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1.
Mol Cell ; 77(3): 571-585.e4, 2020 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-31901448

RESUMO

Сhromatin is critical for genome compaction and gene expression. On a coarse scale, the genome is divided into euchromatin, which harbors the majority of genes and is enriched in active chromatin marks, and heterochromatin, which is gene-poor but repeat-rich. The conserved molecular hallmark of heterochromatin is the H3K9me3 modification, which is associated with gene silencing. We found that in Drosophila, deposition of most of the H3K9me3 mark depends on SUMO and the SUMO ligase Su(var)2-10, which recruits the histone methyltransferase complex SetDB1/Wde. In addition to repressing repeats, H3K9me3 influences expression of both hetero- and euchromatic host genes. High H3K9me3 levels in heterochromatin are required to suppress spurious transcription and ensure proper gene expression. In euchromatin, a set of conserved genes is repressed by Su(var)2-10/SetDB1-induced H3K9 trimethylation, ensuring tissue-specific gene expression. Several components of heterochromatin are themselves repressed by this pathway, providing a negative feedback mechanism to ensure chromatin homeostasis.


Assuntos
Proteínas de Drosophila/metabolismo , Regulação da Expressão Gênica/genética , Proteínas Inibidoras de STAT Ativados/metabolismo , Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/metabolismo , Animais , Proteínas Cromossômicas não Histona/metabolismo , Metilação de DNA/genética , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Eucromatina/metabolismo , Retroalimentação Fisiológica , Expressão Gênica/genética , Inativação Gênica/fisiologia , Heterocromatina/genética , Heterocromatina/metabolismo , Histona-Lisina N-Metiltransferase/genética , Histona-Lisina N-Metiltransferase/metabolismo , Histonas/genética , Histonas/metabolismo , Ligases/genética , Metiltransferases/genética , Proteínas Inibidoras de STAT Ativados/genética , Proteínas Repressoras/metabolismo , Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/genética
2.
Nat Commun ; 10(1): 4872, 2019 10 25.
Artigo em Inglês | MEDLINE | ID: mdl-31653862

RESUMO

It has been hypothesized that individually-rare hidden structural variants (SVs) could account for a significant fraction of variation in complex traits. Here we identified more than 20,000 euchromatic SVs from 14 Drosophila melanogaster genome assemblies, of which ~40% are invisible to high specificity short-read genotyping approaches. SVs are common, with 31.5% of diploid individuals harboring a SV in genes larger than 5kb, and 24% harboring multiple SVs in genes larger than 10kb. SV minor allele frequencies are rarer than amino acid polymorphisms, suggesting that SVs are more deleterious. We show that a number of functionally important genes harbor previously hidden structural variants likely to affect complex phenotypes. Furthermore, SVs are overrepresented in candidate genes associated with quantitative trait loci mapped using the Drosophila Synthetic Population Resource. We conclude that SVs are ubiquitous, frequently constitute a heterogeneous allelic series, and can act as rare alleles of large effect.


Assuntos
Drosophila melanogaster/genética , Eucromatina/genética , Variação Estrutural do Genoma/genética , Locos de Características Quantitativas/genética , Animais , Feminino , Perfilação da Expressão Gênica , Frequência do Gene , Fenótipo
3.
Nucleic Acids Res ; 47(18): e108, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31562528

RESUMO

The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.


Assuntos
Cromossomos/ultraestrutura , DNA/ultraestrutura , Metáfase/genética , Espectrofotometria Infravermelho/métodos , Animais , Núcleo Celular/ultraestrutura , Eucromatina/ultraestrutura , Heterocromatina/ultraestrutura , Humanos , Interfase/genética
4.
Genome Biol ; 20(1): 157, 2019 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-31391082

RESUMO

BACKGROUND: Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS: We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS: H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.


Assuntos
Arabidopsis/genética , Cromatina/química , Histonas/fisiologia , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/metabolismo , Epigênese Genética , Eucromatina/química , Regulação da Expressão Gênica de Plantas , Heterocromatina/química , Histonas/genética , Histonas/metabolismo , Mutação , Nucleossomos
5.
Nat Commun ; 10(1): 2894, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-31263106

RESUMO

The Origin Recognition Complex (ORC) is essential for replication, heterochromatin formation, telomere maintenance and genome stability in eukaryotes. Here we present the structure of the yeast Orc1 BAH domain bound to the nucleosome core particle. Our data reveal that Orc1, unlike its close homolog Sir3 involved in gene silencing, does not appear to discriminate between acetylated and non-acetylated lysine 16, modification states of the histone H4 tail that specify open and closed chromatin respectively. We elucidate the mechanism for this unique feature of Orc1 and hypothesize that its ability to interact with nucleosomes regardless of K16 modification state enables it to perform critical functions in both hetero- and euchromatin. We also show that direct interactions with nucleosomes are essential for Orc1 to maintain the integrity of rDNA borders during meiosis, a process distinct and independent from its known roles in silencing and replication.


Assuntos
Nucleossomos/metabolismo , Complexo de Reconhecimento de Origem/química , Complexo de Reconhecimento de Origem/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Ciclo Celular , Montagem e Desmontagem da Cromatina , Eucromatina/genética , Eucromatina/metabolismo , Heterocromatina/genética , Heterocromatina/metabolismo , Histonas/genética , Histonas/metabolismo , Nucleossomos/genética , Complexo de Reconhecimento de Origem/genética , Ligação Proteica , Domínios Proteicos , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas Reguladoras de Informação Silenciosa de Saccharomyces cerevisiae/genética , Proteínas Reguladoras de Informação Silenciosa de Saccharomyces cerevisiae/metabolismo
6.
Genome Res ; 29(8): 1329-1342, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31201211

RESUMO

Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility at single DNA molecules and thus achieve comprehensive-coverage characterization of the corresponding heterogeneity. MeSMLR-seq offers direct measurements of both nucleosome-occupied and nucleosome-evicted regions on a single DNA molecule, which is challenging for many existing methods. We applied MeSMLR-seq to haploid yeast, where single DNA molecules represent single cells, and thus we could investigate the combinatorics of many (up to 356) nucleosomes at long range in single cells. We illustrated the differential organization principles of nucleosomes surrounding the transcription start site for silent and actively transcribed genes, at the single-cell level and in the long-range scale. The heterogeneous patterns of chromatin status spanning multiple genes were phased. Together with single-cell RNA-seq data, we quantitatively revealed how chromatin accessibility correlated with gene transcription positively in a highly heterogeneous scenario. Moreover, we quantified the openness of promoters and investigated the coupled chromatin changes of adjacent genes at single DNA molecules during transcription reprogramming. In addition, we revealed the coupled changes of chromatin accessibility for two neighboring glucose transporter genes in response to changes in glucose concentration.


Assuntos
Eucromatina/metabolismo , Regulação Fúngica da Expressão Gênica , Histonas/genética , Saccharomyces cerevisiae/genética , Transcrição Genética , Mapeamento Cromossômico , DNA Fúngico/genética , DNA Fúngico/metabolismo , Eucromatina/química , Glucose/metabolismo , Proteínas Facilitadoras de Transporte de Glucose/genética , Proteínas Facilitadoras de Transporte de Glucose/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Histonas/metabolismo , Metiltransferases/química , Proteínas de Transporte de Monossacarídeos/genética , Proteínas de Transporte de Monossacarídeos/metabolismo , Nucleossomos/química , Nucleossomos/metabolismo , Regiões Promotoras Genéticas , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Análise de Célula Única/métodos , Sítio de Iniciação de Transcrição
7.
Nature ; 570(7761): 395-399, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31168090

RESUMO

The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic and inactive heterochromatic regions of the genome1,2. In conventional nuclei, microscopy shows that euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery1,2. Genome-wide chromosome conformation capture (Hi-C) analyses show this segregation as a plaid pattern of contact enrichment within euchromatin and heterochromatin compartments3, and depletion between them. Many mechanisms for the formation of compartments have been proposed, such as attraction of heterochromatin to the nuclear lamina2,4, preferential attraction of similar chromatin to each other1,4-12, higher levels of chromatin mobility in active chromatin13-15 and transcription-related clustering of euchromatin16,17. However, these hypotheses have remained inconclusive, owing to the difficulty of disentangling intra-chromatin and chromatin-lamina interactions in conventional nuclei18. The marked reorganization of interphase chromosomes in the inverted nuclei of rods in nocturnal mammals19,20 provides an opportunity to elucidate the mechanisms that underlie spatial compartmentalization. Here we combine Hi-C analysis of inverted rod nuclei with microscopy and polymer simulations. We find that attractions between heterochromatic regions are crucial for establishing both compartmentalization and the concentric shells of pericentromeric heterochromatin, facultative heterochromatin and euchromatin in the inverted nucleus. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. In addition, our models allow us to rule out mechanisms of compartmentalization that involve strong euchromatin interactions. Together, our experiments and modelling suggest that attractions between heterochromatic regions are essential for the phase separation of the active and inactive genome in inverted and conventional nuclei, whereas interactions of the chromatin with the lamina are necessary to build the conventional architecture from these segregated phases.


Assuntos
Compartimento Celular , Núcleo Celular/metabolismo , Heterocromatina/metabolismo , Animais , Compartimento Celular/genética , Núcleo Celular/genética , Eucromatina/genética , Eucromatina/metabolismo , Heterocromatina/genética , Camundongos , Modelos Biológicos , Lâmina Nuclear/genética , Lâmina Nuclear/metabolismo , Fatores de Tempo
8.
Nat Commun ; 10(1): 2063, 2019 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-31048693

RESUMO

RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bind motifs located in active chromatin states that are depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, we show that REF6 preferentially bind to hypo-methylated CTCTGYTY motifs in vivo, and that CHG methylation decreases REF6 DNA binding affinity in vitro. In addition, crystal structures of ZnF-clusters in complex with DNA oligonucleotides reveal that 5-methylcytosine is unfavorable for REF6 binding. In drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, in which non-CG methylation is significantly reduced, REF6 can ectopically bind a small number of new target loci, most of which are located in or neighbored with short TEs in euchromatic regions. Collectively, our findings reveal that DNA methylation, likely acting in combination with other epigenetic modifications, may partially explain why REF6 binding is depleted in heterochromatic loci.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiologia , Metilação de DNA/fisiologia , Histonas/metabolismo , Histona Desmetilases com o Domínio Jumonji/metabolismo , Fatores de Transcrição/metabolismo , 5-Metilcitosina/metabolismo , Epigênese Genética/fisiologia , Eucromatina/metabolismo , Heterocromatina/metabolismo , Mutação , Plantas Geneticamente Modificadas , Dedos de Zinco/fisiologia
9.
Nature ; 569(7758): 734-739, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31118512

RESUMO

The execution of developmental programs of gene expression requires an accurate partitioning of the genome into subnuclear compartments, with active euchromatin enriched centrally and silent heterochromatin at the nuclear periphery1. The existence of degenerative diseases linked to lamin A mutations suggests that perinuclear binding of chromatin contributes to cell-type integrity2,3. The methylation of lysine 9 of histone H3 (H3K9me) characterizes heterochromatin and mediates both transcriptional repression and chromatin anchoring at the inner nuclear membrane4. In Caenorhabditis elegans embryos, chromodomain protein CEC-4 bound to the inner nuclear membrane tethers heterochromatin through H3K9me3,5, whereas in differentiated tissues, a second heterochromatin-sequestering pathway is induced. Here we use an RNA interference screen in the cec-4 background and identify MRG-1 as a broadly expressed factor that is necessary for this second chromatin anchor in intestinal cells. However, MRG-1 is exclusively bound to euchromatin, suggesting that it acts indirectly. Heterochromatin detachment in double mrg-1; cec-4 mutants is rescued by depleting the histone acetyltransferase CBP-1/p300 or the transcription factor ATF-8, a member of the bZIP family (which is known to recruit CBP/p300). Overexpression of CBP-1 in cec-4 mutants is sufficient to delocalize heterochromatin in an ATF-8-dependent manner. CBP-1 and H3K27ac levels increase in heterochromatin upon mrg-1 knockdown, coincident with delocalization. This suggests that the spatial organization of chromatin in C. elegans is regulated both by the direct perinuclear attachment of silent chromatin, and by an active retention of CBP-1/p300 in euchromatin. The two pathways contribute differentially in embryos and larval tissues, with CBP-1 sequestration by MRG-1 having a major role in differentiated cells.


Assuntos
Caenorhabditis elegans/citologia , Caenorhabditis elegans/genética , Cromatina/genética , Cromatina/metabolismo , Heterocromatina/genética , Heterocromatina/metabolismo , Animais , Caenorhabditis elegans/anatomia & histologia , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas Cromossômicas não Histona/deficiência , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , Eucromatina/genética , Eucromatina/metabolismo , Mutação com Ganho de Função , Genes Reporter/genética , Histona Acetiltransferases/deficiência , Histona Acetiltransferases/genética , Histona Acetiltransferases/metabolismo , Histona-Lisina N-Metiltransferase/genética , Histonas/química , Histonas/metabolismo , Intestinos/citologia , Fatores de Transcrição/deficiência , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
10.
Nucleic Acids Res ; 47(10): 5181-5192, 2019 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-30918956

RESUMO

Eukaryotic cells pack their genomic DNA into euchromatin and heterochromatin. Boundaries between these domains have been shown to be set by boundary elements. In Tetrahymena, heterochromatin domains are targeted for deletion from the somatic nuclei through a sophisticated programmed DNA rearrangement mechanism, resulting in the elimination of 34% of the germline genome in ∼10,000 dispersed segments. Here we showed that most of these deletions occur consistently with very limited variations in their boundaries among inbred lines. We identified several potential flanking regulatory sequences, each associated with a subset of deletions, using a genome-wide motif finding approach. These flanking sequences are inverted repeats with the copies located at nearly identical distances from the opposite ends of the deleted regions, suggesting potential roles in boundary determination. By removing and testing two such inverted repeats in vivo, we found that the ability for boundary maintenance of the associated deletion were lost. Furthermore, we analyzed the deletion boundaries in mutants of a known boundary-determining protein, Lia3p and found that the subset of deletions that are affected by LIA3 knockout contained common features of flanking regulatory sequences. This study suggests a common mechanism for setting deletion boundaries by flanking inverted repeats in Tetrahymena thermophila.


Assuntos
DNA de Protozoário/genética , Deleção de Genes , Heterocromatina/química , Proteínas de Protozoários/genética , Tetrahymena thermophila/genética , Motivos de Aminoácidos , Núcleo Celular/metabolismo , DNA de Protozoário/metabolismo , Eucromatina/química , Regulação da Expressão Gênica , Rearranjo Gênico , Genoma de Protozoário , Domínios Proteicos
11.
Postepy Biochem ; 65(1): 9-20, 2019 Mar 22.
Artigo em Polonês | MEDLINE | ID: mdl-30901179

RESUMO

Genomic DNA is highly packaged in eukaryotic cells and occurs in the form of nucleoprotein complex called chromatin. Although high DNA compaction allows to store large amount of genomic information in the cell nuclei, it also restricts the access to DNA regulatory sequences. Therefore, to overcome this issue, chromatin must be subjected to various alterations which are dependent on few interrelated factors: DNA modification, histones variants and modifications, ncRNA, chromatin remodeling complexes and chromatin architecture in nuclei. They allow to multilayer regulation of fragile balance between transcriptionally active euchromatin and inactive heterochromatin. The newest research describe new chromatin elements, e.g. half nucleosomes, bivalent chromatin marker and pointed to few intermediate states between euchromatin and heterochromatin. Variety and remarkable amount of chromatin modifications require existence of multiprotein complexes reading, editing and integrating genomic information. Some of them are able to remodel nucleosomes in order to control access to particular DNA sequence. Due to the complexity of chromatin structure regulation studies describing these mechanisms are fundamental to understanding the eukaryotes life.


Assuntos
Cromatina/química , Cromatina/metabolismo , DNA/química , DNA/metabolismo , Eucromatina/química , Eucromatina/metabolismo , Heterocromatina/química , Heterocromatina/metabolismo , Histonas/química , Histonas/metabolismo , Nucleossomos/química , Nucleossomos/metabolismo
12.
Diagn Cytopathol ; 47(6): 553-563, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30761780

RESUMO

BACKGROUND: Lobular endocervical glandular hyperplasia (LEGH) was first described by Nucci et al. in 1999 and is believed to be a precancerous lesion of minimal deviation adenocarcinoma and gastric-type adenocarcinoma in the uterine cervix. LEGH lesions do not always exhibit apparent cellular and structural atypia, so are difficult to distinguish from normal endocervical cells (EC cells) with cytological examination. Therefore, we often struggle to make a definite diagnosis of LEGH. METHODS: We used microscopy images of cytological specimens that were diagnosed as EC cells and LEGH cells. Signal intensity in whole nuclear area and in heterochromatin and euchromatin regions, euchromatin area ratio, and nuclear morphological features were quantified in each cell nucleus of the cases. Statistical analyses were conducted to determine statistical significance. Finally, we performed linear support vector machine (LSVM) modeling as a discriminant analysis using the quantified features. RESULTS: Signal intensity in whole nuclear area, and heterochromatin and euchromatin regions of EC cell nuclei were higher than that of the LEGH cell nuclei. Morphologically, EC cell nuclei were larger than LEGH cell nuclei, and nuclei of LEGH cells had irregular nuclear respectively membrane structure and an elongated shape. The LSVM accuracy of 10-fold cross validation and leave-one-case-out cross-validation (LOCOCV) using all measured features were 84.7% to 89.3% and 78.6% to 86.0%, respectively. CONCLUSIONS: The LVSM analysis using features extracted from signal intensity and morphological analysis was useful for discrimination of EC cells vs LEGH cells. We therefore believe that this image analysis method could be used for early detection of LEGH.


Assuntos
Eucromatina/química , Heterocromatina/química , Processamento de Imagem Assistida por Computador , Neoplasias do Colo do Útero/diagnóstico , Neoplasias do Colo do Útero/patologia , Núcleo Celular/patologia , Diagnóstico Diferencial , Feminino , Humanos , Hiperplasia , Reprodutibilidade dos Testes
13.
Nucleic Acids Res ; 47(9): e49, 2019 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-30793190

RESUMO

In most cells, transcriptionally inactive heterochromatin is preferentially localized in the nuclear periphery and transcriptionally active euchromatin is localized in the nuclear interior. Different cell types display characteristic chromatin distribution patterns, which change dramatically during cell differentiation, proliferation, senescence and different pathological conditions. Chromatin organization has been extensively studied on a cell population level, but there is a need to understand dynamic reorganization of chromatin at the single cell level, especially in live cells. We have developed a novel image analysis tool that we term Fluorescence Ratiometric Imaging of Chromatin (FRIC) to quantitatively monitor dynamic spatiotemporal distribution of euchromatin and total chromatin in live cells. A vector (pTandemH) assures stoichiometrically constant expression of the histone variants Histone 3.3 and Histone 2B, fused to EGFP and mCherry, respectively. Quantitative ratiometric (H3.3/H2B) imaging displayed a concentrated distribution of heterochromatin in the periphery of U2OS cell nuclei. As proof of concept, peripheral heterochromatin responded to experimental manipulation of histone acetylation. We also found that peripheral heterochromatin depended on the levels of the inner nuclear membrane protein Samp1, suggesting an important role in promoting peripheral heterochromatin. Taken together, FRIC is a powerful and robust new tool to study dynamic chromatin redistribution in live cells.


Assuntos
Cromatina/genética , Proteínas de Membrana/genética , Imagem Molecular/métodos , Proteínas Nucleares/genética , Acetilação , Linhagem Celular , Núcleo Celular/genética , Eucromatina/genética , Heterocromatina/genética , Histonas/genética , Humanos , Membrana Nuclear/genética , Processamento de Proteína Pós-Traducional/genética
14.
Med Phys ; 46(3): 1501-1511, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30689203

RESUMO

PURPOSE: In this work, we present simulated double-strand breaks (DSBs) obtained for two human cell nucleus geometries. The first cell nucleus represents fibroblasts, filled with DNA molecules in different compaction forms: heterochromatin or euchromatin only. The second one represents an endothelial cell nucleus, either filled with heterochromatin only or with a uniform distribution of 48% of heterochromatin and 52% of euchromatin, obtained from measurements carried out at IRSN. Protons and alpha particles of different energies were used as projectiles. Each cell nucleus model includes a multi-scale description of the DNA target from the molecular level to the whole human genome representation. METHODS: The cell nucleus models were generated using an extended version of the DnaFabric software in which a new model of euchromatin was implemented in addition to the existing model of heterochromatin. Thus, each nucleus model contains the complete human genome (a total of 6 Gbp) in the G0/G1 phase of the cycle, filled with a continuous chromatin fiber per chromosome that can take into account the heterochromatin and the euchromatin compaction. These geometries were then exported to a simulation chain using the Monte Carlo toolkit Geant4-DNA to perform computations of the physical, physicochemical, and chemical stages, in order to evaluate the influence of chromatin compaction on DSB induction and the contribution of direct and indirect damage, as well as DSB complexity. RESULTS: More direct damage and less indirect damage were observed in the heterochromatin than in the euchromatin. Nevertheless, no difference in terms of DSB complexity was observed between those formed in the heterochromatin or the euchromatin models. Yields of DSB/Gy/Gbp show an increase when both heterochromatin and euchromatin models are taken into account, compared to when only heterochromatin is considered. CONCLUSIONS: The results presented indicate that the chromatin compaction decreases DNA damage generated by ionizing radiation and thus, DNA compaction should be considered for the simulation of DNA repair and other cellular outcomes.


Assuntos
Núcleo Celular/genética , Quebras de DNA de Cadeia Dupla , Reparo do DNA , Heterocromatina , Método de Monte Carlo , Radiação Ionizante , Núcleo Celular/efeitos da radiação , Relação Dose-Resposta à Radiação , Eucromatina , Células Endoteliais da Veia Umbilical Humana , Humanos
15.
Mol Biol Cell ; 30(7): 820-827, 2019 03 21.
Artigo em Inglês | MEDLINE | ID: mdl-30625026

RESUMO

During cell division, chromatin is compacted into mitotic chromosomes to aid faithful segregation of the genome between two daughter cells. Posttranslational modifications (PTMs) of histones alter compaction of interphase chromatin, but it remains poorly understood how these modifications affect mitotic chromosome stiffness and structure. Using micropipette-based force measurements and epigenetic drugs, we probed the influence of canonical histone PTMs that dictate interphase euchromatin (acetylation) and heterochromatin (methylation) on mitotic chromosome stiffness. By measuring chromosome doubling force (the force required to double chromosome length), we find that histone methylation, but not acetylation, contributes to mitotic structure and stiffness. We discuss our findings in the context of chromatin gel modeling of the large-scale organization of mitotic chromosomes.


Assuntos
Cromatina/fisiologia , Cromossomos/fisiologia , Histonas/fisiologia , Acetilação , Animais , Fenômenos Biomecânicos/fisiologia , Cromatina/isolamento & purificação , Montagem e Desmontagem da Cromatina/fisiologia , Epigênese Genética , Eucromatina/química , Heterocromatina/química , Histonas/metabolismo , Humanos , Metilação , Mitose/fisiologia , Fosforilação , Processamento de Proteína Pós-Traducional/fisiologia
16.
Cell ; 176(3): 663-675.e19, 2019 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-30661756

RESUMO

In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.


Assuntos
Frequência do Gene/genética , Genoma Humano/genética , Variação Estrutural do Genoma/genética , Alelos , Eucromatina/genética , Genômica/métodos , Humanos , Repetições Minissatélites/genética , Análise de Sequência de DNA/métodos
17.
Gastroenterology ; 156(6): 1834-1848, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30689973

RESUMO

BACKGROUND & AIMS: Little is known about mechanisms that underlie postnatal hepatocyte maturation and fibrosis at the chromatin level. We investigated the transcription of genes involved in maturation and fibrosis in postnatal hepatocytes of mice, focusing on the chromatin compaction the roles of the Polycomb repressive complex 2 histone methyltransferases EZH1 and EZH2. METHODS: Hepatocytes were isolated from mixed background C57BL/6J-C3H mice, as well as mice with liver-specific disruption of Ezh1 and/or Ezh2, at postnatal day 14 and 2 months after birth. Liver tissues were collected and analyzed by RNA sequencing, H3K27me3 chromatin immunoprecipitation sequencing, and sonication-resistant heterochromatin sequencing (a method to map heterochromatin and euchromatin). Liver damage was characterized by histologic analysis. RESULTS: We found more than 3000 genes differentially expressed in hepatocytes during liver maturation from postnatal day 14 to month 2 after birth. Disruption of Ezh1 and Ezh2 in livers caused perinatal hepatocytes to differentiate prematurely and to express genes at postnatal day 14 that would normally be induced by month 2 and differentiate prematurely. Loss of Ezh1 and Ezh2 also resulted in liver fibrosis. Genes with H3K27me3-postive and H3K4me3-positive euchromatic promoters were prematurely induced in hepatocytes with loss of Ezh1 and Ezh2-these genes included those that regulate hepatocyte maturation, fibrosis, and genes not specifically associated with the liver lineage. CONCLUSIONS: The Polycomb repressive complex 2 proteins EZH1 and EZH2 regulate genes that control hepatocyte maturation and fibrogenesis and genes not specifically associated with the liver lineage by acting at euchromatic promoter regions. EZH1 and EZH2 thereby promote liver homeostasis and prevent liver damage. Strategies to manipulate Polycomb proteins might be used to improve hepatocyte derivation protocols or developed for treatment of patients with liver fibrosis.


Assuntos
Diferenciação Celular/genética , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Repressão Epigenética , Regulação da Expressão Gênica/genética , Cirrose Hepática/genética , Complexo Repressor Polycomb 2/genética , Animais , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , Eucromatina , Feminino , Expressão Gênica , Ontologia Genética , Hepatócitos , Histonas/metabolismo , Cirrose Hepática/patologia , Masculino , Metilação , Camundongos , Complexo Repressor Polycomb 2/metabolismo , Regiões Promotoras Genéticas , Fatores de Tempo
18.
Nucleic Acids Res ; 47(2): 700-715, 2019 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-30476274

RESUMO

Mammalian-wide interspersed repeats (MIRs) are retrotransposed elements of mammalian genomes. Here, we report the specific binding of zinc finger protein ZNF768 to the sequence motif GCTGTGTG (N20) CCTCTCTG in the core region of MIRs. ZNF768 binding is preferentially associated with euchromatin and promoter regions of genes. Binding was observed for genes expressed in a cell type-specific manner in human B cell line Raji and osteosarcoma U2OS cells. Mass spectrometric analysis revealed binding of ZNF768 to Elongator components Elp1, Elp2 and Elp3 and other nuclear factors. The N-terminus of ZNF768 contains a heptad repeat array structurally related to the C-terminal domain (CTD) of RNA polymerase II. This array evolved in placental animals but not marsupials and monotreme species, displays species-specific length variations, and possibly fulfills CTD related functions in gene regulation. We propose that the evolution of MIRs and ZNF768 has extended the repertoire of gene regulatory mechanisms in mammals and that ZNF768 binding is associated with cell type-specific gene expression.


Assuntos
Retroelementos , Fatores de Transcrição/metabolismo , Transcrição Genética , Sítios de Ligação , Linhagem Celular Tumoral , Sobrevivência Celular , DNA/química , DNA/metabolismo , Eucromatina/metabolismo , Regulação da Expressão Gênica , Humanos , Motivos de Nucleotídeos , Sequências Repetitivas de Ácido Nucleico , Fatores de Transcrição/química
19.
PLoS Comput Biol ; 14(12): e1006617, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30507936

RESUMO

We investigate spatiotemporal dynamics of human interphase chromosomes by employing a heteropolymer model that incorporates the information of human chromosomes inferred from Hi-C data. Despite considerable heterogeneities in the chromosome structures generated from our model, chromatins are organized into crumpled globules with space-filling (SF) statistics characterized by a single universal scaling exponent (ν = 1/3), and this exponent alone can offer a quantitative account of experimentally observed, many different features of chromosome dynamics. The local chromosome structures, whose scale corresponds to that of topologically associated domains (∼ 0.1 - 1 Mb), display dynamics with a fast relaxation time (≲ 1 - 10 sec); in contrast, the long-range spatial reorganization of the entire chromatin ([Formula: see text] Mb) occurs on a much slower time scale (≳ hour), providing the dynamic basis of cell-to-cell variability and glass-like behavior of chromosomes. Biological activities, modeled using stronger isotropic white noises added to active loci, accelerate the relaxation dynamics of chromatin domains associated with the low frequency modes and induce phase segregation between the active and inactive loci. Surprisingly, however, they do not significantly change the dynamics at local scales from those obtained under passive conditions. Our study underscores the role of chain organization of chromosome in determining the spatiotemporal dynamics of chromatin loci.


Assuntos
Cromatina/química , Cromatina/genética , Cromossomos Humanos/química , Cromossomos Humanos/genética , Interfase/genética , Modelos Genéticos , Algoritmos , Cromossomos Humanos Par 10/química , Cromossomos Humanos Par 10/genética , Biologia Computacional , Simulação por Computador , Eucromatina/química , Eucromatina/genética , Heterocromatina/química , Heterocromatina/genética , Humanos , Linfócitos/química , Conformação Molecular
20.
Proc Natl Acad Sci U S A ; 115(50): 12739-12744, 2018 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-30478042

RESUMO

We use a chromosome-scale simulation to show that the preferential binding of heterochromatin protein 1 (HP1) to regions high in histone methylation (specifically H3K9me3) results in phase segregation and reproduces features of the observed Hi-C contact map. Specifically, we perform Monte Carlo simulations with one computational bead per nucleosome and an H3K9me3 pattern based on published ChIP-seq signals. We implement a binding model in which HP1 preferentially binds to trimethylated histone tails and then oligomerizes to bridge together nucleosomes. We observe a phase reminiscent of heterochromatin-dense and high in H3K9me3-and another reminiscent of euchromatin-less dense and lacking H3K9me3. This segregation results in a plaid contact probability map that matches the general shape and position of published Hi-C data. Analysis suggests that a roughly 20-kb segment of H3K9me3 enrichment is required to drive segregation into the heterochromatic phase.


Assuntos
Cromatina/genética , Segregação de Cromossomos/genética , Epigênese Genética/genética , Proteínas Cromossômicas não Histona/genética , Eucromatina/genética , Heterocromatina/genética , Histonas/genética , Humanos , Método de Monte Carlo , Nucleossomos/genética , Probabilidade
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