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Nuclear matrix-associated poly(ADPribosyl)ation system in rat testis chromatin.

The presence of poly(ADPR)polymerase in the third level of rat testis chromatin, i.e., in stripped chromatin loops and nuclear matrix, was assessed using enzymatic assays, activity blots, and Western blots. The distribution and the size of ADPribose polymers associated to proteins of the same nuclear fractions was analyzed after incubation of intact isolated nuclei with [14C]- or [32P]NAD+. Short ADPribose oligomers, not larger than 3 residues, were found to be associated to tightly bound chromosomal proteins, which resisted extraction by 2 M NaCl, whereas longer oligomers (8-13 residues long) were associated to loosely bound chromosomal proteins. The identity of ADPribose-protein conjugates was determined by autoradiographic analysis of nuclear protein extracts. Tightly bound histone-like proteins appear to be ADPribosylated both in stripped chromatin loops and in nuclear matrix.

Animals↗

Deciphering estrogen receptor alpha-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape.

OBJECTIVE: To investigate estrogen receptor gene 1 (ESR1) and estrogen-driven transcription in human endometrial stromal cells. DESIGN: RNA sequencing (RNA-seq) and Cleavage Under Targets and Release Using Nuclease (Cut&Run) were performed on telomerase-immortalized human endometrial stromal cells with Clustered Regularly Interspaced Short Palindromic Repeats-mediated ESR1 activation. Hi-C-based chromatin architecture analysis (H3K27ac HiChIP) was conducted in primary endometrial stromal cells. SUBJECTS: Biopsies from two healthy, reproductive-aged volunteers with regular menstrual cycles and no history of gynecological malignancies. EXPOSURE: The ESR1-activated and control endometrial stromal cells were treated with estradiol (E2) or vehicle. Primary endometrial stromal cells were treated with vehicle or a decidualization cocktail. MAIN OUTCOME MEASURES: Differential gene expression analysis (RNA-seq) identified ligand-independent and -dependent ESR1 activity. Cut&Run profiled ESR1 genomic binding in ESR1-activated cells. H3K27ac HiChIP mapped hormone-induced changes in chromatin looping in primary cells. RESULTS: Among seven tested guide RNAs (gRNA), the ESR1-3 gRNA induced robust ESR1 activation and restored E2 responsiveness. Bulk RNA-seq revealed both ligand-dependent and -independent ESR1 transcriptional programs regulating inflammation, proliferation, and cancer-related pathways. Notably, 72% of differentially expressed genes overlapped with genes active in human endometrial tissue during the proliferative estrogen-dominant phase, supporting their physiological relevance. The Cut&Run-seq identified genome-wide ESR1 binding sites, with most binding sites located at distal regulatory elements. Integration of Cut&Run data with H3K27ac HiChIP chromatin loops linked distal ESR1 binding sites to gene promoters, including genes involved in decidualization (e.g., FOXO1) and endometrial cancer (e.g., ERRFI1, NRIP1, and EPAS1). Functional assays showed that ESR1 promotes cell viability and, in the presence of E2, enhances migration. CONCLUSION: The CRISPR-mediated ESR1 activation restores estrogen responsiveness in endometrial stromal cells. Combined transcriptomic, cistromic, and chromatin architecture analyses reveal ESR1's role in regulating decidualization and inflammation-related gene networks, with relevance to endometrial pathologies including endometrial cancer. This model serves as a powerful tool to study estrogen signaling in endometrial stromal cell biology and related pathologies.

Humans↗

Genome topology analysis and transcriptomics of human osteoclasts reveals enhancer-promoter interactions at loci for bone traits and diseases.

Genome-wide association studies (GWAS) relevant to osteoporosis have identified hundreds of loci; however, understanding how these variants influence the phenotype is complicated because most reside in non-coding DNA sequence that serves as transcriptional enhancers and repressors. To advance knowledge on these regulatory elements in osteoclasts (OCs), we performed Micro-C analysis, which informs on the genome topology of these cells and integrated the results with transcriptome and GWAS data to further define loci linked to BMD. Using blood cells isolated from 4 healthy participants aged 31-61 yr, we cultured OC in vitro and generated a Micro-C chromatin conformation capture dataset. We characterized chromatin loops (CLs) in OC from among more than 69 million chromatin interactions identified in the genome. Of the CL identified in OC, >16 000 were unique compared to precursor cells. When sentinel single nucleotide polymorphisms from osteoporosis and bone-related GWAS and those in linkage disequilibrium at r 2 > 0.6 were mapped to CL for OC, 12 588 of these variants were observed within chromatin contact regions. Notable in differential gene ontology enrichment analyses of the topology data for OC and precursors were pathways regulating pluripotency of stem cells, Wnt signaling, nucleotide-binding oligomerization domain (NOD)-like receptor signaling and chemokine signaling. These data, in combination with other 3D genome architecture and epigenetic data (eg, histone modifications and chromatin accessibility), will be useful in modeling to predict genome-wide, which enhancers regulate which genes in OC. This data will therefore also be informative for resolving GWAS hits. In conclusion, we have generated a high-resolution genome topology dataset for human OC and have used this to identify CLs relevant to studies of the genetics of osteoporosis. This data will serve as a powerful resource to inform future functional studies of OC biology.

BMD↗

MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.

The mammalian genome is organized into large-scale chromosome territories, compartments, domains, and at the smallest scale, chromatin loops and stripes. The newest element is a chromatin jet, a diffused line perpendicular to the main diagonal in the Hi-C contact map, which was reported in quiescent mammalian lymphocytes supporting a two-sided symmetric cohesin loop extrusion model. A similar structure is observed in Repli-HiC data, where relatively thin and straight chromatin fountains indicate coupling of DNA replication forks. However, the precise biological implications of these jet-like structures are unknown due to the limitations in computational methods. We developed MIA-Jet, a multi-scale ridge detection algorithm that can accurately detect jets of variable lengths, widths, and angles. When tested on Hi-C, Repli-HiC, ChIA-PET, ChIA-Drop, and Micro-C data in mouse, human, roundworm, and zebrafish cells, MIA-Jet outperformed existing methods. In human cells, jets were enriched in cohesin loading sites and early replication initiation zones. Applying MIA-Jet to Hi-C data generated from protein-degraded cells revealed that jets are dependent on cohesin but not YY1, and jet signals are strengthened after depleting WAPL. We envision MIA-Jet to be broadly applicable to any 3D genome mapping data, thereby providing new insights into the functional roles of chromatin jets.

3D genome mapping↗

A physical model for the condensation and decondensation of eukaryotic chromosomes.

During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this paper, we propose a scenario for chromatin structural reorganization during mitosis, which bridges all the different scales involved in chromatin architecture, from nucleosomes to chromatin loops. We build a model for chromatin, based on available data, taking into account both physical and topological constraints DNA has to deal with. Our results suggest that the mitotic chromosome condensation/decondensation process is induced by a structural change at the level of the nucleosome itself.

Cell Cycle↗

Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations.

After mitosis, mammalian chromosomes partially decondense to occupy distinct territories in the cell nucleus. Current models propose that territories are separated by an interchromatin domain, rich in soluble nuclear machinery, where only rare interchromosomal interactions can occur via extended chromatin loops. In contrast, recent evidence for chromatin mobility and high frequency of chromosome translocations are consistent with significant levels of chromosome intermingling, with important consequences for genome function and stability. Here we use a novel high-resolution in situ hybridization procedure that preserves chromatin nanostructure to show that chromosome territories intermingle significantly in the nucleus of human cells. The degree of intermingling between specific chromosome pairs in human lymphocytes correlates with the frequency of chromosome translocations in the same cell type, implying that double-strand breaks formed within areas of intermingling are more likely to participate in interchromosomal rearrangements. The presence of transcription factories in regions of intermingling and the effect of transcription impairment on the interactions between chromosomes shows that transcription-dependent interchromosomal associations shape chromosome organization in mammalian cells. These findings suggest that local chromatin conformation and gene transcription influence the extent with which chromosomes interact and affect their overall properties, with direct consequences for cell-type specific genome stability.

Cells, Cultured↗

Cohesin prevents local mixing of condensed euchromatic domains in living human cells.

The human genome is folded into chromatin loops by the cohesin complex, forming functional chromatin domains that underlie transcription and DNA replication/repair. However, how cohesin organizes these domains in living cells, especially in active euchromatin, remains elusive. Here, to address this question, we combined single-nucleosome imaging/tracking and super-resolution three-dimensional structured illumination microscopy with euchromatin-specific labeling of histone variant H3.3. Using this nanoscopic approach, we revealed that euchromatin forms condensed domains that are constrained by cohesin-mediated loops. This organization refines the classical view of euchromatin as largely open, in line with emerging evidence. Transcription machinery appears to be located near the condensed domain surfaces/borders. Cohesin loss increased nucleosome-level fluidity within these domains without altering their overall compaction, leading to local mixing of domains and compromising transcriptional insulation. These findings suggest a physical role of cohesin in maintaining the integrity of condensed euchromatic domains and ensuring proper higher-order regulation of gene expression.

Humans↗

Assembly of chromatin fibers into metaphase chromosomes analyzed by transmission electron microscopy and scanning electron microscopy.

The higher-order assembly of the approximately 30 nm chromatin fibers into the characteristic morphology of HeLa mitotic chromosomes was investigated by electron microscopy. Transmission electron microscopy (TEM) of serial sections was applied to view the distribution of the DNA-histone-nonhistone fibers through the chromatid arms. Scanning electron microscopy (SEM) provided a complementary technique allowing the surface arrangement of the fibers to be observed. The approach with both procedures was to swell the chromosomes slightly, without extracting proteins, so that the densely-packed chromatin fibers were separated. The degree of expansion of the chromosomes was controlled by adjusting the concentration of divalent cations (Mg2+). With TEM, individual fibers could be resolved by decreasing the Mg2+ concentration to 1.0-1.5 mM. The predominant mode of fiber organization was seen to be radial for both longitudinal and transverse sections. Using SEM, surface protuberances with an average diameter of 69 nm became visible after the Mg2+ concentration was reduced to 1.5 mM. The knobby surface appearance was a variable feature, because the average diameter decreased when the divalent cation concentration was further reduced. The surface projections appear to represent the peripheral tips of radial chromatin loops. These TEM and SEM observations support a "radial loop" model for the organization of the chromatin fibers in metaphase chromosomes.

Calcium↗

Exhausted CD8+ T cell fate is programmed by dynamic CTCF-mediated enhancer activation and invariant CTCF-imposed barriers.

Exhausted CD8+ T (TEX) cells undergo extensive genome reorganization during differentiation, yet the drivers of this process remain elusive. Here we show that CTCF programmed CD8+ TEX cell fates through two distinct modes of action. CTCF acquired de novo binding sites and concordantly induced open chromatin in early CD8+ TEX cells responding to chronic viral infection. The dynamic CTCF binding activated enhancers and promoted chromatin looping. Consequently, genetic ablation of CTCF diminished chromatin accessibility and interaction strength, impairing CD8+ TEX cell proliferation, effector function and bioenergetic mobilization. Conversely, invariant CTCF binding acted as essential chromatin barriers, and loss of CTCF disrupted insulation and caused aberrant chromatin self-association and undue RNA polymerase II pausing, leading to excessive activation of exhaustion- and stemness-linked genes. Thus, CTCF balanced CD8+ TEX cell differentiation by gaining dynamic binding to induce cytotoxicity and sustain metabolic fitness, while its invariant binding compartmentalized exhaustion and stemness program genes to prevent their overexuberant activation.

CCCTC-Binding Factor↗

Changes of nucleosome frequency in nucleolar and non-nucleolar chromatin as a function of transcription: an electron microscopic study.

The morphology of nucleolar and non-nucleolar (lampbrush chromosome loops) chromatin was studied in the electron microscope during states of reduced transcriptional activity in amphibian oocytes (Xenopus laevis, Triturus alpestris, T. cristatus). Reduced transcriptional activity was observed in maturing stages of oocyte development and after treatment with an inhibitor, actinomycin D. Strands of nucleolar chromatin appear smooth and thin, and contain only few, if any, nucleosomal particles in the transcribed units. This is true whether they are densely or only sparsely covered with lateral ribonucleoprotein fibrils. This smooth and non-nucleosomal character is also predominant in the interspersed, apparently nontranscribed rDNA spacer regions. During inactivation, however, nucleolar chromatin frequently and progressively assumes a beaded appearance in extended fibril-free--that is, apparently nontranscribed--regions. In either full-grown oocytes or late after drug treatment, most of the nucleolar chromatin is no longer smooth and thin, but rather shows a beaded configuration indistinguishable from inactive non-nucleolar chromatin. In many chromatin strands, transitions of fibril-associated regions of smooth character into beaded regions without lateral fibrils are seen. Similarly, in the non-nucleolar chromatin of the retracting lampbrush chromosome loops, reduced transcriptional activity is correlated with a change from smooth to beaded morphology. Here, however, beaded regions are also commonly found interspersed between the more or less distant bases of the lateral fibrils, the putative transcriptional complexes. In both sorts of chromatin, detergents (in particular Sarkosyl) that remove most of the chromatin proteins including histones from the DNA axis but leave the RNA polymerases of the transcriptional complexes attached were used to discriminate between polymerases and nucleosomal particles. The results suggest that nucleosomes are absent in heavily transcribed chromatin regions but are reformed after inactivation. In contrast to the findings with inactivated nucleolar genes, in lampbrush chromosome loops the beaded nucleosomal configuration appears to be assumed also in regions within transcriptional units that, perhaps temporarily, are not involved in transcription.

Animals↗

Chromatin: a connection between loops and barriers?

A genetic screen for proteins that can block the spread of silenced heterochromatin has identified components of the nuclear pores with potential barrier activity. These results suggest that formation of loops of chromatin anchored to the pore could be one mechanism of barrier function.

Chromatin↗

The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus.

The nucleus is an intricately structured integration of many functional domains whose complex spatial organization is maintained by a nonchromatin scaffolding, the nuclear matrix. We report here a method for preparing the nuclear matrix with improved preservation of ultrastructure. After the removal of soluble proteins, the structures of the nucleus were extensively cross-linked with formaldehyde. Surprisingly, the chromatin could be efficiently removed by DNase I digestion leaving a well preserved nuclear matrix. The nuclear matrix uncovered by this procedure consisted of highly structured fibers, connected to the nuclear lamina and built on an underlying network of branched 10-nm core filaments. The relative ease with which chromatin and the nuclear matrix could be separated despite extensive prior cross-linking suggests that there are few attachment points between the two structures other than the connections at the bases of chromatin loops. This is an important clue for understanding chromatin organization in the nucleus.

Cells, Cultured↗

Assembly of two transgenes in an artificial chromatin domain gives highly coordinated expression in tobacco.

The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli beta-glucuronidase gene and the firefly luciferase gene, driven by different promoters, were placed between copies of the chicken lysozyme A element, a member of the matrix-associated region (MAR) group of chromatin boundary elements, and introduced in tobacco (Nicotiana tabacum). In plants carrying A elements, quantitative enzyme activities and mRNA levels of both genes show high correlations compared to control plants. The A element thus creates an artificial chromatin domain that yields coordinated expression. Surprisingly, enzyme activities correlated poorly with their respective mRNA levels. We hypothesize that this indicates the occurrence of "error pipelines" in data generation: systematic errors of a given analytical method will point in the same direction and cancel out in correlation analysis, resulting in better correlations. In combining different methods of analysis, however, such errors do not cancel out and as a result relevant correlations can be masked. Such error pipelines will have to be taken into account when different types of (e.g., whole-genome) data sets are combined in quantitative analyses.

Chromatin↗

[DNA-containing polygonal structures detected in somatic nuclei of Bursaria ovata during preparation to cryptobiosis].

Supramolecular chromatin organization of the somatic nucleus (macronucleus--Ma) was studied in a free-living unicellular eukaryotic organism, the ciliate Bursaria ovata Beers 1952, at two late successive stages of its encystment (in the state of preparation to cryptobiosis). A modified Miller's method (Sergejeva et al., 1987) and the same technique in combination with high resolution DNA autoradiography were used. In chromatin spread preparations of Ma, not labeled by 3H-thymidine, numerous electron dense structures (rounded, stick-like and polygonal) were revealed, along with rarely occurring typical supramolecular chromatin structures, such as nucleosomic and not nucleosomic threads, nucleomeres, chromomeres, rosette-like looping chromatin, and electron dense chromonemes (Fig. 1). For DNA visualizing in the revealed polygonal structures, the vegetative cells (trophonts) of B. ovata were inoculated into the culture medium, containing 3H-thymidine and food (ciliates Paramecium caudatum). Here, the ciliates passed through 3-4 successive cell division cycles, thus progressively accumulating the radioactive DNA precursor in Ma. After washing the ciliates in 3H-thymidine-free culture medium, the process of their encystment was induced, and Ma were isolated by hand from the ciliates being at two late successive stages of encystment. Isolated Ma were dispersed in the low ionic solutions, as described elsewhere (Sergejeva et al., 1987). The carbon shadowed electron grids, that contained spread Ma preparations, were individually coated with photographic emulsion, according to the loop interference method (Angelier et al., 1976a; Bouteille, 1976). After a 6 month exposure at 4 degrees C, thymidine incorporation was revealed in fibril crowds, rosette-like structures (Fig. 2), and crystal-like plates of different size and morphology (Fig. 3). In all our experiments, non-specific localization of radioactive DNA precursor was not observed. The above data confirm undoubtedly our earlier assumption (Sergejeva et al., 1987; Sergejeva, Bobyleva, 1988) that the Ma chromatin of Bursaria may undergo crystallization during encystment, i.e. in the state of preparation to cryptobiosis. The present data enable us first to suggest that the looping rosette-like chromatin may be transformed into crystal-like structures ("exotic liquid crystal structures") by means of a peculiar loop packing within the limits of an individual resette (Fig. 2-4), these structural transformations taking place without any visible loop destruction. In this paper, we first describe new morphological types of polygonal plates, differing from those earlier reported elsewhere for the Ma of Bursaria (Sergejeva, Bobylova, 1988), and also from the plates earlier described in studies on liquid crystals both in vivo and in vitro (see: Gianonni et al., 1969; Lerman, 1974; Livolant, 1991: Leforestier et al., 1993, 1997, 1999). The technical approaches used in the present work enabled us to obtain, for the first time, a direct evidence of the presence of DNA in the crystallized structures of somatic nuclei of ciliates during their preparation to cryptobiosis, the DNA-containing polygonal structures being highly morphologically diverse. Further studies into the reasons of this diversity are needed.

Adaptation, Physiological↗

The matrix attachment regions (MARs) associated with the Heat Shock Cognate 80 gene ( HSC80) of tomato represent specific regulatory elements.

Matrix Attachment Regions (MARs) flank certain plant genes and appear in certain cases to be necessary for their proper regulation. For example, we previously demonstrated that the MARs and introns from the Heat Shock Cognate 80 gene of tomato (HSC80) are necessary for efficient expression of HSC80-based transgenes. MARs may exert their effect by anchoring the ends of a chromatin loop to the nuclear matrix, thereby establishing an independent chromatin domain. Alternatively, MARs may facilitate interactions between activating complexes and DNA. In the first case, MARs should enhance the expression of most genes, while in the latter case, their action might be gene-specific. We addressed this problem by testing whether the HSC80 MARs affected the regulation of an unrelated transgene. We constructed a chimeric transgene composed of the Arabidopsis ADENINE PHOSPHORIBOSYLTRANSFERASE (APT) promoter fused to the maize gene Lc, which encodes a regulator of anthocyanin synthesis, and compared the expression of Lc in Arabidopsis transparent testa glabra (ttg) mutants (which lack anthocyanin pigments) transformed with transgene constructs incorporating the MARs or control DNA fragments that do not bind to the nuclear matrix. Quantitative RT-PCR analysis was used to compare Lc expression in the different transgenic lines. Whether the APT-Lc transgene was flanked by the HSC80 MARs or a control fragment had no effect on expression, while the use of a different MAR, the ARS1 MAR from yeast, significantly decreased expression (P=0.03). Comparison of single-copy and multicopy T-DNA insertions indicated that neither the HSC80 MARs nor the ARS1 MAR could protect the APT-Lc transgene from the negative effect of the integration of multiple copies. In conclusion, this work supports a model in which different regulatory elements within the HSC80 locus interact with the nuclear matrix to induce transcriptional competence.

Adenine Phosphoribosyltransferase↗

Identification and characterization of nuclear matrix-attachment regions in the human serpin gene cluster at 14q32.1.

Matrix-attachment regions (MARs) are DNA elements that are defined by their abilities to bind to isolated nuclear matrices in vitro. The DNA sequences of different matrix-binding elements vary widely. The locations of some MARs at the ends of chromatin loops suggest that they may represent boundaries of individual chromatin domains. As such, MARs may play important roles in regulating transcription and chromatin structure. As a first step towards assessing the roles of MARs in these processes, we assayed DNA sequences from the human serine protease inhibitor (serpin) gene cluster at 14q32.1 for matrix-binding activity in vitro. This approximately 150 kb region contains the cell-specific genes encoding alpha1-anti-trypsin (alpha1AT) and corticosteroid-binding globulin (CBG), as well as an antitrypsin-related sequence termed ATR. A DNase I-hypersensitive site (DHS) map of the locus has recently been described. We report here that the alpha1AT-ATR-CBG region contains five distinct MARs. There is a strong matrix-binding element approximately 16 kb upstream of alpha1AT; three MARs are between ATR and CBG and one MAR is within the CBG gene itself. These MARs were matrix-associated in all cell types examined. DNA sequencing indicated that the serpin MARs contained predominantly repetitive DNA, although the types of DNA repeats differed among the MARs.

Base Sequence↗

Relationship of the surface structure of metaphase chromosomes to the higher order organization of chromatin fibers.

Scanning electron microscopy (SEM), as well as transmission electron microscopy (TEM), has been utilized to determine how the surface structure of mitotic chromosomes is related to the organization of the 30 nm chromosomal fibers. SEM revealed the surfaces of isolated, HeLa cell chromosomes to possess a knobby substructure with chromosomes prepared for EM in buffers containing 0.5-1.5 mM Mg2+. These projections had substantially greater widths (65-70 nm) than the underlying chromatin fibers. Reducing the Mg ion concentration to 0.05-0.15 mM resulted in the further expansion of the chromosomes, which flattened the chromosomes for SEM so the fibers became the dominant feature of the micrographs. The surface protuberances are interpreted as representing the peripheral tips of radial chromatin loops. The same procedure of slightly expanding chromosomes by decreasing the Mg2+ concentration in resuspension buffer was also utilized in a TEM, serial sectioning study. Longitudinal sections close to the central chromatid axis showed radially oriented fibers within the planes of the sections. This was replaced by a dot pattern when the longitudinal sections grazed the periphery of the chromatid. Transverse sections displayed more clearly the radial orientation of the fibers. A consistent picture emerges from applying SEM and TEM that supports the "radial loop" model for the primary mode of organization of chromatin fibers in metaphase chromosomes.

Chromatids↗

[Changes in chromatin organization during early development and carcinogenesis].

Similar changes in chromatin organization take place during development and carcinogenesis. The size of chromatin loop domains fixed on the nuclear skeleton (matrix) increased from 20 to approximately 200 kbp. These changes are accompanied by an increased size of replicons and altered specificity of loop attachment to the nuclear matrix. During carcinogenesis, inverse changes in the chromatin structure are observed, neoplastic cells are dedifferentiated and return to the initial state. In this review, we consider new experimental data on organization of the DFNA loops and nuclear matrix in embryogenesis and carcinogenesis.

Animals↗