802 research outputs found
Insulators as mediators of intra- and inter-chromosomal interactions: a common evolutionary theme
Insulator elements mediate intra- and inter-chromosomal interactions. The insulator protein CCCTC-binding factor (CTCF) is important for insulator function in several animals but a report in BMC Molecular Biology shows that Caenorhabditis elegans, yeast and plants lack CTCF. Alternative proteins may have a similar function in these organisms
Visualization of chromatin domains created by the gypsy insulator of Drosophila
Insulators might regulate gene expression by establishing and maintaining the organization of the chromatin fiber within the nucleus. Biochemical fractionation and in situ high salt extraction of lysed cells show that two known protein components of the gypsy insulator are present in the nuclear matrix. Using FISH with DNA probes located between two endogenous Su(Hw) binding sites, we show that the intervening DNA is arranged in a loop, with the two insulators located at the base. Mutations in insulator proteins, subjecting the cells to a brief heat shock, or destruction of the nuclear matrix lead to disruption of the loop. Insertion of an additional gypsy insulator in the center of the loop results in the formation of paired loops through the attachment of the inserted sequences to the nuclear matrix. These results suggest that the gypsy insulator might establish higher-order domains of chromatin structure and regulate nuclear organization by tethering the DNA to the nuclear matrix and creating chromatin loops
YPAR, Critical Whiteness, and Generative Possibilities. A Response to “Sam and Cristina: A Dialogue Between a High School Teacher and Student about the Commoditization of People of Color”
In this response to the article by Tanner and Corrie, the authors provide three critiques of the methodology and theoretical framing of the study with the hopes of informing future scholarship and practice. Specifically, the three critiques addressed in this paper include the integration of CWS frameworks and YPAR methodology, the application and description of CWS and YPAR frameworks, and the role of power in the relationship between educator and student that served as the central medium for the study
The su(Hw) protein bound to gypsy sequences in one chromosome can repress enhancer-promoter interactions in the paired gene located in the other homolog.
Mutant gene phenotypes mediated by a Drosophila melanogaster retrotransposon require sequences homologous to mammalian enhancers.
Architectural proteins, transcription, and the three-dimensional organization of the genome
AbstractArchitectural proteins mediate interactions between distant sequences in the genome. Two well-characterized functions of architectural protein interactions include the tethering of enhancers to promoters and bringing together Polycomb-containing sites to facilitate silencing. The nature of which sequences interact genome-wide appears to be determined by the orientation of the architectural protein binding sites as well as the number and identity of architectural proteins present. Ultimately, long range chromatin interactions result in the formation of loops within the chromatin fiber. In this review, we discuss data suggesting that architectural proteins mediate long range chromatin interactions that both facilitate and hinder neighboring interactions, compartmentalizing the genome into regions of highly interacting chromatin domains
Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators
Long-distance regulatory interactions between enhancers and their target
genes are commonplace in higher eukaryotes. Interposed boundaries or insulators
are able to block these long distance regulatory interactions. The mechanistic
basis for insulator activity and how it relates to enhancer
action-at-a-distance remains unclear. Here we explore the idea that topological
loops could simultaneously account for regulatory interactions of distal
enhancers and the insulating activity of boundary elements. We show that while
loop formation is not in itself sufficient to explain action at a distance,
incorporating transient non-specific and moderate attractive interactions
between the chromatin fibers strongly enhances long-distance regulatory
interactions and is sufficient to generate a euchromatin-like state. Under
these same conditions, the subdivision of the loop into two topologically
independent loops by insulators inhibits inter-domain interactions. The
underlying cause of this effect is a suppression of crossings in the contact
map at intermediate distances. Thus our model simultaneously accounts for
regulatory interactions at a distance and the insulator activity of boundary
elements. This unified model of the regulatory roles of chromatin loops makes
several testable predictions that could be confronted with \emph{in vitro}
experiments, as well as genomic chromatin conformation capture and fluorescent
microscopic approaches.Comment: 10 pages, originally submitted to an (undisclosed) journal in May
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Transcript-indexed ATAC-seq for precision immune profiling.
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy
Disminución de los costes energéticos en la empresa: CDM José Garcés y empresas del Servicio de Apoyo a la Creación de Microempresa de CEOE
Se han estudiado y analizado distintas formas de disminuir los costes energĂ©ticos en cuatro empresas del Servicio de Apoyo a la CreaciĂłn de Microempresas de la ConfederaciĂłn Española de Organizaciones Empresariales (CEOE) y en el CDM JosĂ© GarcĂ©s siguiendo los pasos establecidos por la UNE 216501:2009 para una auditorĂa energĂ©tica y la ISO 50001 para gestiĂłn de energĂa. Demostrando que en el cualquier edificio independiente del tamaño o actividad, se pueden reducir los costes energĂ©ticos, valorando la situaciĂłn energĂ©tica a travĂ©s de la auditorĂa energĂ©tica, determinando el flujo de consumo energĂ©tico y causas de ineficiencia para finalmente proponer mejoras en el consumo energĂ©tico. Destacar que una auditorĂa no se entiende sin un estudio de viabilidad que permita al cliente analizar y decidir la conveniencia de las medidas de ahorro que se proponen
Insulators and imprinting from flies to mammals
The nuclear factor CTCF has been shown to be necessary for the maintenance of genetic imprinting at the mammalian H19/Igf2 locus. MacDonald and colleagues now report in BMC Biology that the mechanisms responsible for maintaining the imprinted state in Drosophila may be evolutionarily conserved and that CTCF may also play a critical role in this process
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