191 research outputs found
Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells
Transcription factors, chromatin components and chromatin modification activities are involved in many diseases including cancer. However, the means by which alterations in these factors influence the epigenotype of specific cell types is poorly understood. One problem that limits progress is that regulatory regions of eukaryotic genes sometimes extend over large regions of DNA. To improve chromatin structure–function analysis over such large regions, we have developed an automated, relatively simple procedure that uses magnetic beads and a capillary sequencer for ligation-mediated-PCR (LM-PCR). We show that the procedure can be used for the rapid examination of chromatin fine-structure, nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation
The architecture of chicken chromosome territories changes during differentiation
BACKGROUND:
Between cell divisions the chromatin fiber of each chromosome is restricted to a subvolume of the interphase cell nucleus called chromosome territory. The internal organization of these chromosome territories is still largely unknown.
RESULTS:
We compared the large-scale chromatin structure of chromosome territories between several hematopoietic chicken cell types at various differentiation stages. Chromosome territories were labeled by fluorescence in situ hybridization in structurally preserved nuclei, recorded by confocal microscopy and evaluated visually and by quantitative image analysis. Chromosome territories in multipotent myeloid precursor cells appeared homogeneously stained and compact. The inactive lysozyme gene as well as the centromere of the lysozyme gene harboring chromosome located to the interior of the chromosome territory. In further differentiated cell types such as myeloblasts, macrophages and erythroblasts chromosome territories appeared increasingly diffuse, disaggregating to separable substructures. The lysozyme gene, which is gradually activated during the differentiation to activated macrophages, as well as the centromere were relocated increasingly to more external positions.
CONCLUSIONS:
Our results reveal a cell type specific constitution of chromosome territories. The data suggest that a repositioning of chromosomal loci during differentiation may be a consequence of general changes in chromosome territory morphology, not necessarily related to transcriptional changes
Wellington : a novel method for the accurate identification of digital genomic footprints from DNase-seq data
The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the great challenges in the gene regulation field is to characterise these elements. This involves the identification of transcription factor (TF) binding sites within regulatory elements that are occupied in a defined regulatory context. Digestion with DNase and the subsequent analysis of regions protected from cleavage (DNase footprinting) has for many years been used to identify specific binding sites occupied by TFs at individual cis-elements with high resolution. This methodology has recently been adapted for high-throughput sequencing (DNase-seq). In this study, we describe an imbalance in the DNA strand-specific alignment information of DNase-seq data surrounding protein–DNA interactions that allows accurate prediction of occupied TF binding sites. Our study introduces a novel algorithm, Wellington, which considers the imbalance in this strand-specific information to efficiently identify DNA footprints. This algorithm significantly enhances specificity by reducing the proportion of false positives and requires significantly fewer predictions than previously reported methods to recapitulate an equal amount of ChIP-seq data. We also provide an open-source software package, pyDNase, which implements the Wellington algorithm to interface with DNase-seq data and expedite analyses
The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken
The replacement histone H2A.Z is variously reported
as being linked to gene expression and preventing the
spread of heterochromatin in yeast, or concentrated
at heterochromatin in mammals. To resolve this
apparent dichotomy, affinity-purified antibodies
against the N-terminal region of H2A.Z, in both a triacetylatedandnon-
acetylatedstate, areusedin native
chromatin immmuno-precipitation experiments with
mononucleosomes from three chicken cell types. The
hyperacetylated species concentrates at the 50 end of
active genes, both tissue specific and housekeeping
but is absent from inactive genes, while the
unacetylated form is absent from both active and
inactive genes. A concentration of H2A.Z is also
found at insulators under circumstances implying a
link to barrier activity but not to enhancer blocking.
Although acetylated H2A.Z is widespread throughout
the interphase genome, at mitosis its acetylation is
erased, the unmodified form remaining. Thus,
although H2A.Z may operate as an epigenetic marker
for active genes, its N-terminal acetylation does not
The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken
The replacement histone H2A.Z is variously reported
as being linked to gene expression and preventing the
spread of heterochromatin in yeast, or concentrated
at heterochromatin in mammals. To resolve this
apparent dichotomy, affinity-purified antibodies
against the N-terminal region of H2A.Z, in both a triacetylatedandnon-
acetylatedstate, areusedin native
chromatin immmuno-precipitation experiments with
mononucleosomes from three chicken cell types. The
hyperacetylated species concentrates at the 50 end of
active genes, both tissue specific and housekeeping
but is absent from inactive genes, while the
unacetylated form is absent from both active and
inactive genes. A concentration of H2A.Z is also
found at insulators under circumstances implying a
link to barrier activity but not to enhancer blocking.
Although acetylated H2A.Z is widespread throughout
the interphase genome, at mitosis its acetylation is
erased, the unmodified form remaining. Thus,
although H2A.Z may operate as an epigenetic marker
for active genes, its N-terminal acetylation does not
The chicken lysozyme locus as a paradigm for the complex developmental regulation of eukaryotic gene loci
Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma
Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported in classical Hodgkin Lymphoma (cHL) that a member of the THE1B class of LTR elements acted as a promoter for the proto-oncogene and growth factor receptor gene CSF1R and that expression of this gene is required for cHL tumour survival. However, to which extent and how such elements participate in globally shaping the unique cHL gene expression programme is unknown. To address this question we mapped the genome-wide activation of THE1-LTRs in cHL cells using a targeted next generation sequencing approach (RACE-Seq). Integration of these data with global gene expression data from cHL and control B cell lines showed a unique pattern of LTR activation impacting on gene expression, including genes associated with the cHL phenotype. We also show that global LTR activation is induced by strong inflammatory stimuli. Together these results demonstrate that LTR activation provides an additional layer of gene deregulation in classical Hodgkin lymphoma and highlight the potential impact of genome-wide LTR activation in other inflammatory diseases
RUNX1/ETO blocks selectin-mediated adhesion via epigenetic silencing of PSGL-1
RUNX1/ETO (RE),the t(8;21)-derived leukemic transcription factor associated with acute myeloid leukemia (AML) development, deregulates genes involved in differentiation, self-renewal and proliferation. In addition, these cells show differences in cellular adhesion behavior whose molecular basis is not well understood. Here, we demonstrate that RE epigenetically silences the gene encoding P-Selectin Glycoprotein Ligand-1 (PSGL-1) and downregulates PSGL-1 expression in human CD34+ and murine lin-hematopoietic progenitor cells. Levels of PSGL-1 inversely and dose-dependently correlate with RE oncogene levels. However, a DNA-binding defective mutant fails to downregulate PSGL-1. We show by ChIP experiments that the PSGL-1 promoter is a direct target of RE and binding is accompanied by high levels of the repressive chromatin mark histone H3K27me3. In t(8;21)+ Kasumi-1 cells, PSGL-1 expression is completely restored at both the mRNA and cell surface protein levels following RE downregulation with short hairpin RNA (shRNA) or RE inhibition with tetramerization-blocking peptides, and at the promoter H3K27me3 is replaced by the activating chromatin mark H3K9ac as well as by RNA polymerase II. Upregulation of PSGL-1 restores the binding of cells to P- and E-selectin and re-establishes myeloid-specific cellular adhesion while it fails to bind to lymphocyte-specific L-selectin. Overall, our data suggest that the RE oncoprotein epigenetically represses PSGL-1 via binding to its promoter region and thus affects the adhesive behavior of t(8;21)+ AML cells
Reduction in the resident intestinal myelomonocytic cell population occurs during ApcMin/+ mouse intestinal tumorigenesis
With its significant contribution to cancer mortality globally, advanced colorectal cancer (CRC) requires new treatment strategies. However, despite recent good results for mismatch repair (MMR)‑deficient CRC and other malignancies, such as melanoma, the vast majority of MMR‑proficient CRCs are resistant to checkpoint inhibitor (CKI) therapy. MMR‑proficient CRCs commonly develop from precursor adenomas with enhanced Wnt‑signalling due to adenomatous polyposis coli (APC) mutations. In melanomas with enhanced Wnt signalling due to stabilized β‑catenin, immune anergy and resistance to CKI therapy has been observed, which is dependent on micro‑environmental myelomonocytic (MM) cell depletion in melanoma models. However, MM populations of colorectal adenomas or CRC have not been studied. To characterize resident intestinal MM cell populations during the early stages of tumorigenesis, the present study utilized the ApcMin/+ mouse as a model of MMR‑proficient CRC, using enhanced green fluorescent protein (EGFP) expression in the mouse lysozyme (M‑lys)lys‑EGFP/+ mouse as a pan‑myelomonocytic cell marker and a panel of murine macrophage surface markers. Total intestinal lamina propria mononuclear cell (LPMNC) numbers significantly decreased with age (2.32±1.39x107 [n=4] at 33 days of age vs. 1.06±0.24x107 [n=8] at 109 days of age) during intestinal adenoma development in ApcMin/+ mice (P=0.05; unpaired Student's t‑test), but not in wild‑type littermates (P=0.35). Decreased total LPMNC numbers were associated with atrophy of intestinal lymphoid follicles and the absence of MM/lymphoid cell aggregates in ApcMin/+ mouse intestine, but not spleen, compared with wild‑type mice. Furthermore, during the early stage of intestinal adenoma development, there was a two‑fold reduction of M‑lys expressing cells (P=0.05) and four‑fold reduction of ER‑HR3 (macrophage sub‑set) expressing cells (P=0.05; two tailed Mann‑Whitney U test) in mice with reduced total intestinal LPMNCs (n=3). Further studies are necessary to determine the relevance of these findings to immune‑surveillance of colorectal adenomas or MMR‑proficient CRC CKI therapy resistance
RUNX1-ETO and RUNX1-EVI1 Differentially Reprogram the Chromatin Landscape in t(8;21) and t(3;21) AML
Acute myeloid leukemia (AML) is a heterogeneous disease caused by mutations in transcriptional regulator genes, but how different mutant regulators shape the chromatin landscape is unclear. Here, we compared the transcriptional networks of two types of AML with chromosomal translocations of the RUNX1 locus that fuse the RUNX1 DNA-binding domain to different regulators, the t(8;21) expressing RUNX1-ETO and the t(3;21) expressing RUNX1-EVI1. Despite containing the same DNA-binding domain, the two fusion proteins display distinct binding patterns, show differences in gene expression and chromatin landscape, and are dependent on different transcription factors. RUNX1-EVI1 directs a stem cell-like transcriptional network reliant on GATA2, whereas that of RUNX1-ETO-expressing cells is more mature and depends on RUNX1. However, both types of AML are dependent on the continuous expression of the fusion proteins. Our data provide a molecular explanation for the differences in clinical prognosis for these types of AML
- …