NIHRDataInsights/HRCSData huggingface dataset:
Title: Defining RNA polymerase II transcription units across the mammalian genome
Funder: Wellcome Trust

Abstract: We will define the extent of RNA polymerase II (Pol II) transcription units (TUs) across mammalian genomes, both protein coding (pc) and long noncoding (lnc). For each TU class, termination sites and mechanisms will be scrutinised, especially by definition of XRN2 “torpedo” entry sites at positions of co-transcriptional endonuclease cleavage. Multiple endonucleases will be investigated including CPSF-73, Drosha and Integrator-S11. For lncRNA their mechanism of transcriptional initiation will also be investigated, especially R-loop dependant promoters. Pilot experiments show that R-loops promote antisense lncRNA particularly at pc-gene promoters and enhancers, so defining a new class of Pol II promoter that we intend to fully characterise at a molecular level. Histone genes represent an unusual, ubiquitous Pol II pc-gene class. We will also characterise the termination mechanism for these genes and in particular the role of the novel endonuclease MBLAC1. Finally, we will study the particular case of the H2AX gene that employs both a histone like, poly(A)- termination mechanism as well as a poly(A)+ mechanism. Overall, we will characterise mechanisms that define gene TUs across mammalian genomes to better inform gene function in the rapidly expanding repertoire of genomic sequences being generated for normal and pathogenic human cells.

Lay abstract: The ease of sequencing human genomes has greatly outstripped understanding of how genes actually work. While between 20-30 thousand genes generate transcripts that directly encode proteins, many more produce noncoding transcripts, often degraded as they are made. We will redress this knowledge imbalance between genome sequence and gene mechanism by focusing on transcriptional termination, a process that separates one gene from the next along a chromosome. In particular we will investigate how genes normally terminate as many cases of cellular pathology such as viral infection and cancer are associated with a breakdown in this process. We will also study a novel mechanism that initiates transcription of noncoding genes and likely explains why these transcripts are so numerous. We predict that while many noncoding genes have no particular function for the cell, they are likely to be important as an evolutionary resource that allows for the creation of new functional genes.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Genome regulation across developmental trajectories
Funder: Wellcome Trust

Abstract: To understand how the genome directs development, we need to know the cell-to-cell changes in genomic activity at individual loci and how changes are regulated. Advances in single-cell profiling provide a new ability to determine the regulatory configuration of individual cells genome-wide through profiling gene expression and chromatin accessibility. However, determining the connections between mother and daughter cells remains difficult. The invariant and known cell lineage of C. elegans solves this problem, making it possible with single-cell profiling to determine locus-specific activity in every cell from the zygote to the differentiated state. In Aim 1 we study the early events of genome quiescence, zygotic genome activation (ZGA), and lineage commitment by profiling all cells from the zygote to the 26-cell stage, and germ cells through their later ZGA. In Aim 2 we use the 20-cell intestine as a paradigm to study progression through a complete developmental trajectory. We will investigate mechanisms of key transitions and further study the relationship of activity patterns to genome 3D structure. In Aim 3, we focus on the impacts and regulation of active and PRC2/Polycomb chromatin domains. Our work will impact understanding of core principles of genome regulation relevant across animals.

Lay abstract: During animal development, the single celled embryo has the remarkable ability to give rise to all of the different cells and tissues of the organism, directed by instructions in the genome sequence. As new cells are produced, their identities are progressively defined by patterns of activation and repression of the genome, which generates correct gene expression programmes. We do not yet know this progressive series of events in any animal. Recent technical advances have made it possible to map which regions of the genome are active in individual cells (single-cell profiling). We will use this technology to study development in the nematode C. elegans, which has just 959 body cells. We will study the precise cell-to-cell changes in genome activity along development, revealing how specific information in the genome sequence is progressively read to produce correct cell types. Our findings will illuminate core principles of development relevant across animals.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Mechanisms and Consequences of Inclusive Inheritance
Funder: Wellcome Trust

Abstract: Heritability has traditionally been thought to be a unique feature of the genetic material of an organism, notably its DNA sequence. However, from studies of a variety of organisms, it is now clear that non-DNA sequence-based inheritance exists from microbes to mammals. The molecular mechanism(s) operating in humans remain opaque. However, understanding the impact of non-DNA sequence-based mechanisms is likely key to a full appreciation of heritability in health and disease. Here we will take ground-breaking steps towards understanding non-DNA sequence-based inheritance mechanisms and consequences. For this work we will focus on the imbred C. elegans model where we have the advantage of extensive genetic tools, a three day generation time and large numbers. In addition, we have identified the African Rift Lake cichlid radiation as a unique opportunity to dissect the contribution of epigenetics to plasticity, adaptation and heritability of phenotype in a vertebrate. While C. elegans gives us the ability to discover new mechanisms de novo we now also have developed paradigms to investigate the role of epigenetic inheritance on the plasticity and adaptivity in C. elegans and in cichlids. The latter is an important step towards a better understanding of inclusive inheritance in vertebrates more generally.

Lay abstract: We know that heritable disorders can be caused by a wide variety of genetic variants, from single nucleotide mutations to short insertions and deletions to larger structural variants. Some genetic variants are caused by the mobilization of genomic elements called transposons. However most research into complex disease has focused on single nucleotide changes of the genome. This overlooks fast evolving parts of the human genome, representing perhaps 50% of the total. Here we will investigate “epigenetic” mechanisms that have evolved to control transposon expression and mobility such as DNA methylation, chromatin modification and non-coding RNAs. These epigenetic mechanisms have been shown to be heritable in a variety of organisms and are able to transfer information about the environment across generations. Here we will use invertebrate and vertebrate animal models to learn more about the mechanisms and impact of such epigenetic inheritance including disease.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Core funding for the Wellcome Centre for Cell Biology
Funder: Wellcome Trust

Abstract: The Wellcome Centre for Cell Biology (WCB) is internationally renowned for discovery of key cellular mechanisms. During the current quinquennium, WCB researchers made transformative advances, aligned with our vision of uncovering cellular epigenetic mechanisms and their impact in disease. Influential breakthroughs in fundamental genome organisation and expression, epigenetic inheritance in fungal resistance and the molecular basis of a neurological disorder provide exemplars of our accomplishments. From these exceptional foundations, we have evolved a new scientific vision for WCB: to understand transitions between cellular states in health and disease. We will determine how cells are developmentally re-programmed and respond to environmental and other stresses, how differentiation goes awry in disease, and how pathogens switch states to evade toxins. We have made recent strategic appointments aligned with these aims, in transcriptomics, cellular development, cell growth and structural epigenetics, and invested in mass spectrometry and Cryo-EM. Future appointments in epigenetic transcriptomics of infectious disease and early development will help deliver this vision. WCB will prioritise building inter-disciplinary connections and changing perceptions around translatable research. Scientific excellence will be underpinned by a strong commitment to growing an exemplary cultural environment. With this holistic vision, WCB is poised to deliver transformative scientific and cultural breakthroughs.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Discovery and early translation of small molecule toxin inhibitors for use as broadly effective, inexpensive, oral, prehospital snakebite treatments
Funder: Wellcome Trust

Abstract: Small molecule toxin inhibitors offer great potential to rapidly deliver inexpensive, safe and efficacious oral interventions in the community soon after a snakebite, prior to subsequent admission to a healthcare facility. Despite such promise, only a handful of toxin inhibitors have been robustly explored to date. We redress this here by expanding the chemical space available for snakebite treatments by employing a comprehensive drug discovery approach. Using toxin-specific assays, we will screen diverse compound libraries (>50,000 molecules), including using the Human Pharmacopoeia and Phase-1 approved molecules in a repurposing approach, for hits that demonstrate broad toxin family neutralisation. Thereafter, we will rationally identify lead series by defining the toxin-specificity, kinetics, phenotypic potency and medicinal chemistry characteristics of hits, before performing murine preclinical efficacy and pharmacokinetic experiments to rationally define oral dosage regimens of lead candidates capable of achieving systemic inhibitory concentrations throughout a snakebite treatment period. Finally, we will evaluate therapeutic combinations of lead candidates by performing dose optimisation via PK/PD modelling, and preclinical efficacy and drug-drug interactions studies. This comprehensive drug discovery pipeline will deliver a portfolio of lead candidates (and numerous backups) ready for translation into clinical studies to assess their tolerability and efficacy as next-generation snakebite therapeutics.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE
Title: Cell fate determination in the vertebrate embryo
Funder: Wellcome Trust

Abstract: Understanding mechanisms underlying cell fate decisions is a central question in developmental biology, stem cell biology, and regenerative medicine. Our goal is to define the “ground-state” for lineage specification and understand the changes to this state that promote differentiation to specific lineages. As our experimental model, we study the vertebrate neural crest, a multipotent embryonic population, that gives rise to a plethora of derivatives, including peripheral neurons and glia, melanocytes, craniofacial cartilage and bone and many others. Due to its unique multipotency and lengthy development, the NC offers notable advantages for studies of cell fate. Our first objective is to uncover the fundamental mechanisms of triggering NC specification by exploring global changes to chromatin and cis-regulatory landscape that initiate the NC programme. Our second objective is to decipher and validate NC developmental trajectories and associated gene regulatory circuits controlling NC fate transitions. We will use a combination of epigenomic, proteomic, genome-editing and single-cell approaches in zebrafish embryos to establish the entire network of transcription factors and chromatin-associated proteins underpinning the process of NC cell fate specification and restriction. The uncovered general mechanisms can be applied to human embryonic stem cells and used in a therapeutic setting in the future.

Lay abstract: Understanding how a single cell can give rise to hundreds of different cell types in the human body is a crucial question in biology. By studying these ‘cell-fate’ decisions, I aspire to decipher the causes of developmental diseases, which occur when these processes go awry during development. My lab studies the neural crest (NC), an emblematic embryonic cell-type that specialises into many derivatives, including nerve cells, bone cells in our skull, and pigment cells in our skin. Errors in NC formation are one of the most common causes of birth anomalies. The NC formation is controlled by a series of genetic on/off switches, known as ‘gene regulatory networks’. We aim to decipher how are these switches activated in future NC cells, and which switches control the future fate they adopt. Untangling the molecular detail controlling NC cell-fate decisions is crucial to our capacity to use those cells for therapeutic purposes.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: OKRE: Opening Knowledge across Research and Entertainment
Funder: Wellcome Trust

Abstract: The proposal outlines the request for funding to support the set-up, operation and activities of OKRE: Opening Knowledge across Research and Entertainment over five years. OKRE is a high-profile strategic initiative for working with the entertainment industries that has been developed in partnership with UKRI. OKRE enables Wellcome to build on the work it has done so far, to scale its impact and create a more sustainable transformation in the engagement of research with mass media. A gap was identified between research and entertainment sectors for a body akin to the Science Media Centre but designed to address the particular challenges of working with the entertainment industries. OKRE's business model has now been developed and the organisation has been registered with Companies House and the Charity Commission. Wellcome is uniquely positioned to establish such a body. Funding enables OKRE to deliver core services in line with Wellcome's new strategic vision. OKRE's objects include promoting research, advancing education of the public and advancing the arts in social, scientific and health-related issues, as well as promoting the efficiency and effectiveness of charities. By sharing infrastructure costs with other funders, OKRE will enable Wellcome to scale the impact of its funding.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: RNA processing and degradation
Funder: Wellcome Trust

Abstract: All living systems – cells or organisms – operate in and must adapt to constantly changing environments. RNA transcription, processing and assembly with protein complexes form the core of the gene expression system, but many key features remain unclear. At times, very substantial changes take place; for example, in response to sudden environmental changes, following infection or during developmental progression. To address unresolved questions in RNA biology, we developed biochemical techniques to identify key, relevant RNA-protein, RNA-RNA and protein-protein interactions. These will be improved and applied in the proposed work, supported by bioinformatics. RNA systems are highly conserved in evolution, so techniques developed in yeast can be adapted for human cells and applied to understand disease. RNA biology in a cellular context is subject to dynamic changes. Kinetic analyses will therefore be applied, particularly during changes in cell state.Specific topics: 1: How is the nascent RNA linked to transcription termination and RNA processing2: How does RNA metabolism respond to environmental stress?3: How is host RNA metabolism remodelled during Coronavirus infection? 4: What are the roles of ncRNAs in neuronal development?The insights generated, and the experimental and bioinformatics techniques developed, will underpin future work by many groups.

Lay abstract: RNA metabolism lies at the heart of the information processing systems that fundamentally distinguish living organisms from sets of biochemical reactions. Alterations in RNA-protein and RNA-interaction are crucial during changes in cell state, but are complex and difficult to map systematically. Many genetic diseases are caused by specific defects in RNA metabolism, which is changed in disease, reprogrammed following stress and during development, and can be manipulated by pathogens. Understanding the molecular mechanisms is essential for future exploitation in therapy. To help achieve this, we have developed, and will further refine, a set of tools to follow complex changes in RNA interactions. These will be applied to identify key interactions that drive alterations in gene expression occur over time courses as cells respond to environmental stress, infection and development. This work will identify key features of RNA metabolism during transitions between cellular states in health and disease.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Genetic Code Compression and Expansion
Funder: Wellcome Trust

Abstract: Genetic code expansion enables the site-specific, incorporation of non-canonical amino acids (ncAAs) into proteins, and has enabled diverse biological discoveries. Most experiments incorporate ncAAs in response to amber stop codons. This strategy is limited to incorporating one type of ncAAs into a protein at a time, and there are no other natural blank codons that can be used for ncAA incorporation. We synthesized a 4 Mb E. coli genome with a compressed genetic code, through the genome-wide substitution of three target codons by defined synonyms. The resulting cell, Syn61, uses 61 codons to encode the 20 canonical amino acids. In Aim 1 we address the limitations of genetic code expansion by encoding multiple distinct ncAAs in response to blank codons in Syn61. This dramatically expands the applications of ncAA incorporation. The recoding of Syn61 was based on the prior identification of a synonymous codon compression scheme (a rule that defines which codons to remove and which codons to replace them with). In Aim 2 and Aim 3 we systematically discover allowed synonymous codon compression schemes that we use to create deeply compressed synthetic genomes using accelerated genome synthesis methods. This creates more blank codons that may be reassigned to ncAAs.

Lay abstract: Proteins, which carry out many of the functions of the cell, are synthesized from genes within the genome. Proteins are polymers of the 20 amino acid and the sequence in which the amino acids are added to the polymer is encoded in sequence of codons in a gene. There are 64 triplet codons (every combination of the 4 DNA bases A,C,G,T), but only 20 amino acids. Most amino acids are encoded by more than one codon. We would like to add amino acids to the genetic code with properties that will help us understand how biology works. To do this we need to compress the number of codons used to encode the normal 20 amino acids to free up some of the code for encoding new amino acids. Our work therefore involves creating genomes with compressed codes and reassigning the free codons to new amino acids.

Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES;1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: TwinsUK (2019-2023) - An Epidemiological and Genomic Resource
Funder: Wellcome Trust

Abstract: The TwinsUK cohort is a major genomic epidemiology resource with longitudinal deep genomic and phenomic data from over 13,500 adult twins who are highly engaged and recallable. We are seeking longer term funding to support operations and management, to continue enhancement of a highly successful programme of international science. The vision is to continue to be the most deeply characterised adult twin cohort in the world, providing a rich platform for scientists to research health and ageing longitudinally. More than 800 data access collaborations and 150,000 samples have been shared with external researchers, resulting in ~600 publications since 2012. In the next 5-year phase of TwinsUK we will integrate electronic health records into an enhanced deep tissue ‘omics resource and introduce dynamic phenotypic testing into clinical visits. The majority of funds requested are to support core staff and to add new enhancements in health records linkage and sociological and environmental data. These developments will not only augment the unique scientific value of the resource but enable co-analysis of these datasets with other world renowned cohorts. The result will be a unique global resource of longitudinal omics and twin research across the life-course, with immense potential for future scientific exploitation.

Lay abstract: TwinsUK is a large-scale health and ageing population study. We have extensive genetic and health data from over 13,500 adult twins, from multiple time points over 25 years. We hope to maintain our highly successful scientific resource: 85% of the requested funds will continue essential staff salaries. We aim to continue to be the twin cohort with the largest amount of data available to scientists to use in the world: since 2012 more than 800 research projects have produced over 600 scientific publications. In the next five years we plan to link twins’ genetic data to their health records and to work with other large UK population studies. We will also measure how different individuals respond to diet and other lifestyle factors. These developments will both enhance the scientific value of TwinsUK and enable us to provide a unique international collaborative resource with huge potential for research across the life-course.

Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION
Health categories: GENERIC HEALTH RELEVANCE
Title: EPSRC Physics of Life
Funder: Wellcome Trust

Abstract: This partnership between Wellcome and UKRI will support the Physics of Life funding call. Which aims support internationally leading research that requires collaborative, interdisciplinary working to address key challenges at the interface of physics and life sciences.The call will fund high-quality proposals that demonstrate deep integration of cutting edge experimental, theoretical and/or computational physics within life sciences research to advance our understanding of living systems in biological or biomedical contexts.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE