Richard Ingram

Bio: Richard Ingram is an academic researcher from St James's University Hospital. The author has contributed to research in topics: Chromatin & Transcription factor. The author has an hindex of 13, co-authored 18 publications receiving 1495 citations. Previous affiliations of Richard Ingram include University of Leeds & University of York.

Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis: New Openings to the MADS World

Abstract: MADS-box transcription factors are key regulators of several plant development processes Analysis of the complete Arabidopsis genome sequence revealed 107 genes encoding MADS-box proteins, of which 84% are of unknown function Here, we provide a complete overview of this family, describing the gene structure, gene expression, genome localization, protein motif organization, and phylogenetic relationship of each member We have divided this transcription factor family into five groups (named MIKC, Mα, Mβ, Mγ, and Mδ) based on the phylogenetic relationships of the conserved MADS-box domain This study provides a solid base for functional genomics studies into this important family of plant regulatory genes, including the poorly characterized group of M-type MADS-box proteins MADS-box genes also constitute an excellent system with which to study the evolution of complex gene families in higher plants

RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis

Abstract: Cell fate decisions during haematopoiesis are governed by lineage-specific transcription factors, such as RUNX1, SCL/TAL1, FLI1 and C/EBP family members. To gain insight into how these transcription factors regulate the activation of haematopoietic genes during embryonic development, we measured the genome-wide dynamics of transcription factor assembly on their target genes during the RUNX1-dependent transition from haemogenic endothelium (HE) to haematopoietic progenitors. Using a Runx1−/− embryonic stem cell differentiation model expressing an inducible Runx1 gene, we show that in the absence of RUNX1, haematopoietic genes bind SCL/TAL1, FLI1 and C/EBPβ and that this early priming is required for correct temporal expression of the myeloid master regulator PU.1 and its downstream targets. After induction, RUNX1 binds to numerous de novo sites, initiating a local increase in histone acetylation and rapid global alterations in the binding patterns of SCL/TAL1 and FLI1. The acquisition of haematopoietic fate controlled by Runx1 therefore does not represent the establishment of a new regulatory layer on top of a pre-existing HE program but instead entails global reorganization of lineage-specific transcription factor assemblies.

A two-step, PU.1-dependent mechanism for developmentally regulated chromatin remodeling and transcription of the c-fms gene.

Abstract: It is now well established that the chromatin of genes expressed in specific hematopoietic lineages is already partly reorganized towards an active state in hematopoietic stem cells (HSCs) and multipotent progenitors, and a number of such genes are expressed at a low level prior to lineage commitment (10, 12, 15, 18, 33). During progressive lineage restriction and cell fate specification this promiscuous gene expression program is then restricted by upregulation of lineage-appropriate genes and silencing of lineage-inappropriate genes (8, 24). These observations indicate that lineage-specific gene priming must occur at an early stage of HSC development. However, due to the low abundance of HSCs and multipotent progenitors little is known about the mechanistic details of how such priming events are achieved and how an active chromatin structure is established that supports high-level transcription later in development. PU.1, a member of the Ets family of DNA-binding proteins, is a transcription factor that is critical for the development of myeloid lineages such as monocytes and granulocytes. Deletion of the PU.1 gene leads to defects in myelopoiesis, including loss of monocytes and macrophages (22, 28). Early myeloid progenitors are generated in PU.1-deficient mice, albeit at reduced numbers, but their differentiation is blocked (6). PU.1−/− myeloid progenitors fail to undergo macrophage differentiation and do not express the colony-stimulating factor 1 (CSF-1) receptor gene (c-fms), one of the most important genes regulating macrophage survival and proliferation. This gene is absolutely required for macrophage development (4). However, rescue of PU.1−/− myeloid progenitor cells with a c-fms expression vector restores macrophage progenitor growth and proliferation but not macrophage differentiation, indicating that PU.1 regulates a larger program of macrophage gene expression (6). c-fms belongs to a class of myeloid genes which are already expressed at a low level in HSCs (24, 34). Tissue-specific expression of c-fms mRNA is regulated by well-defined promoter and intronic enhancer elements (Fig. ​(Fig.1).1). The promoter used in macrophages is a TATA-less promoter, with multiple purine-rich elements bound by Ets family transcription factors (26). Tissue-restricted high-level expression of the c-fms gene is dependent upon the c-fms intron regulatory element termed FIRE, within the first intron (11, 27). Both the promoter and FIRE are bound by PU.1 in macrophages (5, 6, 13, 36). We previously showed by in vivo footprinting that the c-fms locus is already partly occupied by transcription factors in HSCs and becomes fully occupied in committed myeloid progenitor cells (34). In contrast, cell surface expression of CSF-1 receptor protein and high levels of mRNA are readily detected only in committed macrophage precursors (31) and their progeny. An initial mechanistic explanation of why this was the case was provided by in vivo footprinting studies demonstrating that the increase in c-fms mRNA expression during macrophage differentiation correlates with a dynamic assembly and disassembly of transcription factor complexes on the FIRE enhancer (31). However, the molecular details of this dynamic behavior are unknown because the identities of the specific factors and cofactors recruited were not determined in the previous study. It is also not known whether other transcription factors can bind to c-fms in the absence of PU.1 and to what extent chromatin of c-fms is reorganized in PU.1−/− cells. FIG. 1. Map of the mouse c-fms locus and induction of c-fms expression on addition of OHT. (A) Chromatin structure of mouse c-fms locus regulatory regions around the proximal promoter with indications of the transcription factor binding sites, the localization ... To address the above questions, we examined the chromatin fine structure of c-fms by performing in vivo footprinting experiments and chromatin immunoprecipitation (ChIP) assays. For a model system we employed a myeloid progenitor cell line derived from PU.1-deficient mice, which cannot differentiate into macrophages but can proliferate in the presence of interleukin-3. In contrast to wild-type myeloid progenitor cells, the c-fms locus was not occupied by any transcription factors in the PU.1−/− cells. To further study the role of PU.1 in the regulation of the c-fms locus, we employed a well-established derivative of the PU.1−/− cell line (PUER) that expresses an inducible form of PU.1 (36). Significantly, induction of PU.1 in PUER cells that resulted in restoration of macrophage differentiation led to in vivo transcription factor occupancy at the c-fms locus. The promoter was very rapidly occupied by transcription factors, whereas it took significantly longer for the same transcription factors to assemble at FIRE and for elevated levels of c-fms mRNA to be expressed. This delayed kinetics could be explained by our finding that formation of an active enhancer complex at FIRE required the induction of at least one secondary transcription factor, Egr-2, by PU.1. These observations suggest a two-step mechanism of c-fms activation which involves the promoter being active in early progenitor cells, thereby enabling low-level c-fms mRNA expression, whereas activation of FIRE occurs at a later developmental time during the course of macrophage differentiation. We suggest that this mechanism ensures that high levels of c-fms mRNA and CSF-1 receptor protein are expressed only in cells destined to be CSF-1 responsive.

GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox

Abstract: High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data. Users can query the database to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs. Reversely, mining tools allow users to identify genes specifically expressed during selected stresses, growth stages, or in particular organs. Using GENEVESTIGATOR, the gene expression profiles of more than 22,000 Arabidopsis genes can be obtained, including those of 10,600 currently uncharacterized genes. The objective of this software application is to direct gene functional discovery and design of new experiments by providing plant biologists with contextual information on the expression of genes. The database and analysis toolbox is available as a community resource at https://www.genevestigator.ethz.ch.

Transcription factors: from enhancer binding to developmental control.

Abstract: Developmental progression is driven by specific spatiotemporal domains of gene expression, which give rise to stereotypically patterned embryos even in the presence of environmental and genetic variation. Views of how transcription factors regulate gene expression are changing owing to recent genome-wide studies of transcription factor binding and RNA expression. Such studies reveal patterns that, at first glance, seem to contrast with the robustness of the developmental processes they encode. Here, we review our current knowledge of transcription factor function from genomic and genetic studies and discuss how different strategies, including extensive cooperative regulation (both direct and indirect), progressive priming of regulatory elements, and the integration of activities from multiple enhancers, confer specificity and robustness to transcriptional regulation during development.

Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice

Abstract: Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

Pioneer transcription factors: establishing competence for gene expression

Abstract: Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special "pioneer transcription factors" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.