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Niall Dillon

Publications and source records attributed to Niall Dillon.

14 recordsLinked to original sources
PubMed2006

The proteasome restricts permissive transcription at tissue-specific gene loci in embryonic stem cells.

The ability of stem cells to activate different gene expression programs requires the choreographed assembly of trans-acting factors at enhancers and promoters during cell differentiation. In this study, we show that the proteasome acts on specific regulatory regions in embryonic stem (ES) cells to prevent incorrect transcriptional initiation. Chemical or siRNA-mediated inhibition of proteasome activity results in increased transcription factor and RNA polymerase II binding and leads to activation of cryptic promoters. Analysis of the binding profiles of different proteasome subunits in normal ES cells and following RNAi knockdown of individual subunits provides evidence for a targeted assembly of the 26S proteasome at specific regulatory elements. Our results suggest that the proteasome promotes a dynamic turnover of transcription factor and Pol II binding at tissue-specific gene domains in ES cells, thereby restricting permissive transcriptional activity and keeping the genes in a potentiated state, ready for activation at later stages.

Animals↗
PubMed2006

Gene regulation and large-scale chromatin organization in the nucleus.

Regulation of gene expression involves a number of different levels of organization in the cell nucleus. The main agents of transcriptional control are the cis-acting sequences in the immediate vicinity of a gene, which combine to form the functional unit or domain. Contacts between these sequences through the formation of chromatin loops forms the most basic level of organization. The activity of functional domains is also influenced by higher order chromatin structures that impede or permit access of factors to the genes. Epigenetic modifications can maintain and propagate these active or repressive chromatin structures across large genomic regions or even entire chromosomes. There is also evidence that transcription is organized into structures called 'factories' and that this can lead to inter-chromosomal contacts between genes that have the potential to influence their regulation.

Animals↗
PubMed2005

The role of enhancers as centres for general transcription factor recruitment.

Activation of eukaryotic genes requires a tight temporal control of trans-acting-factor binding to different types of sequence elements. General transcription factors (GTFs) have a central role in the regulation of RNA polymerase II (Pol II) function because they are involved in the initiation of transcription at all class II promoters. Recent studies have shown that GTFs and Pol II are recruited to enhancer elements and that this binding is an early event in gene activation. We propose that an important role of some enhancers is to function as nucleation centres for the assembly of the pre-initiation complex to regulate the timing of gene activation during development, differentiation and the cell cycle.

Animals↗
PubMed2005

Mapping and functional analysis of regulatory sequences in the mouse lambda5-VpreB1 domain.

The lambda5 and VpreB genes encode the components of the surrogate light-chain which forms part of the pre-B cell receptor and plays a key role in B cell development. In the mouse, the lambda5 and VpreB1 genes are closely linked and are co-regulated by a multi-component locus control region. To identify the sequences that regulate lambda5 and VpreB1 expression during B cell development, we have comprehensively mapped the DNaseI hypersensitive sites (HS) in the lambda5-VpreB1 functional domain. The active domain contains 12 HS that are distributed at high density across the 18.3 kb region that forms the lambda5 and VpreB1 functional unit. Analysis of a reporter gene driven by the VpreB1 promoter in transgenic mice identified a novel enhancer associated with two HS located upstream of lambda5. The lambda5-VpreB1 locus was also found to be closely linked to the ubiquitously expressed Topoisomerase-3beta (Topo3beta) gene. The VpreB1 and Topo3beta genes have entirely different expression patterns despite the fact that the two promoters are separated by a distance of only 1.5 kb.

Animals↗
PubMed2005

The epigenetic basis for embryonic stem cell pluripotency.

As well as having the remarkable ability to differentiate into all of the cell types in the embryo, embryonic stem (ES) cells also have the capacity to divide and self-renew. Maintenance of pluripotency through repeated cell divisions indicates that the developmental plasticity of ES cells has a specific epigenetic basis. We propose that tightly localised regions of histone modification are formed in ES cells by binding of sequence-specific transcription factors at genes that are destined for expression at later stages of differentiation. These 'early transcription competence marks' would help to maintain pluripotency by preventing the spread of repressive chromatin modifications. We further propose that the presence of discrete histone modification marks in pluripotent cells facilitates the binding of lineage-specific and general transcription factors to the marked regions as ES cells commit to different fates. By helping to organise the precisely timed responses of genes to the signals that determine lineage choice, the gene-specific localised epigenetic marks would play a key role in the establishment of complex gene expression programmes in differentiating cells.

Animals↗
PubMed2005

The lambda5-VpreB1 locus--a model system for studying gene regulation during early B cell development.

The lambda5 and VpreB genes encode the components of the surrogate light-chain, which forms part of the pre-B cell receptor. In mouse, the lambda5 and VpreB1 genes of mouse are closely linked and coordinately regulated by a locus control region (LCR). Activation of the genes in pro-B cells depends on the combined effects of early B cell factor (EBF) and the E2A factors E12 and E47. Silencing of lambda5 expression in mature B cells occurs through the action of Ikaros on the gene promoter where it may compete for binding of EBF and initiate the formation of a silent chromatin structure.

Animals↗
PubMed2005

Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division.

Variant histone H3.3 is incorporated into nucleosomes by a mechanism that does not require DNA replication and has also been implicated as a potential mediator of epigenetic memory of active transcriptional states. In this study, we have used chromatin immunoprecipitation analysis to show that H3.3 is found mainly at the promoters of transcriptionally active genes. We also show that H3.3 combines with H3 acetylation and K4 methylation to form a stable mark that persists during mitosis. Our results suggest that H3.3 is deposited principally through the action of chromatin-remodelling complexes associated with transcriptional initiation, with deposition mediated by RNA polymerase II elongation having only a minor role.

Animals↗
PubMed2005

Formation of an active tissue-specific chromatin domain initiated by epigenetic marking at the embryonic stem cell stage.

The differentiation potential of stem cells is determined by the ability of these cells to establish and maintain developmentally regulated gene expression programs that are specific to different lineages. Although transcriptionally potentiated epigenetic states of genes have been described for haematopoietic progenitors, the developmental stage at which the formation of lineage-specific gene expression domains is initiated remains unclear. In this study, we show that an intergenic cis-acting element in the mouse lambda5-VpreB1 locus is marked by histone H3 acetylation and histone H3 lysine 4 methylation at a discrete site in embryonic stem (ES) cells. The epigenetic modifications spread from this site toward the VpreB1 and lambda5 genes at later stages of B-cell development, and a large, active chromatin domain is established in pre-B cells when the genes are fully expressed. In early B-cell progenitors, the binding of haematopoietic factor PU.1 coincides with the expansion of the marked region, and the region becomes a center for the recruitment of general transcription factors and RNA polymerase II. In pre-B cells, E2A also binds to the locus, and general transcription factors are distributed across the active domain, including the gene promoters and the intergenic region. These results suggest that localized epigenetic marking is important for establishing the transcriptional competence of the lambda5 and VpreB1 genes as early as the pluripotent ES cell stage.

Acetylation↗
PubMed2004

The regulated long-term delivery of therapeutic proteins by using antigen-specific B lymphocytes.

Memory lymphocytes are important mediators of the immune response. These cells are long-lived and undergo clonal expansion upon reexposure to specific antigen, differentiating into effector cells that secrete Ig or cytokines while maintaining a residual pool of memory T and B lymphocytes. Here, the ability of antigen-specific lymphocytes to undergo repeated cycles of antigen-driven clonal expansion and contraction is exploited in a therapeutic protocol aimed at regulating protein delivery. The principle of this strategy is to introduce genes encoding proteins of therapeutic interest into a small number of antigen-specific B lymphocytes. Output of therapeutic protein can then be regulated in vivo by manipulating the size of the responder population by antigen challenge. To evaluate whether such an approach is feasible, we developed a mouse model system in which Emu- and Iglambda-based vectors were used to express human erythropoietin (hEPO) gene in B lymphocytes. These mice were then immunized with the model antigen phycoerythrin (PE), and immune splenocytes (or purified PE-specific B lymphocytes) were adoptively transferred to normal or mutant (EPO-deficient) hosts. High levels of hEPO were detected in the serum of adoptively transferred normal mice after PE administration, and this responsiveness was maintained for several months. Similarly, in EPO-deficient anemic recipients, antigen-driven hEPO expression was shown to restore hematocrit levels to normal. These results show that antigen-mediated regulation of memory lymphocytes can be used as a strategy for delivering therapeutic proteins in vivo.

Adoptive Transfer↗
PubMed2004

Heterochromatin structure and function.

Although heterochromatin has long been used as a model for studying chromatin condensation and heritable gene silencing, it is only relatively recently that detailed information has become available on the mechanisms that underlie its structure. Current evidence suggests that these operate on at least three different levels. A regular nucleosome array may facilitate packaging of the chromatin into a highly condensed configuration. Methylation of histone H3 lysine 9 and lysine 27 generates heterochromatin marks that are recognised through binding of heterochromatin proteins such as HP1. Finally, very recent studies using genetic and biochemical approaches have indicated that the RNAi machinery plays an important role in the formation of heterochromatin.

Animals↗
PubMed2003

Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication.

Temporal control of DNA replication has been implicated in epigenetic regulation of gene expression on the basis of observations that certain tissue-specific genes replicate earlier in expressing than non-expressing cells. Here, we show evidence that several leukocyte-specific genes replicate early in lymphocytes regardless of their transcription and also in fibroblasts, where these genes are never normally expressed. Instead, the heritable silencing of some genes (Rag-1, TdT, CD8alpha and lambda5) and their spatial recruitment to heterochromatin domains within the nucleus of lymphocytes resulted in a markedly delayed resolution of sister chromatids into doublet signals discernable by 3D fluorescence in situ hybridization (FISH). Integration of transgenes within heterochromatin (in cis) did, however, confer late replication and this was reversed after variegated transgene expression. These findings emphasise that chromosomal location is important for defining the replication timing of genes and show that retarded sister-chromatid resolution is a novel feature of inactive chromatin.

Animals↗
PubMed2002

Unravelling heterochromatin: competition between positive and negative factors regulates accessibility.

Heterochromatin mediates many diverse functions in the cell nucleus, including centromere function, gene silencing and nuclear organization. The condensed structure of pericentromeric heterochromatin is associated with the presence of a regular arrangement of nucleosomes, which might be due in part to the underlying sequence of the satellite repeats. Recent studies identified methylation of the histone H3 tail as an epigenetic mark that affects acetylation and phosphorylation of histone tail residues and also acts as a recognition signal for binding of heterochromatin protein 1 (HP1). The decision to silence or activate heterochromatic genes appears to be the result of a balance between negative factors that promote the formation of condensed higher-order chromatin structure, and positively acting transcription factors that bind to regulatory sequences and activate gene expression.

Acetylation↗