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PubMed1996

Localization of mouse Rad51 and Lim15 proteins on meiotic chromosomes at late stages of prophase 1.

BACKGROUND: In meiosis, eukaryotic chromosomes show a series of morphological changes, during which chromosomes synapse and recombine. To understand the mechanisms of the morphological changes and recombination of chromosomes, we examined stage-specific localization of the Rad51 and Lim15 proteins on the chromosomes in meiotic prophase 1. These proteins are homologous with the RecA protein and have general properties of searching and pairing of homologous DNA sequences. We used mouse chromosomes whose small sizes allow us to identify the locations of these proteins on the entire structures of the chromosomes. RESULTS: In the leptotene and zygotene stages, the Rad51 protein was present on chromatin loops of mouse testis chromosomes then the protein left the loops. In the pachytene stage, the Rad51 protein was present almost exclusively along the core of the synaptonemal complexes (SC). When the stage proceeded to diplotene, the protein was present in the synaptic regions of chromosomes, in particular, in the chiasma regions. The protein was not present on separated homologous SC cores. On the other hand, the Lim15 protein that was found on chromatin loops in early prophase 1, was present almost exclusively at both ends of the SC cores throughout the late stages of prophase 1. CONCLUSION: The Rad51 and Lim15 proteins are present in chromatin loops when chromosomes form SC. The proteins may promote pairing of homologous DNA sequences that would lead formation of SC. The Rad51 protein in the SC cores may be involved in chiasma formation in late stages. The Lim15 protein, instead, may be involved in recombination in the telomeric region or in cohesion of sister chromatids for segregation.

Adenosine Triphosphatases↗

PubMed1990

Topological DNA target size model.

This study presents a model that explains the difference in radiosensitivity between dividing and resting mammalian non-lymphoid tissue cells (liver, kidney, respiratory tract, muscle cells, neurons), based on the topological organization of DNA. In dividing cells, the target for radiation might be identified in replicon clusters or domains (7 X 10(8)-5.8 X 10(9) Da of DNA), in contrast with resting cells, in which the target could be limited to the size of chromatin loops or replicons (10(7)-10(8) Da). Hence, the target theory, D37(cGy) = 0.58 X 10(12)/weight of DNA in Da, indicates that the D37 dose (low-LET radiation) needed to inactivate 63% of the replicon clusters contained by the genome is around 100-850 cGy, and the D37 doses that could damage 63% of chromatin loops increase to 5800-58,000 cGy, with a value of 10,000 cGy for medium size replicons (5.8 X 10(7) Da). Accordingly, most dividing cells have D37 doses of 35 to 650 cGy, and the D37 values for the interphase death of non-lymphoid resting cells increase to several tens of Gy or more. These data are consistent with the idea that killing of dividing cells is correlated with the inactivation of most replicon clusters (about 720-6000 domains per genome), induced mainly by DNA single-strand breaks (SSBs), associated with double-strand breaks (DSBs); while the death of resting cells occurs when the majority of replicons comprised by the cell nucleus (about 72,000 chromatin loops) are damaged by radiation (SSBs, DSBs), which might prevent the process of transcription.

Cell Division↗

PubMed2004

Persistence length of chromatin determines origin spacing in Xenopus early-embryo DNA replication: quantitative comparisons between theory and experiment.

In Xenopus early embryos, replication origins neither require specific DNA sequences nor is there an efficient S/M checkpoint, even though the whole genome (3 billion bases) is completely duplicated within 10-20 minutes. This leads to the "random-completion problem" of DNA replication in embryos, where one needs to find a mechanism that ensures complete, faithful, timely reproduction of the genome without any sequence dependence of replication origins. We analyze recent DNA replication data in Xenopus laevis egg extracts and find discrepancies with models where replication origins are distributed independently of chromatin structure. Motivated by these discrepancies, we have investigated the role that chromatin looping may play in DNA replication. We find that the loop-size distribution predicted from a wormlike-chain model of chromatin can account for the spatial distribution of replication origins in this system quantitatively. Together with earlier findings of increasing frequency of origin firings, our results can explain the random-completion problem. The agreement between experimental data (molecular combing) and theoretical predictions suggests that the intrinsic stiffness of chromatin loops plays a fundamental biological role in DNA replication in early-embryo Xenopus in regulating the origin spacing.

Animals↗

PubMed2003

Non-random features of loop-size chromatin fragmentation.

Upon isolation of DNA from normal eukaryotic cells by standard methods involving extensive proteolytic treatment, a rather homogeneous population of loop-size, double-stranded DNA fragments is regularly obtained. These DNA molecules can be efficiently end-labeled by the DNA polymerase I Klenow fragment, as well as by a 3'- to -5'-exonuclease-free Klenow enzyme, but not by terminal transferase (TdT) unless the ends have been filled up by Klenow, suggesting that dominantly 5' protruding termini are generated upon fragmentation. The filled-up termini were used for cloning the distal parts of the approximately 50 kb fragments. BLAST analysis of the sequence of several clones allowed us to determine the sequence of the non-cloned side of the breakpoints. Comparison of 25, 600 bp-long breakpoint sequences demonstrated prevalence of repetitive elements. Consensus motives characteristic of the breakpoint sequences have been identified. Several sequences exhibit peculiar computed conformational characteristics, with sharp transition or center of symmetry located exactly at the breakpoint. Our data collectively suggest that chromatin fragmentation involves nucleolytic cleavages at fragile/hypersensitive sites delimiting loop-size fragments in a non-random manner. Interestingly, the sequence characteristics of the breakpoints are reminiscent of certain breakpoint cluster regions frequently subject to gene rearrangements.

Animals↗

PubMed2026

Folding a broken genome: the versatile roles of cohesin in genome maintenance.

Cohesin is a protein complex that shapes 3D genome organization through two distinct mechanisms. First, cohesin tethers replicated chromatids from DNA replication until mitosis. This process, known as sister chromatid cohesion, ensures accurate chromosome segregation and enables high-fidelity DNA repair through homologous recombination between the sister chromatids. Second, cohesin organizes the genome during interphase by dynamically extruding chromatin loops, structures that have key roles in gene regulation. Recent work has shown that, in addition to the well-established repair functions of sister chromatid cohesion, cohesin-mediated chromatin looping is closely linked to the repair of DNA double-strand breaks - one of the most toxic DNA lesions. In this Review, we discuss the central roles of cohesin in maintaining genome stability, with emphasis on the cellular response to DNA double-strand breaks. We review how dynamic loop structures facilitate signalling of repair events and promote long-range chromatin motions that underpin the repair process. Overall, its dual mode of action - cohesion and loop extrusion - positions cohesin as a central regulator of chromatin architecture and genome maintenance.

Cohesins↗

PubMed1999

Intranuclear relocalization of matrix binding sites during T cell activation detected by amplified fluorescence in situ hybridization.

We describe a method for analyzing the nuclear localization of specific DNA sequences, with special emphasis on their binding status to the nuclear matrix, depending on the developmental stage of the cells. This method employs high-resolution fluorescence in situ hybridization procedures. For our studies, it was important to examine the nuclear localization of a particular gene locus. Previously, however, it was not possible to detect a single-copy genomic sequence using a DNA probe less than several kilobases in size. We describe here a signal amplification technique based on tyramide which makes such a task possible. Using this method, we monitored single-copy loci using a short, 509-bp DNA sequence that binds in vivo to the T cell factor SATB1 within T cell nuclei, high-salt-extracted nuclei (histone-depleted nuclei generating "halos" with distended chromatin loops), and the nuclear matrix, before and after T cell activation. We found that these loci were anchored onto the nuclear matrix, creating new bases of chromatin loops, only after T cell activation. This experimental strategy, therefore, enabled us to detect the changes in higher order chromatin structure upon activation and study gene regulation at a new dimension: the loop domain structure. The methods shown here can be widely applied to explore other functions involving chromatin, including recombination and replication.

Binding Sites↗

PubMed2025

FoxP3 forms a head-to-head dimer in vivo and stabilizes its multimerization on adjacent microsatellites.

FoxP3, the master regulator of Tregs, employs two DNA-binding modes to recognize diverse DNA sequences. It multimerizes on long TnG repeats (n = 2-5) to bridge DNA segments and stabilize chromatin loops, and it forms head-to-head (H-H) dimers on inverted repeat forkhead motifs (IR-FKHM) without bridging DNA. Although genomic data confirm its multimeric role, in vivo evidence for H-H dimerization has been elusive. Here, unbiased pull-down sequencing uncovers a range of relaxed motifs that drive H-H dimerization, enabling systematic genome-wide analysis. We demonstrate that FoxP3 binds genomic DNA as both H-H dimers and multimers in Tregs, with H-H binding often seeding and stabilizing multimerization on adjacent TnG repeats-especially on shorter, suboptimal repeats. While multimerization is conserved across FoxP family members, H-H dimerization is unique to FoxP3 orthologs, conferred by its divergent accessory loop. This dual-mode strategy broadens FoxP3's sequence repertoire and enhances its architectural function in chromatin looping.

Journal Article↗

PubMed2003

The insulator binding protein CTCF associates with the nuclear matrix.

Nuclear DNA is organized into chromatin loop domains. At the base of these loops, matrix-associated regions (MARs) of the DNA interact with nuclear matrix proteins. MARs act as structural boundaries within chromatin, and MAR binding proteins may recruit multiprotein complexes that remodel chromatin. The potential tumor suppressor protein CTCF binds to vertebrate insulators and is required for insulator activity. We demonstrate that CTCF is associated with the nuclear matrix and can be cross-linked to DNA by cisplatin, an agent that preferentially cross-links nuclear matrix proteins to DNA in situ. These results suggest that CTCF anchors chromatin to the nuclear matrix, suggesting that there is a functional connection between insulators and the nuclear matrix. We also show that the chromatin-modifying enzymes HDAC1 and HDAC2, which are intrinsic nuclear matrix components and thought to function as corepressors of CTCF, are incapable of associating with CTCF. Hence, the insulator activity of CTCF apparently involves an HDAC-independent association with the nuclear matrix. We propose that CTCF may demarcate nuclear matrix-dependent points of transition in chromatin, thereby forming topologically independent chromatin loops that may support gene silencing.

Amino Acid Sequence↗

PubMed2005

Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

Recent evidence suggests that long-range enhancers and gene promoters are in close proximity, which might reflect the formation of chromatin loops. Here, we examined the mechanism for DNA looping at the beta-globin locus. By using chromosome conformation capture (3C), we show that the hematopoietic transcription factor GATA-1 and its cofactor FOG-1 are required for the physical interaction between the beta-globin locus control region (LCR) and the beta-major globin promoter. Kinetic studies reveal that GATA-1-induced loop formation correlates with the onset of beta-globin transcription and occurs independently of new protein synthesis. GATA-1 occupies the beta-major globin promoter normally in fetal liver erythroblasts from mice lacking the LCR, suggesting that GATA-1 binding to the promoter and LCR are independent events that occur prior to loop formation. Together, these data demonstrate that GATA-1 and FOG-1 are essential anchors for a tissue-specific chromatin loop, providing general insights into long-range enhancer function.

Animals↗

PubMed2003

Structure of human chromosomes studied by atomic force microscopy.

In this work human chromosomes have been treated with RNase and pepsin to remove the layer of cellular material that covers the standard preparations on glass slides. This allows characterization of the topography of chromosomes at nanometer scale in air and in physiological solution by atomic force microscopy. Imaging of the dehydrated structure in air indicates radial arrangement of chromatin loops as the last level of DNA packing. However, imaging in liquid reveals a last level of organization consisting of a hierarchy of bands and coils. Additionally force curves between the tip and the chromosome in liquid are consistent with radial chromatin loops. These results and previous electron microscopy studies are analyzed, and a model is proposed for the chromosome structure in which radial loops and helical coils coexist.

Chromatin↗

PubMedDate not supplied

Nuclear topography of beta-like globin gene cluster in IL-3-stimulated human leukemic K-562 cells.

The beta-like globin genes, Ggamma, Agamma, delta and beta, forming specific clusters on chromosome 11, are transcriptionally regulated by the locus control region (LCR). The members of beta-like globin gene cluster (11p15.4) are variously switched during ontogenetic dependent erythropoiesis; however, changes of globin gene expression can be also observed during erythroid differentiation of bone marrow cells. In our experiments, interleukin-3 (IL-3)-stimulated human leukemic K-562 cells were used as a model system in which nuclear organization and expression of the beta-like globin gene cluster was investigated. In addition, the influence of IL-3 on the arrangement of chromosome 11 territory was analyzed. We observed that the beta-globin gene is not expressed in progenitor (nondifferentiated) K-562 cells, but is, however, activated after IL-3 stimulation of the K-562 population. A similar nuclear location of beta-like globin gene clusters was found in both control and IL-3-treated cells, which indicates that changes in cluster gene expression are accompanied by conserved nuclear topography of the gene cluster studied. On the other hand, the studied type of cell differentiation was characterized by relocation of chromosome 11 and its centromeric regions closer to the nuclear periphery, which seems to be a general feature of many pathways of cellular maturation. The beta-like globin gene cluster was observed on chromatin loops extended away from compact chromosome 11 territories that were more condensed in regions closer to the nuclear membrane. The relocation of chromosome 11 territories towards the nuclear periphery and simultaneous appearance of chromatin loops may explain the conserved nuclear positioning of the gene cluster studied.

Cell Differentiation↗

PubMed1994

Cisplatin induces apoptosis in a human ovarian carcinoma cell line without concomitant internucleosomal degradation of DNA.

After treatment of the human ovarian carcinoma cell line, CH1, with cisplatin, cells detached from the culture dish in a time- and dose-dependent fashion. These cells showed morphological changes indicative of apoptosis. Their DNA had not been degraded into oligonucleosomal fragments, but the DNA had been cut into larger fragments (30 kbp) of a size associated with chromatin loops. We conclude that cisplatin killed these ovarian cells by inducing apoptosis. However, in these cells, apoptosis was not accompanied by internucleosomal degradation of DNA. Our data are consistent with the hypothesis that the introduction of a double-strand break at a specific site in the chromatin loops is an early event in apoptosis. This degradation is accompanied by morphologically observable changes in chromatin structure. Internucleosomal degradation, when it occurs, is a late event.

Apoptosis↗

PubMed1984

A serial section study of nuclear pockets and loops.

A serial section study of nuclear pockets in a lymphoma of the stomach showed that: 1) no tumour cell nucleus was free of pockets; 2) approximately 10 to 50 pockets occur on a nucleus; and 3) the pockets show a focal rather than a diffuse distribution on the nucleus. In most pockets cytoplasmic material is completely sequestrated and no channel of communication remains between the cytoplasm and the contents of the pocket. While most pockets contain cytoplasmic material, a few contain nuclear material. It would appear that these are two distinct and different lesions and that one does not evolve from the other. A serial section study of the so-called 'chromatin loops' shows that they are no more than fortuitous sections through pockets. The idea that 'chromatin loops' are cast off from the nucleus receives no support from our studies.

Cell Nucleus↗

PubMed1988

Elevated expression of c-myc and N-myc produces distinct changes in nuclear fine structure and chromatin organization.

The proto-oncogenes c-myc and N-myc encode nuclear phosphoproteins with unknown function. Here, c-myc or N-myc, or hybrid constructs of the two, were transfected into fibroblastic cells (CV-1) using SV40-based high expression vectors. The cells were studied by indirect immunofluorescence microscopy and transmission electron microscopy to determine the localization of the two myc proteins within the nucleus and their influence on nuclear fine structure and chromatin organization. In c-myc transfected cells the overproduced protein product accumulated in large amorphous globules that displaced the normal chromatin and did not stain for DNA. In N-myc transfected cells condensed chromatin loops were formed. They were attached to the nuclear envelope and by traction in the latter they may have contributed to give the nucleus its irregular shape in these cells. During mitosis the chromatin loops persisted as clearly identifiable entities within the chromosomes, suggesting a rigid conformation that did not allow normal chromosome packaging. These findings suggest that the c-myc and N-myc proteins bind to different structures and may have different functions. Observations on cells transfected with hybrid constructs indicated that both the second and third exon of c-myc were required to yield a product that behaved like the c-myc protein. In contrast, domains encoded by the second exon of N-myc were sufficient to give rise to a product that morphologically behaved like the N-myc protein.

Animals↗

PubMed2006

Meiotic cohesins modulate chromosome compaction during meiotic prophase in fission yeast.

The meiotic cohesin Rec8 is required for the stepwise segregation of chromosomes during the two rounds of meiotic division. By directly measuring chromosome compaction in living cells of the fission yeast Schizosaccharomyces pombe, we found an additional role for the meiotic cohesin in the compaction of chromosomes during meiotic prophase. In the absence of Rec8, chromosomes were decompacted relative to those of wild-type cells. Conversely, loss of the cohesin-associated protein Pds5 resulted in hypercompaction. Although this hypercompaction requires Rec8, binding of Rec8 to chromatin was reduced in the absence of Pds5, indicating that Pds5 promotes chromosome association of Rec8. To explain these observations, we propose that meiotic prophase chromosomes are organized as chromatin loops emanating from a Rec8-containing axis: the absence of Rec8 disrupts the axis, resulting in disorganized chromosomes, whereas reduced Rec8 loading results in a longitudinally compacted axis with fewer attachment points and longer chromatin loops.

Cell Cycle Proteins↗

PubMed1998

Mechanisms of radiation-induced chromatid breaks.

Chromatid breaks are thought to result from DNA double-strand breaks (dsb) but the mechanisms are not yet understood. The early (but still prevailing) 'breakage-first' hypothesis fails to explain the large size of chromatid breaks; many of which are estimated to represent the apparent loss of between 15 and 45 Mbp (up to 30% of an average chromatid). The alternative 'exchange' hypothesis of Revell has potential for explaining the large sizes of deletions, but assumes the interaction of two lesions which therefore predicts a quadratic dependence of chromatid breaks on radiation dose. The exchange hypothesis is not tenable for mammalian cells since chromatid breaks are observed to be induced linearly with dose in both human and rodent cells. An alternative 'signal' model of chromatid breaks is outlined whereby a single dsb, occurring within a large looped chromatin domain, is signalled (possibly by molecules such as DNAPK or ATM protein) and triggers the cell to undergo a recombinational exchange, either within a chromatid or between sister chromatids. If incomplete, such recombinational exchanges would appear as chromatid breaks at metaphase. It is suggested that the large looped chromatin domains could be equivalent to one or more likely several replication 'factories' in which the DNA processing enzymes required for exchange formation would be located.

Animals↗

PubMed1997

Preferential localization of DNA damage induced by depurination and bleomycin in a plasmid containing a scaffold-associated region.

Recent evidence suggests that DNA damage of various origins is not randomly distributed in the genome but appears to be clustered in unidentified hypersensitive regions of the chromatin. A model was proposed that stipulates that unpaired DNA stretches, such as those found in scaffold- (or matrix)-associated regions (SARs) under torsional strain, are candidate regions of hypersensitivity to DNA damage in vivo. In this study, we assessed in vitro the relative susceptibility of supercoiled plasmids containing a SAR or chromatin loop DNA segment to DNA damage induced by acid-catalyzed depurination or FeIII-bleomycin. Single-strand specific S1 nuclease was used in combination with 3'-end-labeling to detect single-strand breaks or gaps, after cleavage of abasic sites or removal of 3'-phosphoglycolates by Escherichia coli endonuclease IV. The optimal conditions of DNA cleavage specificity by S1 nuclease were determined. Using these conditions, the DNA cleavage patterns obtained showed (i) a preferential localization of S1 hypersensitive sites in the SAR DNA as compared with plasmid or chromatin loop DNA and (ii) a strikingly similar localization of DNA damage with the two clastogenic treatments.

Base Composition↗

PubMed1998

Chromosome cores and chromatin at meiotic prophase.

We review the synaptonemal complex, SC, of the synapsed homologous chromosomes at meiotic prophase in insects and mammals in terms of its formation, and the association of specific chromatin elements with the synaptonemal complexes. The focus is: (1) The SC as visualized with a variety of techniques; (2) The nature of the chromatin loops where they are associated with the SCs--the bases of the loops may be instrumental in recombinant events judging from the presence of Rad51 protein and late recombination nodules at the SCs; (3) Differences in DNA content of similarly sized loops; (4) Requirements for chromatin attachment to the chromosome cores, requirements that are apparently lacking in foreign DNA inserts; (5) Regulation of loop size by the position along the chromosome; (6) The structural correlates of recombination at the SCs--these comments are based on studies of SC structure, DNA-core protein associations, fluorescent in situ hybridization to visualize specific DNA segments, and fluorescent immunocytology to visualize the chromosome core proteins.

Animals↗