We have identified a direct functional interaction between PIP5K1A, which synthesises PIP2, and an essential core component of all MLL-SET complexes. We suggest that nuclear PIP2 regulates H3K4 methylation by interacting with this core component. We will use an array of molecular and structural technologies to identify: A. components that constitute the nuclear PIP2/H3K4 methylation pathway; B. how PIP5K1A and PIP2 interact with the MLL-SET core component and C. how these interactions might regulate MLL-SET activity in vitro and in cells. Next generation sequencing will investigate how nuclear PIP2 influences global transcriptional output and H3K4 methylation. Finally, we will develop novel technologies to investigate how different sub-nuclear pools of PIP2 impact on H3K4 methylation and transcription.
Epigenetics will provide novel targets to impact on healthy ageing and diseases. Defining how small molecule such as PIP2 might allosterically regulate MLL-SET activity will likely provide highly selective, less toxic approaches to intervene in H3K4 methylation signalling.
Planned Impact
People. This project has the potential to impact directly on the general public through impacting on health. PI and epigenetic signalling are implicated in cancer, muscular degeneration and in mental health and inflammatory diseases. Our studies bring these two pathways together and in doing so reveal novel target sites for the potential development of therapies that could be used to combat these diseases. Furthermore recent studies in model organisms show that PI and epigenetic signalling impact on the ageing process and on health span, potentially placing our studies of value in this area. The western world has an increasing aged population above 65 and both medicinal and non-medicinal interventions will be essential to maximise the health span of the population. Therefore the outputs from this research and their further commercial developments have potentially enormous impact on public health, although the realistic timescales to such therapeutic use are in the order of tens of years.
The increased knowledge gained from this proposal and its impact on human health and ageing are topics frequently highlighted in the news and are of direct interest to the public. Engaging the public in discussions of the wider issues encompassing our research increases knowledge and fosters an information based society which indirectly impacts on the ability of research councils and universities to lobby government on research funding policies.
Industrial beneficiaries. The research outputs outlined in this proposal could impact on industrial beneficiaries such as small and larger scale pharmaceutical companies. Development of therapies aimed at components of PI and epigenetic signalling pathways are already being developed illustrating their known potential in human health. Our studies will define exactly how a small regulatory molecule, PIP2, interacts with and controls an epigenetic signalling complex providing novel target sites for commercially exploitation. Industrial partnerships could be instigated within two years. These partnerships will likely be aimed at developing proof of principle cellular and animal models. Within the time frame of the grant we would hope to strengthen and generate productive industrial partnership interactions.
Economy. If target molecules can be realised then the potential to the overall economy is large. Revenue from the technology and its exploitation together with increased societal health will impact on the economy of the nation. The second potential for impact into the economy is through training and teaching. The research participants within this project will be trained in sophisticated biological and non-biological areas thereby enabling their contribution to both the academic and professional science base as well as non-academic environments. This research will also provide research placements and lecture material for undergraduate students, thereby contributing to the development of an educated workforce.
The increased knowledge gained from this proposal and its impact on human health and ageing are topics frequently highlighted in the news and are of direct interest to the public. Engaging the public in discussions of the wider issues encompassing our research increases knowledge and fosters an information based society which indirectly impacts on the ability of research councils and universities to lobby government on research funding policies.
Industrial beneficiaries. The research outputs outlined in this proposal could impact on industrial beneficiaries such as small and larger scale pharmaceutical companies. Development of therapies aimed at components of PI and epigenetic signalling pathways are already being developed illustrating their known potential in human health. Our studies will define exactly how a small regulatory molecule, PIP2, interacts with and controls an epigenetic signalling complex providing novel target sites for commercially exploitation. Industrial partnerships could be instigated within two years. These partnerships will likely be aimed at developing proof of principle cellular and animal models. Within the time frame of the grant we would hope to strengthen and generate productive industrial partnership interactions.
Economy. If target molecules can be realised then the potential to the overall economy is large. Revenue from the technology and its exploitation together with increased societal health will impact on the economy of the nation. The second potential for impact into the economy is through training and teaching. The research participants within this project will be trained in sophisticated biological and non-biological areas thereby enabling their contribution to both the academic and professional science base as well as non-academic environments. This research will also provide research placements and lecture material for undergraduate students, thereby contributing to the development of an educated workforce.
People |
ORCID iD |
Nullin Divecha (Principal Investigator) |
Publications
Andrews DM
(2022)
Identification and optimization of a novel series of selective PIP5K inhibitors.
in Bioorganic & medicinal chemistry
Bowler EH
(2019)
Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine.
in Journal of proteome research
Devitt G
(2024)
Mechanisms of SARS-CoV-2 Inactivation Using UVC Laser Radiation.
in ACS photonics
Divecha N
(2016)
Phosphoinositides in the nucleus and myogenic differentiation: how a nuclear turtle with a PHD builds muscle.
in Biochemical Society transactions
Fiume R
(2016)
PIP4K2B: Coupling GTP Sensing to PtdIns5P Levels to Regulate Tumorigenesis.
in Trends in biochemical sciences
Fiume R
(2019)
Nuclear Phosphoinositides: Their Regulation and Roles in Nuclear Functions.
in International journal of molecular sciences
Lundquist MR
(2018)
Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy.
in Molecular cell
Poli A
(2023)
PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1.
in Nature communications
Poli A
(2019)
Phosphatidylinositol 5 Phosphate (PI5P): From Behind the Scenes to the Front (Nuclear) Stage.
in International journal of molecular sciences
Description | we have discovered where nuclear PIP2 is localised and that this pool of nuclear PIP2 is controlled by a nuclear PIP5K1A. surprisingly we have also shown nuclear PIP2 appears to be essential for cells to survive. In the context of a knockout of PIP5k1A , the nuclear Pool of PIP2 strongly decreases but within a number of days, the pool of PIP2 is reconstituted. How this occurs is not clear but suggests a highly dynamic mechanism employed in the nucleus to maintain its effects on transcriptional output. we have also developed a number of novel cell lines in which we have targeted lipid phosphatase domains to the nucleus in order to monitor if they can be used ot modulate the levels of nuclear PIP2 and thereby generate a technology to control PIP2 at will. Furthermore using CRISPR cas9 we have developed PIP5K1A knock out lines and have targeted luciferase to the last exon of a PIP2 dependent gene. this latter cell lines enables us to easily monitor effects of changing PIP2 on transcriptional output both in vivo and in vitro. we have now discovered how PI interact with ASH2l and have novel data showing that the interaction of PIP2 with ASh2L is important for regulating output signalling by ASh2L and the h3k4methylase complex. our studies also suggest that targeting the interaction domain could be useful as a target to prevent cancer cell growth using the data obtained of how ASH2L is regulated by PIP2 we have generated cell lines that are depleted of their endogenous expression and reconstituted them with wild type or mutant ASH2L unable to interact with PIP2. these cells expressing the mutant ASH2L appear to be compromised in terms of cell growth, histone methylation and gene expression . moreover with our collaborators we have assessed how these mutants impact on the activity of the methylation complex in vitro. |
Exploitation Route | our studies suggest that a number of components that constitute this nuclear transcriptional signalling unit might be useful as targets for a number of different signaling inputs as well as being a target for cancer therapeutic development. furthermore we believe our cell lines will be useful to the research community and that there could be possibilities to develop the luciferase cell line as a bioassay for TNF signalling. we are interested in targeting the pI interaction site to develop novel allosteric regulators of H3K4me 3 signalling |
Sectors | Creative Economy Healthcare Pharmaceuticals and Medical Biotechnology |
Description | Crispr Cas 9 genetic editing for researchers |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | educating research students at the beginning of their studies on how to develop and utilise CRISPR gene editing has induced capacity to perform complex experiments that enhance the reach of their science to the wider community. |
Description | IFLS cell biology joint theme lead |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | increased awareness of cell biology and instigated cross disciplinary collaborations |
Description | biochemistry and cell biology journal club |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | increased education of research students with respect to technological breakthroughs. increased their awareness of the wider impacts of research outside of their individual field. this will have direct impacts on economics of the country as it increases the research capacity and awareness of potential researchers that enter into the economic field |
Description | theme lead for molecular bioscience |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Membership of a guideline committee |
Impact | the molecular bioscience group constitutes 12 group leaders that span biological research ranging from structural biology to nuclear genome organisation. as theme lead i sit on a number of committees including the research and strategy board which dictates the environment of research within the institute and thus impacts on how we work, the facilities that we build capacity and how resources are utilised. |
Description | understanding the remit of BBSRC funding at the university of Southampton |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | novel review process have been inplemented and guidance to the BBSRC has been sent |
Description | 'How Is PtdIns(4,5)P2, A Membrane Lipid Messenger, Localised And Regulated In Splicing Speckles, A Membrane Less Compartment Within The Nucleus? |
Amount | £1,100,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2024 |
End | 01/2028 |
Description | Investigating the role of nuclear phosphoinositides in DNA damage responses |
Amount | £60,000 (GBP) |
Organisation | Rajiv Gandhi Charitable Trust |
Sector | Charity/Non Profit |
Country | India |
Start | 01/2023 |
End | 01/2026 |
Description | The role of nuclear PPIns in the control of LADS |
Amount | £80,000 (GBP) |
Funding ID | Mayflower Studentship |
Organisation | University of Southampton |
Sector | Academic/University |
Country | United Kingdom |
Start | 08/2023 |
End | 09/2028 |
Description | The role of nuclear PPIns in the control of LADS |
Amount | £25,000 (GBP) |
Organisation | The Gerald Kerkut Charitable Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 12/2022 |
End | 05/2023 |
Description | biological sciences studentship |
Amount | £70,000 (GBP) |
Organisation | University of Southampton |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2019 |
End | 09/2022 |
Description | invstigating a role for nuclear PPIns in muscle cell differentiation |
Amount | £100,000 (GBP) |
Organisation | University of Southampton |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2024 |
End | 01/2028 |
Title | ASH2l mutatnt cell lines |
Description | we have characterised how ASh2L interacts with phosphoinositides and made mutants that non longer interact with it. we have generated cell lines in which these mutants replace the endogenous ASH2L enabling us to assess their role in regulating transcriptional histone methylation and transcriptional output. |
Type Of Material | Cell line |
Year Produced | 2020 |
Provided To Others? | No |
Impact | we have carried out RNA seq and esablished how interacton with PI modulate transcription |
Title | ASHL wild type and PI interaction mutant reconstitution cell lines |
Description | we have determined how ASH2l interacts with phosphoinositides and therefore to assess how PI interaction modulates ASH2L outcomes we have developed a cell line that expresses wild type or mutant ASH2l. the endogenous protein can be removed using allele specific RNAI constructs. |
Type Of Material | Model of mechanisms or symptoms - in vitro |
Year Produced | 2019 |
Provided To Others? | No |
Impact | we have used this to demonstrate the importance of the PI interaction site on ASH2l in controlling various epigenetic signalling outputs as well as tumour cell growth |
Title | C2C12 expressing TIR1 (for inducible degradation of degron tagged alleles) |
Description | in order to degrade AID tagged proteins, a cell lines needs to express the TIR1 protein. TIR1 is auxin sensitive and targets the AID tagged proteins for degradation. we have generated a C2C12 cell line that expresses a doxycyclin inducible TIR1 construct. |
Type Of Material | Cell line |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | this has enabled us to control the expression of PIP4k2B rapidly and reversibly in order to study downstream effects such as differentiation, cell cycle progression and myoblast fusion. in addition we expect that there will be interest in this cell line from the scientific community. has been used to tag PIP4k2B PIp4k2A in human cells |
Title | CRISPR knockout constructs for PPIns modulating enzymes |
Description | We have generated and validated a panel of tools that can be used to knockdown/out proteins involved in regulating PPIns metabolism |
Type Of Material | Technology assay or reagent |
Year Produced | 2021 |
Provided To Others? | No |
Impact | we have knocked out numerous PPIns modulating enzymes and assesed how they impact on cell behaviour, nuclear PPIns regulation and have used them to validate commerically available antibody characteristics |
Title | CRISPR-KNockout U2OS cells |
Description | using the tools described we have developed knockout cells lines for various PPINs modulating enzymes. these lines will be made available to the reserach community through publicaiton |
Type Of Material | Cell line |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | we have used these cells to assess how their knockout impacts on various cell biological outputs including mitophagy, cell proliferation, nuclear PPIns and gene transcription |
Title | CRISPR_knockout of PIP5K1A in U2OS cells |
Description | using CRISPR-CAS9 we have generated a number of PIP5K1A knock out cell lines. |
Type Of Material | Cell line |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | these are being used to assess how PIP5K1A modulates gene expression and epigenetic signalling. they will also be used to enhance our collaboration with Babraham institute to assess nuclear PIP2 levels |
Title | Purified protein domain of SRSF2 |
Description | we have produced this domain in bacteria and purified it in order to assess its ability to interact with PPIns |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | we have shown that this domain interacts with PPIns and are now characterising how it influences nuclear PPins |
Title | U2OS cell line with ASH2 tagged with GFP |
Description | CRISPR cas9 used to generate a GFP tagged ASh2l which will be used for chip-seq, analysis of interaction partners and for live cell imaging |
Type Of Material | Cell line |
Year Produced | 2019 |
Provided To Others? | No |
Impact | used chip interaction partner analysis |
Title | U2OS cells line with knockin flag tag into the endogenous ASH2 loci |
Description | we have used CRISPR CAS9 to generate a cell line in which ASH2L has been tagged with the FLAG epitope. |
Type Of Material | Cell line |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | the antibodies to ASH2l are not sufficiently good enough to be used for CHIP-seq studies. we have developed this line in order to establish a tool for this technique. this should be useful to the epigenetic community |
Title | lentiviral knockout lines |
Description | utilisation of lentiviral mediated disruption of genes |
Type Of Material | Cell line |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | the lentiviral knockout system that we implemented has been widely used within the research community at biological Sciences. many of these researchers are funded by UKRI and as such the implementation of this technology has or will impact on their research outputs. Additionally we use this technology to teach out undergraduates about CRISPR gene editing and there fore increase their capacity and knowledge for their access into research and into the pharmaceutical industry. |
Title | manipulating nuclear phosphoinositides |
Description | We have generated a panel of U2OS cells lines that express various nuclear targeted PIP2 phosphatases. these are all Ha tagged and will be used to assess how they might manipulate nuclear PIP2 |
Type Of Material | Cell line |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | these are being used by two other projects within the lab. we will also advertise these on our web site. |
Title | monitoring PIP2 dependent modulation of the transcription of the BIRC3 gene |
Description | in order to easily monitor in vivo and in vitro the effect of PIP2 on transcription we have used CRISP -CAS9 to knockin a luciferase gene into the last exon of BIRC3 . The luciferase is expressed downstream of BIRC3, under the control of P2A self cleavage site, and is a direct measure of BIRC3 transcription. |
Type Of Material | Cell line |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | we have shown that the transcription of this gene is strongly regulated by TNFa in both a PIP2 and histone methylation dependent manner. The stimulation by TNF suggests that is is a highly sensitive assay that could also be used to generate a bioassay for TNFa have used this line to assess how PIP5K and ash2l depletion modulates luciferase activity. is being used as a screen to test for PI and H3K4me3 modulators in the control of Birc3 |
Title | selection plasmids in order to generate knockin alleles tagged with the auxin inducible degron (AID) domain |
Description | In order to carry out rapid and reversible degradation of a protein we have utilised the AID tagging system. In order to use this in the most rigourous manner tagging the endogenous allele in cells is a requisite. the simplest way to do this is to utilise CRISPR CAS9. however the efficiency of tagging is still low especially as both alleles need to be tagged. we have generated a set of plasmids that allow selection of tagging using seven different types of selection markers. Some of these are based on antibiotic selection and others are based on their use with fluorescence cell sorting (FACS) in addition we have incorporated |
Type Of Material | Biological samples |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | this tool has now been used to generate AID Knockin alleles for two separate projects within the department (update 2018) and has been used by others in our department to knockin AID into various endogenous loci |
Title | tools to deplete nuclear phosphoinostides |
Description | we have generated genetically encoded lipid phosphatases that are targeted to the nucleus. the phosphatase domains from 10 different lipid phosphatases known to regulate PIP2 have been cloned in to inducible vectors that target the protein domain to the nucleus. |
Type Of Material | Biological samples |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | these tools are being utilised to assess the role of nuclear PIP2 in nuclear functions. |
Title | Genes regulated by PIP4K2B/2C in T regulatory cells |
Description | PIP4K2B/2C were depleted in Human T regulatory cells and Gene transcriptional changes were assess using RNA seq. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | this dataset has established that PIP4K are relevant targets with which to influence T regulatory cell activity |
URL | https://www.pnas.org/doi/10.1073/pnas.2010053118?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr... |
Title | genes regualate by the interacton of ASH2L with PI |
Description | the data set is derived from RNA seq of cell lines in which the endogenous ASH2L has been deleted and the cells have been reconstituted with wild type ASH2L or mutant ASh2L unable to interact with PI |
Type Of Material | Data handling & control |
Year Produced | 2020 |
Provided To Others? | No |
Impact | we have shown that if ASh2L cannot interact with PI this leads to a selective loss of gene transcriptional outputs |
Title | genes regulated by changes in PIP5K1A |
Description | gene expression array data set after knocking down PIP5K1A |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | No |
Impact | we have been able to define a set of genes that are regulated by changes in PIP5K1A |
Title | impact of PIP5K1A modulation on H3K4me3 |
Description | data set to understand how PIP5K1A modulates histone methylation and its relationship to ASH2L |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | No |
Impact | defining mechanistically how nuclear PIP2 impacts on gene expression. data has been curated and used to show that PIP5K modulates H3K4me3 signalling similarly to ASH2L |
Description | PIP4K2B as a mechanosensor |
Organisation | AIRC Foundation for Cancer Research in Italy |
Department | FIRC Institute of Molecular Oncology Foundation |
Country | Italy |
Sector | Academic/University |
PI Contribution | we generated knockout cells lines, contributed to the role of PIP4K2B in cancer cells as a mechanosensor and provided advice, reagents and project input |
Collaborator Contribution | carried out experiments to investigate the role of PIP4K2B in regulating YAP signalling. |
Impact | PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1 DOI: 10.1038/s41467-023-37064-0 PMID: 36918565 |
Start Year | 2022 |
Description | interaction of PPIns with nuclear proteins |
Organisation | University of Southampton |
Department | Faculty of Natural and Environmental Sciences |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | provided purified proteins |
Collaborator Contribution | carried out NMR studies to assess the interaction of lipids with these purified protein domains |
Impact | none yet. this is a multidisciplinary approach |
Start Year | 2021 |
Description | measuring nuclear PIP2 in response to depletion of kinases, phosphatases and phospholipases |
Organisation | Babraham Institute |
Department | Signalling |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | we are knocking down various enzymes that are known to regulate PIP2 levels and isolating nuclei to bu used to measure the levels of nuclear PIP2 |
Collaborator Contribution | They are measuring the levels of nuclear PIP2 using mass spectroscopy |
Impact | multi disciplinary : encompassing genetic modulation of enzyme components with the use of mass spectroscopy. |
Start Year | 2018 |
Description | measuring the impact of PIP2 depletion on histone modifications |
Organisation | University of Southampton |
Department | Centre for Biological Sciences |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | we are generating PIP5K1A knockdown and CRISP cas 9 knockout cells and are measuring the extent of PIP2 depletion. we have already shown that this leads to a decrease in nuclear PIP2 levels and in decrease in the extent of H3K3Me3 at specific loci. |
Collaborator Contribution | They are using Mass spectrometry to determine the extent of other histone modifications that might also act directly downstream of changes in nuclear PIP2 |
Impact | this is a multidisciplinary collaboration encompassing genetic modulation of components of a nuclear phosphoinositide pathway with quantitative mass spectrometry to determine changes in histone modification. |
Start Year | 2018 |
Description | the role of PIP2 in regulating histone methylation complexes |
Organisation | State University of New York |
Country | United States |
Sector | Academic/University |
PI Contribution | We are identifying how PIP2 interacts with components of the histone methylation complex in order to identify mutants that may no longer interact. |
Collaborator Contribution | they are measuring how PIP2 might impact on the in vitro activity of the methylation complex. they have purified and reconstituted a core methylation complex composed of ASH2l, wdr5, wd-40 and a methylation subunit such as the set domain from MLL1. |
Impact | outcomes 1. we have asessed how mutants of ASH2l that cannot interact with PIP2 impact on the in vitro methylation activity of histone methylation complex. 2. we have assessed how PIP2 impacts on the methylation complex this crosses 1. protein production in bacteria. 2. reconstitution of biological complex activities 3. understanding the role of these complexes in vivo |
Start Year | 2018 |
Description | Cell biology theme lead increasing awareness and generating new collaborative interactions within the cell biology sector of the university of southampton |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | the intention is to describe and increase awareness of cell biological applications and concepts around the university of Southampton and in the broader sphere of the SOCO_bio phd DTP (BBSRC) |
Year(s) Of Engagement Activity | 2021,2022,2023 |
Description | developement of CRISPR CAS9 techonology for education |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | we developed a CRISPR CAS9 project in order to illustrate the potential of the ues of this technology to students . in essence 18 students were associated with six different research groups and carried out CRISPR to develop novel models of knockouts and knockins for primary research activity. these models have been taken further by researchers within the department and likely will form a basis for novel grant proposals. the project was developed primarily to enable undergraduate students to experience the excitement of primary research |
Year(s) Of Engagement Activity | 2018,2019 |
Description | hosting summer students within the laboratory |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | six week placement for two summer students to experience primary research activity. of the two participants (Steven John and Lakshay Nayyar) steven has now taken up a Ph.D studentship within the department. |
Year(s) Of Engagement Activity | 2017,2018,2019 |
Description | university open day |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | to increase awareness of school students and parents of the educational and research objectives of the centre for biological sciences |
Year(s) Of Engagement Activity | 2017,2018,2019,2020 |