Composition of a regulatory locus and the impact on phenotype and disease
Lead Research Organisation:
University of Edinburgh
Department Name: UNLISTED
Abstract
It was assumed that most mutations/variations that cause human diseases would be due to changes in the coding regions of genes affecting the structure of proteins. This view has changed dramatically over recent years and it is now clear that the majority of mutations related to disease predisposition and even variability within the human population occur outside genes. The assumption is that these differences reside in regions of the DNA (known as regulatory domains or enhancers) that control protein production in the cell. Our research focusses on how changes in these regulatory domains can lead to congenital abnormalities. Although development of the human foetus is highly reliable, in approximately 1 in 100 cases deformities occur. Some of the most frequent abnormalities that occur affect the skeleton of the arms and legs and structure of the head and face. We have identified mutations in regulatory domains responsible for a spectrum of deformities in these features of the newborn, by using mammalian model systems such as the mouse and our goals are to investigate the mechanism by which this class of mutations causes congenital defects.
Technical Summary
Genome wide association studies (GWAS) highlight SNPs (single nucleotide polymorphisms) in noncoding DNA associated with disease traits for complex or common diseases. Undoubtedly, cis-regulatory mutations cause multiple human congenital defects which show a direct association of regulatory mutations with effects on gene expression. Enhancer adoption and recently, ectopic enhancer activity were shown to occur in patients with chromosomal deletions or duplications that remove TAD boundaries. Hence, examination of the mechanisms by which regulatory mutations perturb gene expression is fundamental to understanding the basis of congenital defects.
We showed that disrupted gene regulation of the signalling molecule SHH is responsible for skeletal abnormalities and others have shown involvement in brain and craniofacial defects. Mutations in the Shh limb-specific cis-regulator, the ZRS, cause appendicular skeletal defects which has subsequently, led to the categorization of a broad spectrum of defects into the ‘ZRS associated syndromes’. Our studies range from defining causative mutations to attempting to identify regulatory processes involved in disease, focusing on causative mechanisms and investigating general principles that underlie long range gene activation. We showed that dominant regulatory mutations result from both gain and loss of transcription factor binding capacity. One series of point mutations in human hijacks the normal regulatory machinery involved in setting the Shh expression boundary to generate ectopic expression and skeletal defects.
In addition we are investigating the role that chromatin organization plays in supporting enhancer activity and controlling gene expression. In general, we are investigation the overall architectural components required for cis-regulators to operate over large genomic distances. Known chromatin organizers such as CTCF binding sites are being surveyed to understand their direct role on gene expression and their contribution to the phenotype of the developing mouse. Systematic removal of CTCF sites in the large Shh regulatory domain results in change in 3D chromatin organization and one site underlies the appearance of the holoprosencephaly (craniofacial and brain defects) spectrum in mouse. We are presently developing imaging techniques to map chromatin changes that occur during developmental gene activation and to observe the dynamics in live cells. Our pursuit of long-range regulatory mechanisms are important in understanding developmental gene activation, and the contribution of non-coding mutations to congenital abnormalities.
We showed that disrupted gene regulation of the signalling molecule SHH is responsible for skeletal abnormalities and others have shown involvement in brain and craniofacial defects. Mutations in the Shh limb-specific cis-regulator, the ZRS, cause appendicular skeletal defects which has subsequently, led to the categorization of a broad spectrum of defects into the ‘ZRS associated syndromes’. Our studies range from defining causative mutations to attempting to identify regulatory processes involved in disease, focusing on causative mechanisms and investigating general principles that underlie long range gene activation. We showed that dominant regulatory mutations result from both gain and loss of transcription factor binding capacity. One series of point mutations in human hijacks the normal regulatory machinery involved in setting the Shh expression boundary to generate ectopic expression and skeletal defects.
In addition we are investigating the role that chromatin organization plays in supporting enhancer activity and controlling gene expression. In general, we are investigation the overall architectural components required for cis-regulators to operate over large genomic distances. Known chromatin organizers such as CTCF binding sites are being surveyed to understand their direct role on gene expression and their contribution to the phenotype of the developing mouse. Systematic removal of CTCF sites in the large Shh regulatory domain results in change in 3D chromatin organization and one site underlies the appearance of the holoprosencephaly (craniofacial and brain defects) spectrum in mouse. We are presently developing imaging techniques to map chromatin changes that occur during developmental gene activation and to observe the dynamics in live cells. Our pursuit of long-range regulatory mechanisms are important in understanding developmental gene activation, and the contribution of non-coding mutations to congenital abnormalities.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Cancer Research UK (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- University of California, San Francisco (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- University of Cape Town (Collaboration)
People |
ORCID iD |
Robert Hill (Principal Investigator) |
Publications
Dorà NJ
(2018)
A conditional Pax6 depletion study with no morphological effect on the adult mouse corneal epithelium.
in BMC research notes
Crane-Smith Z
(2021)
A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development.
in Frontiers in cell and developmental biology
Kane L
(2022)
Cohesin is required for long-range enhancer action at the Shh locus.
in Nature structural & molecular biology
West JD
(2018)
Computer simulation of neutral drift among limbal epithelial stem cells of mosaic mice.
in Stem cell research
Ushiki A
(2021)
Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
in Nature communications
Williamson I
(2019)
Developmentally regulated Shh expression is robust to TAD perturbations.
in Development (Cambridge, England)
Oh JDH
(2024)
Insights into digit evolution from a fate map study of the forearm using Chameleon, a new transgenic chicken line.
in Development (Cambridge, England)
Mellis D
(2021)
Ubiquitin-protein ligase Ubr5 cooperates with hedgehog signalling to promote skeletal tissue homeostasis.
in PLoS genetics
Related Projects
Project Reference | Relationship | Related To | Start | End | Award Value |
---|---|---|---|---|---|
MC_UU_00007/1 | 31/03/2018 | 30/03/2023 | £662,000 | ||
MC_UU_00007/2 | Transfer | MC_UU_00007/1 | 31/03/2018 | 30/03/2023 | £3,730,000 |
MC_UU_00007/3 | Transfer | MC_UU_00007/2 | 31/03/2018 | 30/05/2022 | £3,053,000 |
MC_UU_00007/4 | Transfer | MC_UU_00007/3 | 31/03/2018 | 30/03/2023 | £1,772,000 |
MC_UU_00007/5 | Transfer | MC_UU_00007/4 | 31/03/2018 | 30/03/2023 | £4,524,000 |
MC_UU_00007/6 | Transfer | MC_UU_00007/5 | 31/03/2018 | 30/03/2023 | £2,878,000 |
MC_UU_00007/7 | Transfer | MC_UU_00007/6 | 31/03/2018 | 30/03/2023 | £2,829,000 |
MC_UU_00007/8 | Transfer | MC_UU_00007/7 | 31/03/2018 | 31/12/2022 | £4,072,000 |
MC_UU_00007/9 | Transfer | MC_UU_00007/8 | 31/03/2018 | 30/03/2023 | £3,137,000 |
MC_UU_00007/10 | Transfer | MC_UU_00007/9 | 31/03/2018 | 30/03/2023 | £6,948,000 |
MC_UU_00007/11 | Transfer | MC_UU_00007/10 | 31/03/2018 | 30/03/2023 | £2,421,000 |
MC_UU_00007/12 | Transfer | MC_UU_00007/11 | 31/03/2018 | 30/03/2023 | £1,205,000 |
MC_UU_00007/13 | Transfer | MC_UU_00007/12 | 31/03/2018 | 30/03/2023 | £1,174,000 |
MC_UU_00007/14 | Transfer | MC_UU_00007/13 | 31/03/2018 | 30/03/2023 | £1,838,000 |
MC_UU_00007/15 | Transfer | MC_UU_00007/14 | 31/03/2018 | 30/03/2023 | £2,551,000 |
MC_UU_00007/16 | Transfer | MC_UU_00007/15 | 31/03/2018 | 30/03/2023 | £1,496,000 |
MC_UU_00007/17 | Transfer | MC_UU_00007/16 | 31/03/2018 | 30/03/2023 | £1,886,000 |
Description | Masters Programme |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | Developed Masters by research programme for Edinburgh University |
Title | Mice with chromosome 5 engineered |
Description | Serial deletions of large region of Chromosome 5 that include the Shh locus |
Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
Provided To Others? | No |
Impact | Gain insight into developmental regulation of brain, limb and gut |
Title | Model for studying the human condition holoprosencephaly |
Description | A regulatory mutations that lowers the expression of the sonic hedgehog |
Type Of Material | Model of mechanisms or symptoms - human |
Year Produced | 2017 |
Provided To Others? | No |
Impact | These findings will be published in the upcoming year |
Title | Skeletal Changes |
Description | Modification of skeletal development by creating a series of mutations using the CRISPR/Cas genome engineering system |
Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
Provided To Others? | No |
Impact | Manuscript being prepared |
Title | limb cell lines |
Description | A cohort of immortalised cell lines from developing limb tissues. New lines now contain a fluorescent marker for Shh expression for genetic screens |
Type Of Material | Cell line |
Year Produced | 2010 |
Provided To Others? | Yes |
Impact | These lines have provided deeper insights into limb development and Shh signaling. |
Title | osteoarthritis model |
Description | A mouse mutations that results in osteoarthritis that shows a novel pathway responsible for joint inflammation and deformation. Also shows a number of symptoms related to osteochondromas. |
Type Of Material | Model of mechanisms or symptoms - human |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | A better understanding of the molecular mechanism responsible for osteoarthritis |
Description | Acardi-Goutieres Syndrome |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Provided specialised methodology and intellectual input |
Collaborator Contribution | Has provided mutation data and phenotypic analyses |
Impact | Generated a mouse model for Aicardi-Goutieres Syndrome |
Start Year | 2007 |
Description | Congenital disease and genome conformation |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Contribution to a body of work to unravel a disease mechanism |
Collaborator Contribution | Contribution to work and provided patient samples |
Impact | Publications |
Start Year | 2020 |
Description | Congenital disease and genome conformation |
Organisation | University of California, San Francisco |
Department | Department of Bioengineering and Therapeutic Sciences |
Country | United States |
Sector | Academic/University |
PI Contribution | Contribution to a body of work to unravel a disease mechanism |
Collaborator Contribution | Contribution to work and provided patient samples |
Impact | Publications |
Start Year | 2020 |
Description | Corneal development |
Organisation | University of Edinburgh |
Department | Centre for Integrative Physiology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Contribute experimental information and advice to students and Postdoc. |
Collaborator Contribution | Contribute experimental information and data |
Impact | 19387074 doi.org/10.1016/j.scr.2015.10.016 doi.org/10.1016/j.exer.2016.05.021 |
Description | Embryonic growth and patterning |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Meier Gorlin Syndrome has been identified in patients and we made a genetic model to further probe the molecular disease mechanism Mouse model for analyzing cell proliferation and pattern formation in limb development |
Collaborator Contribution | Provides a genetic means to determine growth rate on organogensis. Also brought in a student to work collaboratively on the project |
Impact | A mouse model for the Meier-Gorlin (primitive dwarfism) syndrome. |
Start Year | 2011 |
Description | Genomic architecture |
Organisation | University of California, San Francisco |
Country | United States |
Sector | Academic/University |
PI Contribution | Generated a number of mutations targeted to affect chromatin organization |
Collaborator Contribution | provided the expertise in analysing the chromatin structure |
Impact | Data generated for a publication |
Start Year | 2017 |
Description | Innate immunity |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Provided specialised methodology and intellectual input |
Collaborator Contribution | provided basic immunology data to advance our understanding of the innate immune system |
Impact | Generated a number of mouse mutations which affect the innate immunity system |
Description | Long-Range Regulation |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | expertise, intellectual input,access to data, |
Collaborator Contribution | expertise, intellectual input |
Impact | Multidisciplinary. One manuscripts in preparation and work ongoing on nsecond |
Start Year | 2015 |
Description | Matthew wood Syndrome |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Provided specialised methodology and intellectual input |
Collaborator Contribution | Provided studentship and patient data |
Impact | Analysis of genetic models (mouse and zebrafish) to understand retinoic acid involvement in Matthew Wood (PDAC) syndrome |
Start Year | 2008 |
Description | Preaxial Polydactyly Patients |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Sharing patient information |
Collaborator Contribution | Sharing information on patientsProvided patient data |
Impact | 18463159 |
Start Year | 2007 |
Description | Preaxial Polydactyly Patients |
Organisation | University of Oxford |
Department | Weatherall Institute of Molecular Medicine (WIMM) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Sharing patient information |
Collaborator Contribution | Sharing information on patientsProvided patient data |
Impact | 18463159 |
Start Year | 2007 |
Description | Syndactyly |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Chromosomal analysis and molecular biological data |
Collaborator Contribution | Provided patient data and phenotype analysis and chromosomal analysis |
Impact | Generated an animal model for human syndactylism DOI:10.1002/humu.21615 |
Start Year | 2006 |
Description | UBR5 |
Organisation | Cancer Research UK |
Department | Edinburgh Cancer Research UK Centre |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Intellectual input, experimental resources and technical assistance |
Collaborator Contribution | Studentship |
Impact | Collaborative studentship doi:10.1371/journal.pone.0157079 |
Start Year | 2009 |
Description | Wt1 |
Organisation | Medical Research Council (MRC) |
Department | MRC Human Genetics Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Provided specialised methodology and intellectual input |
Collaborator Contribution | Basic biochemistry analysis |
Impact | Multidisciplinary (mouse genetics and Biochemistry) doi:10.1038/ng.494 |
Start Year | 2006 |
Description | evolution of Shh |
Organisation | University of Cape Town |
Department | Department of Zoology |
Country | South Africa |
Sector | Academic/University |
PI Contribution | Functional analysis of Shh in mammalian flight |
Collaborator Contribution | Initial identification of element |
Impact | Manuscript in prepaation |
Start Year | 2012 |
Description | Interview for National Radio Program (Radio 4) |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | General discussion of genes and their roles for the layperson |
Year(s) Of Engagement Activity | 2020 |
Description | Interview for a lay science book on evolution and development |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Several interviews by the author of a science book for the general public. Our work was discussed extensively in one chapter |
Year(s) Of Engagement Activity | 2019 |