NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular mechanisms of mRNA polyadenylation and deadenylation
Funder: Medical Research Council

Abstract: Gene expression is tightly regulated to allow rapid responses to cellular stimuli. This is controlled through transcription, mRNA stability and the efficiency of translation into protein. Many of the post-transcriptional mechanisms of gene regulation are mediated by polyadenosine (polyA) tails which are found at the 3´-end of almost every eukaryotic mRNA. PolyA tails act in many diverse processes including the expression of genes in the inflammatory response, microRNA-targeted gene silencing and expression of maternal mRNAs in oocyte development. They are deregulated in human disease including cancer and viral infection. My laboratory aims to understand the molecular mechanisms of addition and removal of mRNA polyA tails, thereby providing fundamental insight into the regulation of gene expression. We use an integrated, multidisciplinary approach combining structural, biochemical, biophysical, and functional techniques. We are determining high-resolution structures of Cleavage and Polyadenylation Factor (CPF), Ccr4–Not and Pan2–Pan3 protein complexes to elucidate how they determine polyA tail position and length. We will define fundamental principles underlying their assembly, gain insight into their activities and regulation, and establish the functions of individual subunits. Specifically, we purify endogenous protein complexes as well as overexpressed (sub)complexes, to determine their structures and characterise their functions. We use electron cryo-microscopy (cryo-EM), alongside x-ray crystallographic, biophysical, biochemical and genetic techniques. We have developed methods for cryo-EM by designing new substrates that improve image quality, enabling structure determination of more difficult proteins than was previously possible. An understanding of the structures and functions of CPF, Pan2–Pan3 and Ccr4-Not will provide fundamental biological insights into this exciting field.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Specificity in the ubiquitin system
Funder: Medical Research Council

Abstract: Protein ubiquitination emerges as a key regulatory posttranslational modification, which is utilised both in degradative processes regulating the half-life of target proteins, as well as in signal transduction where it serves non-degradative functions. During ubiquitination, the small protein ubiquitin is attached covalently to target proteins. Ubiquitin can be ubiquitinated itself, generating ubiquitin polymers. The versatility of the ubiquitin system is achieved by the ability of ubiquitin to form at least eight types of polymers, and proteomic analysis has shown that all different ubiquitin linkages are present in cells. To date, functional and structural data is available for only three types of polyubiquitin chains. These are the well-studied Lys48-linked polyubiquitin chain, that targets modified proteins for proteasomal degradation, as well as Lys63-linked polyubiquitin that are implicated in cell signalling processes. Independent functions for the remaining chain types are emerging. We aim to generate and study the remaining ubiquitin chain types, and understand their roles in the cell. For this, we need to study ubiquitin chain assembly systems. This work has led us to determine the structure of the E3 ubiquitin ligase Parkin, explaining many mutations of individuals with early-onset Parkinson’s disease, shedding new light on the role of ubiquitin in neurodegenerative disorders. Moreover, we have identified E2 and E3 enzymes to generate Lys6- and Lys11-linked polyubiquitin chains. Availability of novel chain linkages is important to understand the molecular basis for specificity in the ubiquitin system, especially specificity of deubiquitinases and ubiquitin binding domains. Deubiquitinating enzymes hydrolyse ubiquitin chains, and are therefore key regulators of the ubiquitin system. Currently, limited information is available as how this important class of enzymes is regulated. We perform structural and functional studies on deubiquitinases of the Ovarian Tumour family, to understand how they affect cell signalling pathways at the molecular level.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Cellular Stress
Funder: Medical Research Council

Abstract: The overall aim of the Group is to increase our understanding of the regulation of energy metabolism. Defects in energy metabolism underlie a number of diseases including type 2 diabetes and obesity, and the prevalence of these diseases is increasing at an alarming rate. A growing body of evidence has shown that the AMP-activated protein kinase (AMPK) plays a key role in maintaining energy homeostasis. AMPK acts as a sensor of energy status and regulates a wide range of metabolic pathways, adjusting energy production with energy expenditure. We are investigating the physiological role of the AMPK cascade, with a particular emphasis on metabolic diseases. Our studies combine in vivo models in which components of the AMPK cascade have been altered genetically, together with cell based models and in vitro techniques using recombinant protein preparations. The recent identification of two upstream kinases in the AMPK cascade, calcium and calmodulin dependent protein kinase kinase (CaMKK) beta and LKB1, provides additional models and reagents with which to explore the role and regulation of AMPK. CaMKKbeta is involved in calcium signalling and so we are investigating the role of AMPK in cellular responses involving increased calcium levels. Mutations in LKB1 lead to a cancer pre-disposition syndrome in humans, termed Peutz-Jeghers syndrome, and we have begun to explore the possibility that AMPK may be involved in the regulation of cell proliferation and tumorogenesis. The specific aims of the programme are: 1. Investigating the role of AMPK in vivo using a novel gain-of-function mouse model; 2. Identification of new AMPK activators; 3. Biochemical and biophysical studies to understand the basis of AMPK regulation; examining the role of AMPK subunit isoforms in the regulation of AMPK.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Cell Cycle
Funder: Medical Research Council

Abstract: "Work will focus on the biology of chromosome assembly and segregation. The research effort will be concentrated on (i) continuing the characterisation of Cdc14 function, and (ii) analysing the uncharacterised protein complex SMC5/6. Our long term goal is to analyse these factors in mammalian cells.||1. Biology of Smc5-Smc6 complex|(i) To characterise the molecular role of Smc5-Smc6 in the coordination of DNA DSB repair;|(ii) To develop new assays to study site-specific damage during DNA replication in order to further analyse the function of Smc5-Smc6 in replication fork stability;|(iii) To isolate novel targets and regulators of Smc5-Smc6;||2. Cdc14 and the control of chromosome segregation|(i) To elucidate the physical nature of sister-chromatid linkages in cdc14 mutants;|(ii) To characterise the molecular regulation of Cdc14 role during nucleolar segregation."


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: DNA Replication
Funder: Medical Research Council

Abstract: The precise duplication of chromosomal DNA is essential to preserve the genetic complement of the cell. In multicellular organisms mistakes during genetic inheritance can lead to a cell population that proliferates uncontrolled. To ensure that chromosomes only replicate once per cell cycle the process of chromosome duplication is divided into discrete steps which have to happen in a specific order for successful assembly of a DNA replication machine. The first major step is licensing of chromosomes during late in mitosis or early G1 phase. This reaction involves i.) Binding of the six-subunit Origin Recognition Complex (ORC) to origin DNA and ii.) Cdc6 and Cdt1 dependent loading of Mini-Chromosome maintenance proteins (MCM), a putative DNA helicase, onto chromatin to form the pre-replicative complex (pre-RC). Once the cell is committed to cell division and DNA replication, Dbf4 Dependent Kinase (DDK) and Cyclin Dependent Kinases (CDKs) get activated. In the second major step several proteins are recruited to origins, including Replication Protein A (RPA) and DNA polymerases, which lead to pre-initiation complex (pre-IC) formation and DNA replication. Origins that replicated get inactivated by S-phase specific cyclins to restrict DNA replication to once per cell cycle.||We are interested in understanding the function, mechanism and regulation of the multiprotein machine that assembles in a multistep process on DNA resulting in duplication of the genome. To address these questions we use yeast as a model system, since it is the only biochemical accessible system available that allow sequence specific complex assembly and will serve as good basis for a general understanding of eukaryotic DNA replication. The 1st aim is to determine the basic mechanisms in assembly and regulation of the preRC. Recently we analyzed the role of ORC and Cdc6 in pre-RC formation. Now our focus will be on Cdt1 and MCM proteins in pre-RC formation. We will analyze the interactions between Cdt1-MCM2-7 and ORC/Cdc6 in solution and on DNA using biochemical assays. We are interested in the question how Cdt1-MCM2-7 modifies the previously studied ORC-Cdc6-DNA complex. To analyze the function of MCM proteins we do assemble the entire pre-RC and also understand the binding/loading of MCM proteins. In collaboration with Huilin Li (Brokkhaven National Laboratory, USA) we will determine the 3D structures of multiple complexes on DNA with ORC, Cdc6, Cdt1 and MCM proteins. Structural and biochemical data will be consequently integrated into a model describing the function and mechanism in pre-RC formation. This information will be used to understand the consequences of pre-RC misregulation in cancer.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Reprogramming and Chromatin
Funder: Medical Research Council

Abstract: The process of epigenetic reprogramming requires global resetting of epigenetic memory at the level of DNA methylation and chromatin modifications. This process leads to major shifts in gene expression profile and can lead to a change in cell fate.||In mammals, under physiological conditions epigenetic reprogramming occurs in the course of development and potentially to some extent also as a part of the regenerative processes during wound healing. Aberrantly, similar processes that reverse cell fate decisions might be partially recapitulated during cellular dedifferentiation observed in cancer. ||In vitro, several reprogramming systems have been described that could be used to revert somatic cell phenotype and to regenerate pluripotency: somatic cell nuclear transfer (SCNT), generation of induced pluripotent cells (iPS), cell fusion or permeabilisation of cells followed by incubation with protein extracts - amongst others.||However, these in vitro reprogramming systems are very inefficient, show high degree of variability and often generate cells with intermediate phenotypes. In order to gain deep mechanistic insights into the molecular processes underlying epigenetic reprogramming we decided to focus on the naturally occurring reprogramming that operates very efficiently in the course of embryonic development. Detailed understanding of these processes can add to our ability to efficiently reprogramme cells in vitro.||Our lab uses mouse zygotes and developing germ line (primordial germ cells PGCs) as in vivo models where epigenetic reprogramming occurs naturally in vivo. The germ line carries unique epigenetic properties, since the reprogramming process involves both genome wide DNA demethylation (including erasure of genomic imprints) and chromatin remodelling. In comparison, the reprogramming process in zygotes involves genome wide DNA demethylation that affects only the paternal genome a few hours after fertilisation.||In order to decipher molecular mechanisms underlying the reprogramming processes we concentrate on 2 main areas:||1) Mechanisms underlying DNA demethylation and erasure of genomic imprints|We have previously documented the kinetics of erasure of DNA methylation and genomic imprints during the development of mouse primordial germ cells (Hajkova et al, 2002, Hajkova et al 2008). Based on the kinetics of the process we suggested that DNA demethylation driven through DNA repair pathway is the most likely scenario to operate in germ cells. We are currently testing this hypothesis.||2) Interplay between DNA demethylation and chromatin dynamics ||Besides our efforts to decipher the mechanisms responsible for large scale loss of DNA methylation in germ cells and zygotes, we are particularly interested in the cross-talk and regulation between DNA demethylation and large scale chromatin remodelling.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Meiosis
Funder: Medical Research Council

Abstract: The ultimate goal of our group is to understand the molecular mechanisms that ensure the faithful segregation of chromosomes during meiosis, the specialized cell division program that forms haploid gametes from diploid germ cells. Correct chromosome partitioning during meiosis is achieved through a series of complex changes at the level of DNA molecules, chromosome structure and nuclear organization. These include: pairing of homologous chromosomes, the assembly of a proteinaceous scaffold (the synaptonemal complex) between the homologues, and the formation of crossover recombination events between DNA molecules of paired homologues. Crucially, inter-homologue crossovers provide the basis of a temporary physical link that holds homologues together until they segregate from each other on the first meiotic spindle. A failure to form crossovers results in the creation of aneuploid gametes, one of the leading causes of miscarriages and birth defects in humans. Our main focus is to elucidate the mechanisms that control the formation and distribution of inter-homologue crossovers during meiosis. We are using C. elegans as an experimental organism and a combination of different experimental approaches including: genetics, biochemistry, molecular biology and three-dimensional microscopy. Our research program is divided into two main areas: first, we are performing genetic screens to isolate mutants that display a reduced number of crossovers and second, we are investigating the molecular mechanisms by which HTP-1, a component of meiotic chromosome axes, promotes proper homologue pairing and crossover formation. We are also studying the interplay between crossovers and meiotic chromosome structure. We have shown that crossovers trigger a remodelling of chromosome axis composition that is required for proper homologue segregation, and that HTP-1 is a key player in this remodelling process. We are trying to identify proteins that collaborate with HTP-1 in this process. Studies are also directed at understanding the mechanisms that control the distribution of crossovers across the genome.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Mitochondria and Cell Death Regulation following toxic injury
Funder: Medical Research Council

Abstract: The focus of our research is to better understand the control of cellular death processes in normal cells and in pathological states with alterations of these processes. Our aim is to achieve a better understanding of the regulatory mechanisms controlling cell death. Understanding the basic biology of these processes can provide insights that are aimed to deliver field-changing mechanistic insights into toxicology and disease. Part of our research addresses the function of mitochondrial proteins such as the protease HtrA2 and PINK1 and their role in stress responses. Mutations in HtrA2 and PINK1 are linked to Parkinson’s disease and we identified a mitochondrial stress-sensing pathway that involves the interaction between these two proteins. Our work focuses on mitochondrial signaling pathways of toxicity associated with neurodegenerative diseases. The aim of this work is to target these pathways to improve neuronal health in models of Parkinson’s disease and other diseases related to mitochondrial dysfunction. We use the fruit fly as a model system to study organs and tissues with high energetic demand, such as the brain and muscles, that are susceptible to toxic insults.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE
Title: Cilia Development & Disease
Funder: Medical Research Council

Abstract: Cilia are microtubule based extensions of the centriole that are present in almost every cells of the body. Specialised motile cilia function in the trachea, ependyma of the brain and the reproductive tract; during development cilia are also required for establishing left-right patterning. In contrast, most cells have a single non-motile primary cilium. Primary cilia have been implicated in cell-cell signalling (particularly the hedgehog pathway), planar cell polarity, stress perception, hearing, vision and obesity leading some to describe them as the cellular antenna. Defective cilia are known to result in a broad range of diseases including Primary Ciliary Dyskinesia (PCD), Polycystic Kidney Disease (PKD), Bardet Biedl Syndrome (BBS), Meckel Syndrome (MKS) and Orofaciodigital Syndrome (OFD). While individual and distinct, these disorders result in a range of overlapping defects and together have become known as the ciliopathies. We are interested in the role of cilia in mammalian disease and development. Using mouse genetics, cell biological and biochemical approaches we are studying ciliogenesis, left-right patterning and cilia related disease. The aim of this programme is to understand the normal function of cilia, the effects of defective cilial function and to develop mouse models of human ciliopathies with the ultimate goal of identifying and developing therapeutic strategies. Current work concentrates on mechanisms by which cilia generate flow and the role of cilia in flow detection. This is of particular relevance to PCD, PKD and to left-right patterning. Our other major area of research is characterising the genetic control of the process of ciliogenesis and has resulted in the identification of a novel transcriptional regulator and a major target of this regulation.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Bioinformatics for mouse genomics and genetics
Funder: Medical Research Council

Abstract: The BioComputing Group research is in two key areas; mouse phenotyping and next generation sequencing. Both areas are critical to mouse genetics and interlink with research programmes at MRC Harwell and activities in wider consortia in the community in which MRC Harwell is intimately involved. The group's specific areas of interest include the development of tools and novel approaches for the annotation of mouse phenotypes, which underpins the development, utilisation and dissemination of disease models - a vital broader remit for MRC Harwell. This research includes developing phenotype databases (www.europhenome.org) for the acquisition and dissemination of mouse phenotyping information, an activity that is interlinked with our leading involvement in the coordination of European and International programmes in mouse phenotyping (www.mousephenotype.org). We are also leading the Data Coordination Centre (DCC) for the NIH KOMP2 program in collaboration with the WTSI and EBI. Our sequence analysis work focusses on the interpretation of Next-Generation Sequencing data as they relate to major projects going on in the MGU, with particular emphasis at present on SNP identification in homozygous and heterozygous ENU mutant lines. This is leading to the more rapid identification of point mutations involved in the phenotypes of these lines.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE
Title: Basse Health and Demographic Surveillance System
Funder: Medical Research Council

Abstract: The Basse Health and Demographic Surveillance System (BHDSS) was established in July 2007, primarily to support Basse’s participation in the Global Enteric Multicentre Study (GEMS) and the ongoing Pneumococcal Surveillance Project (PSP). It covers a population of about 170,000 in 219 settlements in the Fulladu East and Kantora Districts of the Upper River Region of The Gambia, a setting typical of much of rural Sub-Saharan and with a high burden of communicable and preventable diseases. In addition to the GEMS and PSP projects, it hosts and facilitates the implementation of a range of other projects and studies. The BHDSS, with a similar operational design as the Farafenni HDSS, constitutes a potential valuable resource to establish benchmarks and monitor progress towards the achievement of post-2015 global and regional health indicators that the international community will be expected to set. Specific strategies to be adopted to maximise the scientific output of the BHDSS include: • Potential linkage of DSS data with Basse Major Health Centre records (in recognition of its potential upgrading to a District Hospital), thus broadening the scope for medical research to include, among other things, disease-specific morbidity burden estimation for both communicable and non-communicable diseases, and their respective impact on quality of life. • Enhance capacity to support the placement of PhD students in the fields of Demography, Epidemiology, Sociology, etc, and build multi-disciplinary capacity for optimal utilisation of the data generated by the platform. • Fully engage government stakeholders in the utilisation of the platform database to inform public health policy formulation and review; as well as generating the necessary evidence base required to guide rational health care delivery planning and resource allocation.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: GENERIC HEALTH RELEVANCE