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1.
Int J Mol Sci ; 22(18)2021 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-34575948

RESUMO

Chromatin conformation plays an important role in a variety of genomic processes, including genome replication, gene expression, and gene methylation. Hi-C data is frequently used to analyze structural features of chromatin, such as AB compartments, topologically associated domains, and 3D structural models. Recently, the genomics community has displayed growing interest in chromatin dynamics. Here, we present 4DMax, a novel method, which uses time-series Hi-C data to predict dynamic chromosome conformation. Using both synthetic data and real time-series Hi-C data from processes, such as induced pluripotent stem cell reprogramming and cardiomyocyte differentiation, we construct smooth four-dimensional models of individual chromosomes. These predicted 4D models effectively interpolate chromatin position across time, permitting prediction of unknown Hi-C contact maps at intermittent time points. Furthermore, 4DMax correctly recovers higher order features of chromatin, such as AB compartments and topologically associated domains, even at time points where Hi-C data is not made available to the algorithm. Contact map predictions made using 4DMax outperform naïve numerical interpolation in 87.7% of predictions on the induced pluripotent stem cell dataset. A/B compartment profiles derived from 4DMax interpolation showed higher similarity to ground truth than at least one profile generated from a neighboring time point in 100% of induced pluripotent stem cell experiments. Use of 4DMax may alleviate the cost of expensive Hi-C experiments by interpolating intermediary time points while also providing valuable visualization of dynamic chromatin changes.


Assuntos
Cromatina/ultraestrutura , Cromossomos/ultraestrutura , Biologia Computacional , Algoritmos , Cromatina/genética , Cromossomos/genética , Genoma/genética , Humanos , Conformação Molecular
3.
Nucleic Acids Res ; 49(15): 8934-8946, 2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34352093

RESUMO

Giardia lamblia is a pathogenic unicellular eukaryotic parasite that causes giardiasis. Its genome encodes the canonical histones H2A, H2B, H3, and H4, which share low amino acid sequence identity with their human orthologues. We determined the structure of the G. lamblia nucleosome core particle (NCP) at 3.6 Å resolution by cryo-electron microscopy. G. lamblia histones form a characteristic NCP, in which the visible 125 base-pair region of the DNA is wrapped in a left-handed supercoil. The acidic patch on the G. lamblia octamer is deeper, due to an insertion extending the H2B α1 helix and L1 loop, and thus cannot bind the LANA acidic patch binding peptide. The DNA and histone regions near the DNA entry-exit sites could not be assigned, suggesting that these regions are asymmetrically flexible in the G. lamblia NCP. Characterization by thermal unfolding in solution revealed that both the H2A-H2B and DNA association with the G. lamblia H3-H4 were weaker than those for human H3-H4. These results demonstrate the uniformity of the histone octamer as the organizing platform for eukaryotic chromatin, but also illustrate the unrecognized capability for large scale sequence variations that enable the adaptability of histone octamer surfaces and confer internal stability.


Assuntos
Microscopia Crioeletrônica , Giardia lamblia/ultraestrutura , Histonas/genética , Nucleossomos/ultraestrutura , Sequência de Aminoácidos/genética , Cromatina/genética , Cromatina/ultraestrutura , Giardia lamblia/genética , Histonas/ultraestrutura , Humanos , Estrutura Molecular , Nucleossomos/genética
4.
Cells ; 10(7)2021 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-34359832

RESUMO

Primary cilia biogenesis has been closely associated with cell cycle progression. Cilia assemble when cells exit the cell cycle and enter a quiescent stage at the post-mitosis phase, and disassemble before cells re-enter a new cell cycle. Studies have focused on how the cell cycle coordinates with the cilia assembly/disassembly process, and whether and how cilia biogenesis affects the cell cycle. Appropriate regulation of the functions and/or expressions of ciliary and cell-cycle-associated proteins is pivotal to maintaining bodily homeostasis. Epigenetic mechanisms, including DNA methylation and histone/chromatin modifications, are involved in the regulation of cell cycle progression and cilia biogenesis. In this review, first, we discuss how epigenetic mechanisms regulate cell cycle progression and cilia biogenesis through the regulation of DNA methylation and chromatin structures, to either promote or repress the transcription of genes associated with those processes and the modification of cytoskeleton network, including microtubule and actin. Next, we discuss the crosstalk between the cell cycle and ciliogenesis, and the involvement of epigenetic regulators in this process. In addition, we discuss cilia-dependent signaling pathways in cell cycle regulation. Understanding the mechanisms of how epigenetic regulators contribute to abnormal cell cycle regulation and ciliogenesis defects would lead to developing therapeutic strategies for the treatment of a wide variety of diseases, such as cancers, polycystic kidney disease (PKD), and other ciliopathy-associated disorders.


Assuntos
Pontos de Checagem do Ciclo Celular/genética , Cílios/metabolismo , Ciliopatias/genética , Epigênese Genética , Neoplasias/genética , Doenças Renais Policísticas/genética , Processamento de Proteína Pós-Traducional , Actinas/genética , Actinas/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Cromatina/metabolismo , Cromatina/ultraestrutura , Cílios/ultraestrutura , Ciliopatias/metabolismo , Ciliopatias/patologia , Citoesqueleto/metabolismo , Citoesqueleto/ultraestrutura , Metilação de DNA , Histonas/genética , Histonas/metabolismo , Humanos , Microtúbulos/metabolismo , Microtúbulos/ultraestrutura , Neoplasias/metabolismo , Neoplasias/patologia , Doenças Renais Policísticas/metabolismo , Doenças Renais Policísticas/patologia , Transdução de Sinais , Pesquisa Médica Translacional
5.
Science ; 372(6549)2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34324427

RESUMO

The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.


Assuntos
Repetições de Dinucleotídeos , Proteína 2 de Ligação a Metil-CpG/metabolismo , Repetições de Microssatélites , Nucleossomos/metabolismo , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/química , 5-Metilcitosina/metabolismo , Animais , Células Cultivadas , Cromatina/química , Cromatina/metabolismo , Cromatina/ultraestrutura , Citosina/química , Citosina/metabolismo , Metilação de DNA , Células-Tronco Embrionárias/metabolismo , Fibroblastos , Lobo Frontal/metabolismo , Proteína 2 de Ligação a Metil-CpG/química , Proteína 2 de Ligação a Metil-CpG/genética , Camundongos , Neurônios/metabolismo , Conformação de Ácido Nucleico , Oxirredução , Ligação Proteica , Domínios Proteicos , Síndrome de Rett/genética , Síndrome de Rett/metabolismo , Transcrição Genética
6.
Nucleic Acids Res ; 49(14): 8007-8023, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34233004

RESUMO

The 'open' and 'compact' regions of chromatin are considered to be regions of active and silent transcription, respectively. However, individual genes produce transcripts at different levels, suggesting that transcription output does not depend on the simple open-compact conversion of chromatin, but on structural variations in chromatin itself, which so far have remained elusive. In this study, weakly crosslinked chromatin was subjected to sedimentation velocity centrifugation, which fractionated the chromatin according to its degree of compaction. Open chromatin remained in upper fractions, while compact chromatin sedimented to lower fractions depending on the level of nucleosome assembly. Although nucleosomes were evenly detected in all fractions, histone H1 was more highly enriched in the lower fractions. H1 was found to self-associate and crosslinked to histone H3, suggesting that H1 bound to H3 interacts with another H1 in an adjacent nucleosome to form compact chromatin. Genome-wide analyses revealed that nearly the entire genome consists of compact chromatin without differences in compaction between repeat and non-repeat sequences; however, active transcription start sites (TSSs) were rarely found in compact chromatin. Considering the inverse correlation between chromatin compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.


Assuntos
Cromatina/ultraestrutura , Nucleossomos/genética , Sítio de Iniciação de Transcrição , Transcrição Genética , Centrifugação , Cromatina/genética , Montagem e Desmontagem da Cromatina/genética , Genoma Humano/genética , Histonas/genética , Humanos , Nucleossomos/ultraestrutura , Ligação Proteica/genética , Fatores de Transcrição/genética
7.
Nucleic Acids Res ; 49(14): 8097-8109, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34320189

RESUMO

During RNA polymerase II (RNA Pol II) transcription, the chromatin structure undergoes dynamic changes, including opening and closing of the nucleosome to enhance transcription elongation and fidelity. These changes are mediated by transcription elongation factors, including Spt6, the FACT complex, and the Set2-Rpd3S HDAC pathway. These factors not only contribute to RNA Pol II elongation, reset the repressive chromatin structures after RNA Pol II has passed, thereby inhibiting aberrant transcription initiation from the internal cryptic promoters within gene bodies. Notably, the internal cryptic promoters of infrequently transcribed genes are sensitive to such chromatin-based regulation but those of hyperactive genes are not. To determine why, the weak core promoters of genes that generate cryptic transcripts in cells lacking transcription elongation factors (e.g. STE11) were replaced with those from more active genes. Interestingly, as core promoter activity increased, activation of internal cryptic promoter dropped. This associated with loss of active histone modifications at the internal cryptic promoter. Moreover, environmental changes and transcription elongation factor mutations that downregulated the core promoters of highly active genes concomitantly increased their cryptic transcription. We therefore propose that the chromatin-based regulation of internal cryptic promoters is mediated by core promoter strength as well as transcription elongation factors.


Assuntos
Cromatina/genética , Chaperonas de Histonas/genética , MAP Quinase Quinase Quinases/genética , Metiltransferases/genética , RNA Polimerase II/genética , Proteínas de Saccharomyces cerevisiae/genética , Fatores de Elongação da Transcrição/genética , Cromatina/ultraestrutura , Proteínas de Ligação a DNA/genética , Regulação Fúngica da Expressão Gênica/genética , Proteínas de Grupo de Alta Mobilidade/genética , Histona Desacetilases/genética , Histonas/genética , Nucleossomos/genética , Nucleossomos/ultraestrutura , Regiões Promotoras Genéticas/genética , Saccharomyces cerevisiae/genética , Transdução de Sinais/genética
8.
Int J Mol Sci ; 22(11)2021 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-34072879

RESUMO

Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis-Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.


Assuntos
Cromatina/ultraestrutura , Cromossomos/ultraestrutura , DNA/genética , Imageamento Tridimensional , Cromatina/genética , Cromossomos/genética , DNA/ultraestrutura , Humanos , Modelos Moleculares
9.
Methods Mol Biol ; 2324: 203-217, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34165717

RESUMO

There is accumulating evidence that pseudogenes can produce functionally relevant lncRNAs in a tightly controlled manner. This class of transcripts has been demonstrated to play an important role in development and disease, by controlling parental gene expression. Classically, pseudogene derived lncRNAs compete with parental transcripts for miRNAs or factors that control parental mRNA metabolisms. Recently, pseudogene lncRNAs were demonstrated to take over the control of classic chromatin modifying enzymes and alter parental gene promoter activity or genome wide gene expression. Here, we discuss a new mechanism of parental gene expression controlled by the mOct4P4 lncRNA, a sense transcript derived from the murine Oct4 pseudogene 4. mOct4P4 lncRNA specifically interacts with the RNA binding protein FUS and the Histone Methyltransferase SUV39H1 to target heterochromatin formation at the parental Oct4 promoter in trans. In addition, we will address key issues for the functional dissection of epigenetic control of parental gene promoters by pseudogene lncRNAs.


Assuntos
Cromatina/metabolismo , Epigênese Genética/genética , Regiões Promotoras Genéticas/genética , Pseudogenes/genética , RNA Longo não Codificante/genética , Alelos , Animais , Sistemas CRISPR-Cas , Proteínas do Capsídeo/metabolismo , Cromatina/genética , Cromatina/ultraestrutura , Imunoprecipitação da Cromatina , Células-Tronco Embrionárias , Regulação da Expressão Gênica , Humanos , Levivirus/genética , Metiltransferases/metabolismo , Camundongos , Fator 3 de Transcrição de Octâmero/genética , RNA Mensageiro/metabolismo , RNA Viral/metabolismo , Proteína FUS de Ligação a RNA/metabolismo , Proteínas Repressoras/metabolismo
10.
Nat Commun ; 12(1): 3968, 2021 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-34172755

RESUMO

Cellular heterogeneity in the human brain obscures the identification of robust cellular regulatory networks, which is necessary to understand the function of non-coding elements and the impact of non-coding genetic variation. Here we integrate genome-wide chromosome conformation data from purified neurons and glia with transcriptomic and enhancer profiles, to characterize the gene regulatory landscape of two major cell classes in the human brain. We then leverage cell-type-specific regulatory landscapes to gain insight into the cellular etiology of several brain disorders. We find that Alzheimer's disease (AD)-associated epigenetic dysregulation is linked to neurons and oligodendrocytes, whereas genetic risk factors for AD highlighted microglia, suggesting that different cell types may contribute to disease risk, via different mechanisms. Moreover, integration of glutamatergic and GABAergic regulatory maps with genetic risk factors for schizophrenia (SCZ) and bipolar disorder (BD) identifies shared (parvalbumin-expressing interneurons) and distinct cellular etiologies (upper layer neurons for BD, and deeper layer projection neurons for SCZ). Collectively, these findings shed new light on cell-type-specific gene regulatory networks in brain disorders.


Assuntos
Doença de Alzheimer/genética , Transtorno Bipolar/genética , Cromatina/ultraestrutura , Esquizofrenia/genética , Acetilação , Doença de Alzheimer/patologia , Transtorno Bipolar/patologia , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , Sequenciamento de Cromatina por Imunoprecipitação , Elementos Facilitadores Genéticos , Epigênese Genética , Neurônios GABAérgicos/metabolismo , Regulação da Expressão Gênica , Estudo de Associação Genômica Ampla , Histonas/metabolismo , Humanos , Lisina/metabolismo , Neuroglia/patologia , Neuroglia/ultraestrutura , Neurônios/patologia , Neurônios/ultraestrutura , Regiões Promotoras Genéticas , Esquizofrenia/patologia
11.
Sci Rep ; 11(1): 13195, 2021 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-34162976

RESUMO

Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson-Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.


Assuntos
Cromatina/ultraestrutura , Desoxirribonucleotídeos/metabolismo , Lamina Tipo A/fisiologia , Lâmina Nuclear/patologia , Progéria/genética , Homeostase do Telômero/genética , Telômero/patologia , Adulto , Animais , Células Cultivadas , Senescência Celular/genética , Dano ao DNA , Replicação do DNA , Fibroblastos , Genes Reporter , Proteínas de Fluorescência Verde , Código das Histonas , Humanos , Recém-Nascido , Lamina Tipo A/análise , Lamina Tipo A/deficiência , Lamina Tipo A/genética , Lamina Tipo B/análise , Camundongos , Camundongos Knockout , Progéria/patologia , Proteínas Recombinantes de Fusão/metabolismo , Pele/patologia
12.
Aging (Albany NY) ; 13(12): 15917-15941, 2021 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-34139671

RESUMO

The G-quadruplex (G4-DNA or G4) is a secondary DNA structure formed by DNA sequences containing multiple runs of guanines. While it is now firmly established that stabilized G4s lead to enhanced genomic instability in cancer cells, whether and how G4s contribute to genomic instability in brain cells is still not clear. We previously showed that, in cultured primary neurons, small-molecule G4 stabilizers promote formation of DNA double-strand breaks (DSBs) and downregulate the Brca1 gene. Here, we determined if G4-dependent Brca1 downregulation is unique to neurons or if the effects in neurons also occur in astrocytes and microglia. We show that primary neurons, astrocytes and microglia basally exhibit different G4 landscapes. Stabilizing G4-DNA with the G4 ligand pyridostatin (PDS) differentially modifies chromatin structure in these cell types. Intriguingly, PDS promotes DNA DSBs in neurons, astrocytes and microglial cells, but fails to downregulate Brca1 in astrocytes and microglia, indicating differences in DNA damage and repair pathways between brain cell types. Taken together, our findings suggest that stabilized G4-DNA contribute to genomic instability in the brain and may represent a novel senescence pathway in brain aging.


Assuntos
Astrócitos/metabolismo , Quadruplex G , Microglia/metabolismo , Neurônios/metabolismo , Aminoquinolinas/farmacologia , Animais , Astrócitos/efeitos dos fármacos , Astrócitos/ultraestrutura , Proteína BRCA1/genética , Proteína BRCA1/metabolismo , Sequência de Bases , Linhagem Celular , Cromatina/efeitos dos fármacos , Cromatina/metabolismo , Cromatina/ultraestrutura , Dano ao DNA , Camundongos , Microglia/efeitos dos fármacos , Microglia/ultraestrutura , Neurônios/efeitos dos fármacos , Neurônios/ultraestrutura , Ácidos Picolínicos/farmacologia , Regiões Promotoras Genéticas/genética , Ratos
13.
Dev Cell ; 56(11): 1562-1573, 2021 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-33984271

RESUMO

Understanding how complex cell-fate decisions emerge at the molecular level is a key challenge in developmental biology. Despite remarkable progress in decoding the contribution of the linear epigenome, how spatial genome architecture functionally informs changes in gene expression remains unclear. In this review, we discuss recent insights in elucidating the molecular landscape of genome folding, emphasizing the multilayered nature of the 3D genome, its importance for gene regulation, and its spatiotemporal dynamics. Finally, we discuss how these new concepts and emergent technologies will enable us to address some of the outstanding questions in development and disease.


Assuntos
Linhagem da Célula/genética , Cromatina/ultraestrutura , Epigenoma/genética , Genoma Humano/genética , Diferenciação Celular/genética , Cromatina/genética , Regulação da Expressão Gênica/genética , Humanos
14.
Nat Struct Mol Biol ; 28(4): 382-387, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33846633

RESUMO

Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA.


Assuntos
Proteínas Cromossômicas não Histona/ultraestrutura , Proteínas de Ligação a DNA/ultraestrutura , Proteínas de Grupo de Alta Mobilidade/ultraestrutura , Proteínas de Saccharomyces cerevisiae/ultraestrutura , Transcrição Genética , Fatores de Elongação da Transcrição/ultraestrutura , Cromatina/genética , Cromatina/ultraestrutura , Montagem e Desmontagem da Cromatina , Proteínas Cromossômicas não Histona/genética , Proteínas de Ligação a DNA/genética , Proteínas de Grupo de Alta Mobilidade/genética , Histonas/genética , Complexos Multiproteicos/genética , Complexos Multiproteicos/ultraestrutura , Nucleossomos/genética , Nucleossomos/ultraestrutura , RNA Polimerase II/genética , RNA Polimerase II/ultraestrutura , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/ultraestrutura , Proteínas de Saccharomyces cerevisiae/genética , Fatores de Elongação da Transcrição/genética
15.
Philos Trans A Math Phys Eng Sci ; 379(2199): 20200298, 2021 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-33896203

RESUMO

Structured Illumination Microscopy (SIM) is a widespread methodology to image live and fixed biological structures smaller than the diffraction limits of conventional optical microscopy. Using recent advances in image up-scaling through deep learning models, we demonstrate a method to reconstruct 3D SIM image stacks with twice the axial resolution attainable through conventional SIM reconstructions. We further demonstrate our method is robust to noise and evaluate it against two-point cases and axial gratings. Finally, we discuss potential adaptions of the method to further improve resolution. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.


Assuntos
Aprendizado Profundo , Microscopia de Fluorescência/métodos , Animais , Cromatina/ultraestrutura , Simulação por Computador , Humanos , Processamento de Imagem Assistida por Computador/métodos , Processamento de Imagem Assistida por Computador/estatística & dados numéricos , Imageamento Tridimensional/métodos , Imageamento Tridimensional/estatística & dados numéricos , Microscopia Confocal/métodos , Microscopia Confocal/estatística & dados numéricos , Microscopia de Fluorescência/estatística & dados numéricos , Fenômenos Ópticos
16.
Int J Mol Sci ; 22(7)2021 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-33807337

RESUMO

In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a "double-edged sword"-it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.


Assuntos
Cromatina/genética , Dano ao DNA/genética , Neoplasias/genética , Linhagem Celular Tumoral , Cromatina/ultraestrutura , Quebras de DNA de Cadeia Dupla/efeitos da radiação , Dano ao DNA/efeitos da radiação , Reparo do DNA/genética , Reparo do DNA/efeitos da radiação , Células HeLa , Humanos , Microscopia/métodos , Radiação Ionizante , Imagem Individual de Molécula/métodos
17.
Brief Bioinform ; 22(5)2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-33751027

RESUMO

DNase I hypersensitive site (DHS) refers to the hypersensitive region of chromatin for the DNase I enzyme. It is an important part of the noncoding region and contains a variety of regulatory elements, such as promoter, enhancer, and transcription factor-binding site, etc. Moreover, the related locus of disease (or trait) are usually enriched in the DHS regions. Therefore, the detection of DHS region is of great significance. In this study, we develop a deep learning-based algorithm to identify whether an unknown sequence region would be potential DHS. The proposed method showed high prediction performance on both training datasets and independent datasets in different cell types and developmental stages, demonstrating that the method has excellent superiority in the identification of DHSs. Furthermore, for the convenience of related wet-experimental researchers, the user-friendly web-server iDHS-Deep was established at http://lin-group.cn/server/iDHS-Deep/, by which users can easily distinguish DHS and non-DHS and obtain the corresponding developmental stage ofDHS.


Assuntos
Arabidopsis/genética , DNA/genética , Aprendizado Profundo , Desoxirribonuclease I/genética , Oryza/genética , Software , Arabidopsis/metabolismo , Cromatina/metabolismo , Cromatina/ultraestrutura , DNA/química , DNA/metabolismo , Conjuntos de Dados como Assunto , Desoxirribonuclease I/metabolismo , Elementos Facilitadores Genéticos , Loci Gênicos , Humanos , Internet , Oryza/metabolismo , Regiões Promotoras Genéticas , Ligação Proteica , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcrição Genética
18.
Brief Bioinform ; 22(5)2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-33783485

RESUMO

Tumor suppressor genes (TSGs) exhibit distinct evolutionary features. We speculated that TSG promoters could have evolved specific features that facilitate their tumor-suppressing functions. We found that the promoter CpG dinucleotide frequencies of TSGs are significantly higher than that of non-cancer genes across vertebrate genomes, and positively correlated with gene expression across tissue types. The promoter CpG dinucleotide frequencies of all genes gradually increase with gene age, for which young TSGs have been subject to a stronger evolutionary pressure. Transcription-related features, namely chromatin accessibility, methylation and ZNF263-, SP1-, E2F4- and SP2-binding elements, are associated with gene expression. Moreover, higher promoter CpG dinucleotide frequencies and chromatin accessibility are positively associated with the ability of TSGs to resist downregulation during tumorigenesis. These results were successfully validated with independent datasets. In conclusion, TSGs evolved specific promoter features that optimized cancer resistance through achieving high expression in normal tissues and resistance to downregulation during tumorigenesis.


Assuntos
Cromatina/metabolismo , Biologia Computacional/métodos , Resistencia a Medicamentos Antineoplásicos/genética , Evolução Molecular , Genes Supressores de Tumor , Neoplasias/genética , Regiões Promotoras Genéticas , Antineoplásicos/uso terapêutico , Carcinogênese/genética , Carcinogênese/metabolismo , Carcinogênese/patologia , Linhagem Celular Tumoral , Cromatina/ultraestrutura , Ilhas de CpG , Metilação de DNA , Conjuntos de Dados como Assunto , Regulação Neoplásica da Expressão Gênica , Ontologia Genética , Humanos , Anotação de Sequência Molecular , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Neoplasias/patologia , Domínios e Motivos de Interação entre Proteínas , Transcrição Genética
19.
Plant J ; 106(3): 588-600, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33788333

RESUMO

Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.


Assuntos
Cromatina/ultraestrutura , Citrullus/genética , Duplicação Gênica/genética , Regulação da Expressão Gênica de Plantas/genética , Cromatina/genética , Cromatina/metabolismo , Cromossomos de Plantas/genética , Cromossomos de Plantas/metabolismo , Cromossomos de Plantas/ultraestrutura , Citrullus/metabolismo , Epigenoma/genética , Estudos de Associação Genética , Genoma de Planta/genética , Poliploidia , Tetraploidia
20.
Brief Bioinform ; 22(5)2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-33634313

RESUMO

Three-dimensional (3D) architecture of the chromosomes is of crucial importance for transcription regulation and DNA replication. Various high-throughput chromosome conformation capture-based methods have revealed that CTCF-mediated chromatin loops are a major component of 3D architecture. However, CTCF-mediated chromatin loops are cell type specific, and most chromatin interaction capture techniques are time-consuming and labor-intensive, which restricts their usage on a very large number of cell types. Genomic sequence-based computational models are sophisticated enough to capture important features of chromatin architecture and help to identify chromatin loops. In this work, we develop Deep-loop, a convolutional neural network model, to integrate k-tuple nucleotide frequency component, nucleotide pair spectrum encoding, position conservation, position scoring function and natural vector features for the prediction of chromatin loops. By a series of examination based on cross-validation, Deep-loop shows excellent performance in the identification of the chromatin loops from different cell types. The source code of Deep-loop is freely available at the repository https://github.com/linDing-group/Deep-loop.


Assuntos
Fator de Ligação a CCCTC/genética , Cromatina/metabolismo , Genoma Humano , Redes Neurais de Computação , Fator de Ligação a CCCTC/metabolismo , Cromatina/ultraestrutura , Conjuntos de Dados como Assunto , Regulação da Expressão Gênica , Humanos , Células K562 , Células MCF-7 , Conformação Molecular , Motivos de Nucleotídeos , Software
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