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1.
Nucleic Acids Res ; 52(11): 6234-6252, 2024 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-38647066

RESUMEN

Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit a distinct structure in neurons, characterized by an increase in short-range interactions and a decrease in long-range ones.


Asunto(s)
Cromatina , Genoma Humano , Proteínas del Grupo Polycomb , Humanos , Encéfalo/metabolismo , Encéfalo/citología , Cromatina/metabolismo , Cromatina/genética , Histonas/metabolismo , Histonas/genética , Neuronas/metabolismo , Proteínas del Grupo Polycomb/metabolismo , Proteínas del Grupo Polycomb/genética , Regiones Promotoras Genéticas
2.
Brief Bioinform ; 24(2)2023 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-36759336

RESUMEN

The chromatin interaction assays, particularly Hi-C, enable detailed studies of genome architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mechanisms mediated by epigenetics. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach, HiConfidence, eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not substantially influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and topologically associating domains. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases, that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in histone acetylation pattern affect chromatin organization in Drosophila melanogaster S2 cells. The method is freely available at GitHub: https://github.com/victorykobets/HiConfidence.


Asunto(s)
Drosophila melanogaster , Genoma , Animales , Drosophila melanogaster/genética , Cromatina/genética , Cromosomas , Sesgo
3.
Biochemistry (Mosc) ; 89(3): 441-450, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38648764

RESUMEN

The Siberian frog Rana amurensis has a uniquely high tolerance to hypoxia among amphibians, as it is able to withstand several months underwater with almost no oxygen (0.2 mg/liter) vs. several days for other studied species. Since it was hypothesized that hypoxia actives the antioxidant defense system in hypoxia-tolerant animals, one would expect similar response in R. amurensis. Here, we studied the effect of hypoxia in the Siberian frog based on the transcriptomic data, activities of antioxidant enzyme, and content of low-molecular-weight antioxidants. Exposure to hypoxia upregulated expression of three relevant transcripts (catalase in the brain and two aldo-keto reductases in the liver). The activities of peroxidase in the blood and catalase in the liver were significantly increased, while the activity of glutathione S-transferase in the liver was reduced. The content of low-molecular-weight antioxidants (thiols and ascorbate) in the heart and liver was unaffected. In general, only a few components of the antioxidant defense system were affected by hypoxia, while most remained unchanged. Comparison to other hypoxia-tolerant species suggests species-specific adaptations to hypoxia-related ROS stress.


Asunto(s)
Antioxidantes , Hipoxia , Ranidae , Animales , Antioxidantes/metabolismo , Ranidae/metabolismo , Hipoxia/metabolismo , Hígado/metabolismo , Estrés Oxidativo , Catalasa/metabolismo
4.
Nucleic Acids Res ; 50(6): 3203-3225, 2022 04 08.
Artículo en Inglés | MEDLINE | ID: mdl-35166842

RESUMEN

Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis - in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters' detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.


Asunto(s)
Cromatina , Drosophila , Animales , Diferenciación Celular/genética , Cromatina/genética , Compensación de Dosificación (Genética) , Drosophila/genética , Células Germinativas , Masculino
5.
Genome Res ; 30(5): 776-789, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32424074

RESUMEN

Identification of gene expression traits unique to the human brain sheds light on the molecular mechanisms underlying human evolution. Here, we searched for uniquely human gene expression traits by analyzing 422 brain samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well as 88,047 cell nuclei composing three of these regions. Among 33 regions, cerebral cortex areas, hypothalamus, and cerebellar gray and white matter evolved rapidly in humans. At the cellular level, astrocytes and oligodendrocyte progenitors displayed more differences in the human evolutionary lineage than the neurons. Comparison of the bulk tissue and single-nuclei sequencing revealed that conventional RNA sequencing did not detect up to two-thirds of cell-type-specific evolutionary differences.


Asunto(s)
Encéfalo/metabolismo , Transcriptoma , Animales , Encéfalo/citología , Evolución Molecular , Humanos , Inmunohistoquímica , Macaca/genética , Neuronas/metabolismo , Pan paniscus/genética , Pan troglodytes/genética , RNA-Seq , Análisis de la Célula Individual
6.
Int J Mol Sci ; 22(15)2021 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-34360852

RESUMEN

Fluoxetine is an antidepressant commonly prescribed not only to adults but also to children for the treatment of depression, obsessive-compulsive disorder, and neurodevelopmental disorders. The adverse effects of the long-term treatment reported in some patients, especially in younger individuals, call for a detailed investigation of molecular alterations induced by fluoxetine treatment. Two-year fluoxetine administration to juvenile macaques revealed effects on impulsivity, sleep, social interaction, and peripheral metabolites. Here, we built upon this work by assessing residual effects of fluoxetine administration on the expression of genes and abundance of lipids and polar metabolites in the prelimbic cortex of 10 treated and 11 control macaques representing two monoamine oxidase A (MAOA) genotypes. Analysis of 8871 mRNA transcripts, 3608 lipids, and 1829 polar metabolites revealed substantial alterations of the brain lipid content, including significant abundance changes of 106 lipid features, accompanied by subtle changes in gene expression. Lipid alterations in the drug-treated animals were most evident for polyunsaturated fatty acids (PUFAs). A decrease in PUFAs levels was observed in all quantified lipid classes excluding sphingolipids, which do not usually contain PUFAs, suggesting systemic changes in fatty acid metabolism. Furthermore, the residual effect of the drug on lipid abundances was more pronounced in macaques carrying the MAOA-L genotype, mirroring reported behavioral effects of the treatment. We speculate that a decrease in PUFAs may be associated with adverse effects in depressive patients and could potentially account for the variation in individual response to fluoxetine in young people.


Asunto(s)
Antidepresivos/efectos adversos , Conducta Animal/efectos de los fármacos , Fluoxetina/efectos adversos , Metabolismo de los Lípidos/efectos de los fármacos , Trastornos Mentales/tratamiento farmacológico , Animales , Ácidos Grasos Insaturados/metabolismo , Macaca mulatta , Masculino
7.
BMC Genomics ; 20(1): 399, 2019 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-31117933

RESUMEN

BACKGROUND: The three epidemiologically important Opisthorchiidae liver flukes Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, are believed to harbour similar potencies to provoke hepatobiliary diseases in their definitive hosts, although their populations have substantially different ecogeographical aspects including habitat, preferred hosts, population structure. Lack of O. felineus genomic data is an obstacle to the development of comparative molecular biological approaches necessary to obtain new knowledge about the biology of Opisthorchiidae trematodes, to identify essential pathways linked to parasite-host interaction, to predict genes that contribute to liver fluke pathogenesis and for the effective prevention and control of the disease. RESULTS: Here we present the first draft genome assembly of O. felineus and its gene repertoire accompanied by a comparative analysis with that of O. viverrini and Clonorchis sinensis. We observed both noticeably high heterozygosity of the sequenced individual and substantial genetic diversity in a pooled sample. This indicates that potency of O. felineus population for rapid adaptive response to control and preventive measures of opisthorchiasis is higher than in O. viverrini and C. sinensis. We also have found that all three species are characterized by more intensive involvement of trans-splicing in RNA processing compared to other trematodes. CONCLUSION: All revealed peculiarities of structural organization of genomes are of extreme importance for a proper description of genes and their products in these parasitic species. This should be taken into account both in academic and applied research of epidemiologically important liver flukes. Further comparative genomics studies of liver flukes and non-carcinogenic flatworms allow for generation of well-grounded hypotheses on the mechanisms underlying development of cholangiocarcinoma associated with opisthorchiasis and clonorchiasis as well as species-specific mechanisms of these diseases.


Asunto(s)
Cricetinae/parasitología , Cyprinidae/parasitología , Genoma de los Helmintos , Genómica/métodos , Proteínas del Helminto/genética , Opistorquiasis/epidemiología , Opisthorchis/genética , Secuencia de Aminoácidos , Animales , Clonorquiasis/epidemiología , Clonorquiasis/genética , Clonorquiasis/parasitología , Clonorchis sinensis/genética , Opistorquiasis/genética , Opistorquiasis/parasitología , Homología de Secuencia
8.
J Cell Biochem ; 120(3): 4494-4503, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30260021

RESUMEN

Chromosomes in many organisms, including Drosophila and mammals, are folded into topologically associating domains (TADs). Increasing evidence suggests that TAD folding is hierarchical, wherein subdomains combine to form larger superdomains, instead of a sequence of nonoverlapping domains. Here, we studied the hierarchical structure of TADs in Drosophila. We show that the boundaries of TADs of different hierarchical levels are characterized by the presence of different portions of active chromatin, but do not vary in the binding of architectural proteins, such as CCCTC binding factor or cohesin. The apparent hierarchy of TADs in Drosophila chromosomes is not likely to have functional importance but rather reflects various options of long-range chromatin folding directed by the distribution of active and inactive chromatin segments and may represent population average.


Asunto(s)
Factor de Unión a CCCTC/metabolismo , Cromatina/metabolismo , Cromosomas de Insectos/metabolismo , Proteínas de Drosophila/metabolismo , Animales , Factor de Unión a CCCTC/genética , Cromatina/genética , Cromosomas de Insectos/genética , Proteínas de Drosophila/genética , Drosophila melanogaster
9.
Mol Biol Evol ; 35(8): 1947-1957, 2018 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-29762743

RESUMEN

Lipids are essential structural and functional components of cells. Little is known, however, about the evolution of lipid composition in different tissues. Here, we report a large-scale analysis of the lipidome evolution in six tissues of 32 species representing primates, rodents, and bats. While changes in genes' sequence and expression accumulate proportionally to the phylogenetic distances, <2% of the lipidome evolves this way. Yet, lipids constituting this 2% cluster in specific functions shared among all tissues. Among species, human show the largest amount of species-specific lipidome differences. Many of the uniquely human lipidome features localize in the brain cortex and cluster in specific pathways implicated in cognitive disorders.


Asunto(s)
Evolución Biológica , Metabolismo de los Lípidos , Mamíferos/genética , Mamíferos/metabolismo , Animales , Corteza Cerebral/metabolismo , Humanos , Especificidad de la Especie
10.
Genome Res ; 26(1): 70-84, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-26518482

RESUMEN

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)(+) RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.


Asunto(s)
Cromatina/genética , Drosophila melanogaster/genética , Genoma de los Insectos , Transcripción Genética , Animales , Línea Celular , Ensamble y Desensamble de Cromatina , Mapeo Cromosómico , Simulación por Computador , Modelos Moleculares , Nucleosomas/genética , Nucleosomas/metabolismo , Cromosomas Politénicos/genética , Análisis de Secuencia de ARN
11.
BMC Genet ; 18(Suppl 1): 110, 2017 12 28.
Artículo en Inglés | MEDLINE | ID: mdl-29297395

RESUMEN

BACKGROUND: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. RESULTS: We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts. CONCLUSIONS: Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.


Asunto(s)
Emigración e Inmigración/historia , Etnicidad/genética , Genética de Población , Algoritmos , Asia , ADN , Conjuntos de Datos como Asunto , Europa (Continente) , Femenino , Variación Genética , Técnicas de Genotipaje , Historia del Siglo XV , Historia del Siglo XVI , Historia del Siglo XVII , Historia del Siglo XVIII , Historia del Siglo XIX , Historia del Siglo XX , Historia del Siglo XXI , Historia Antigua , Historia Medieval , Humanos , Masculino , Federación de Rusia
12.
PLoS Genet ; 9(10): e1003856, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24146627

RESUMEN

The U1 small nuclear ribonucleoprotein (snRNP)-specific U1C protein participates in 5' splice site recognition and regulation of pre-mRNA splicing. Based on an RNA-Seq analysis in HeLa cells after U1C knockdown, we found a conserved, intra-U1 snRNP cross-regulation that links U1C and U1-70K expression through alternative splicing and U1 snRNP assembly. To investigate the underlying regulatory mechanism, we combined mutational minigene analysis, in vivo splice-site blocking by antisense morpholinos, and in vitro binding experiments. Alternative splicing of U1-70K pre-mRNA creates the normal (exons 7-8) and a non-productive mRNA isoform, whose balance is determined by U1C protein levels. The non-productive isoform is generated through a U1C-dependent alternative 3' splice site, which requires an adjacent cluster of regulatory 5' splice sites and binding of intact U1 snRNPs. As a result of nonsense-mediated decay (NMD) of the non-productive isoform, U1-70K mRNA and protein levels are down-regulated, and U1C incorporation into the U1 snRNP is impaired. U1-70K/U1C-deficient particles are assembled, shifting the alternative splicing balance back towards productive U1-70K splicing, and restoring assembly of intact U1 snRNPs. Taken together, we established a novel feedback regulation that controls U1-70K/U1C homeostasis and ensures correct U1 snRNP assembly and function.


Asunto(s)
Empalme Alternativo/genética , Precursores del ARN/genética , Empalme del ARN/genética , Ribonucleoproteína Nuclear Pequeña U1/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Sitios de Unión , Análisis Mutacional de ADN , Embrión no Mamífero , Técnicas de Silenciamiento del Gen , Células HeLa , Humanos , Sitios de Empalme de ARN/genética , Empalmosomas/genética , Pez Cebra/genética , Pez Cebra/crecimiento & desarrollo
13.
Int J Mol Sci ; 16(10): 25353-76, 2015 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-26512651

RESUMEN

Quantum chemical methods allow screening and prediction of peptide antioxidant activity on the basis of known experimental data. It can be used to design the selective proteolysis of protein sources in order to obtain products with antioxidant activity. Molecular geometry and electronic descriptors of redox-active amino acids, as well as tyrosine and methionine-containing dipeptides, were studied by Density Functional Theory method. The calculated data was used to reveal several descriptors responsible for the antioxidant capacities of the model compounds based on their experimentally obtained antioxidant capacities against ABTS (2,2'-Azino-bis-(3-ethyl-benzothiazoline-6-sulfonate)) and peroxyl radical. A formula to predict antioxidant activity of peptides was proposed.


Asunto(s)
Antioxidantes/química , Dipéptidos/química , Antioxidantes/farmacología , Dipéptidos/farmacología , Metionina/química , Relación Estructura-Actividad Cuantitativa , Tirosina/química
14.
RNA ; 18(1): 1-15, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-22128342

RESUMEN

Pre-mRNA structure impacts many cellular processes, including splicing in genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 gene using minigenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.


Asunto(s)
Empalme Alternativo , Precursores del ARN/química , Precursores del ARN/genética , Empalme del ARN , Animales , Secuencia de Bases , Secuencia Conservada , Quinasas Similares a Doblecortina , Células HEK293 , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Proteínas Serina-Treonina Quinasas/genética , Sitios de Empalme de ARN , Análisis de Secuencia de ARN
15.
RNA Biol ; 11(2): 146-55, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24526010

RESUMEN

Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a multifunctional RNA-binding protein that is involved in many different processes, such as regulation of transcription, translation, and RNA stability. We have previously characterized hnRNP L as a global regulator of alternative splicing, binding to CA-repeat, and CA-rich RNA elements. Interestingly, hnRNP L can both activate and repress splicing of alternative exons, but the precise mechanism of hnRNP L-mediated splicing regulation remained unclear. To analyze activities of hnRNP L on a genome-wide level, we performed individual-nucleotide resolution crosslinking-immunoprecipitation in combination with deep-sequencing (iCLIP-Seq). Sequence analysis of the iCLIP crosslink sites showed significant enrichment of C/A motifs, which perfectly agrees with the in vitro binding consensus obtained earlier by a SELEX approach, indicating that in vivo hnRNP L binding targets are mainly determined by the RNA-binding activity of the protein. Genome-wide mapping of hnRNP L binding revealed that the protein preferably binds to introns and 3' UTR. Additionally, position-dependent splicing regulation by hnRNP L was demonstrated: The protein represses splicing when bound to intronic regions upstream of alternative exons, and in contrast, activates splicing when bound to the downstream intron. These findings shed light on the longstanding question of differential hnRNP L-mediated splicing regulation. Finally, regarding 3' UTR binding, hnRNP L binding preferentially overlaps with predicted microRNA target sites, indicating global competition between hnRNP L and microRNA binding. Translational regulation by hnRNP L was validated for a subset of predicted target 3'UTRs.


Asunto(s)
Regiones no Traducidas 3' , Empalme Alternativo , Ribonucleoproteína Heterogénea-Nuclear Grupo L/metabolismo , Intrones , MicroARNs/metabolismo , ARN Mensajero/metabolismo , Regulación de la Expresión Génica , Técnicas de Silenciamiento del Gen , Redes Reguladoras de Genes , Genoma Humano , Células HeLa , Ribonucleoproteína Heterogénea-Nuclear Grupo L/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Inmunoprecipitación
16.
Int J Mol Sci ; 15(9): 16351-80, 2014 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-25229820

RESUMEN

Antioxidant capacity (AOC) against peroxyl radical and 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) radical cation was measured for a series of p-hydroxybenzoic (HB) and p-hydroxycinnamic (HC) acids at different pH. Quantum-chemical computation was performed using Gaussian 3.0 software package to calculate the geometry and energy parameters of the same compounds. Significant correlations were revealed between AOC and a number of calculated parameters. The most significant AOC descriptors for the studied compounds against peroxyl radical were found to be HOMO energy, rigidity (η) and Mulliken charge on the carbon atom in m-position to the phenolic hydroxyl. The most significant descriptor of the antioxidant properties against the ABTS radical cation at рН 7.40 is electron transfer enthalpy from the phenolate ion. The mechanism of AOC realization has been proposed for HB and HC acids against both radicals.


Asunto(s)
Antioxidantes/química , Hidroxibenzoatos/química , Algoritmos , Ácidos Cumáricos/química , Concentración de Iones de Hidrógeno , Cinética , Parabenos/química , Propionatos , Teoría Cuántica , Programas Informáticos
17.
Epigenetics Chromatin ; 17(1): 18, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38783373

RESUMEN

The three-dimensional organization of the genome plays a central role in the regulation of cellular functions, particularly in the human brain. This review explores the intricacies of chromatin organization, highlighting the distinct structural patterns observed between neuronal and non-neuronal brain cells. We integrate findings from recent studies to elucidate the characteristics of various levels of chromatin organization, from differential compartmentalization and topologically associating domains (TADs) to chromatin loop formation. By defining the unique chromatin landscapes of neuronal and non-neuronal brain cells, these distinct structures contribute to the regulation of gene expression specific to each cell type. In particular, we discuss potential functional implications of unique neuronal chromatin organization characteristics, such as weaker compartmentalization, neuron-specific TAD boundaries enriched with active histone marks, and an increased number of chromatin loops. Additionally, we explore the role of Polycomb group (PcG) proteins in shaping cell-type-specific chromatin patterns. This review further emphasizes the impact of variations in chromatin architecture between neuronal and non-neuronal cells on brain development and the onset of neurological disorders. It highlights the need for further research to elucidate the details of chromatin organization in the human brain in order to unravel the complexities of brain function and the genetic mechanisms underlying neurological disorders. This research will help bridge a significant gap in our comprehension of the interplay between chromatin structure and cell functions.


Asunto(s)
Encéfalo , Cromatina , Neuronas , Humanos , Neuronas/metabolismo , Neuronas/citología , Cromatina/metabolismo , Animales , Encéfalo/metabolismo , Proteínas del Grupo Polycomb/metabolismo , Proteínas del Grupo Polycomb/genética , Ensamble y Desensamble de Cromatina
18.
Aging Cell ; : e14283, 2024 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-39072888

RESUMEN

Epigenetic aging clocks have been widely used to validate rejuvenation effects during cellular reprogramming. However, these predictions are unverifiable because the true biological age of reprogrammed cells remains unknown. We present an analytical framework to consider rejuvenation predictions from the uncertainty perspective. Our analysis reveals that the DNA methylation profiles across reprogramming are poorly represented in the aging data used to train clock models, thus introducing high epistemic uncertainty in age estimations. Moreover, predictions of different published clocks are inconsistent, with some even suggesting zero or negative rejuvenation. While not questioning the possibility of age reversal, we show that the high clock uncertainty challenges the reliability of rejuvenation effects observed during in vitro reprogramming before pluripotency and throughout embryogenesis. Conversely, our method reveals a significant age increase after in vivo reprogramming. We recommend including uncertainty estimation in future aging clock models to avoid the risk of misinterpreting the results of biological age prediction.

19.
Commun Biol ; 7(1): 783, 2024 Jun 29.
Artículo en Inglés | MEDLINE | ID: mdl-38951619

RESUMEN

Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Here, using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.


Asunto(s)
Cromatina , Proteínas de Drosophila , Interfase , Proteínas de Complejo Poro Nuclear , Poro Nuclear , Animales , Sitios de Unión , Núcleo Celular/metabolismo , Cromatina/metabolismo , Drosophila melanogaster/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/embriología , Proteínas de Drosophila/metabolismo , Proteínas de Drosophila/genética , Poro Nuclear/metabolismo , Proteínas de Complejo Poro Nuclear/metabolismo , Proteínas de Complejo Poro Nuclear/genética
20.
Nat Commun ; 15(1): 4455, 2024 May 25.
Artículo en Inglés | MEDLINE | ID: mdl-38796479

RESUMEN

Lipids are the most abundant but poorly explored components of the human brain. Here, we present a lipidome map of the human brain comprising 75 regions, including 52 neocortical ones. The lipidome composition varies greatly among the brain regions, affecting 93% of the 419 analyzed lipids. These differences reflect the brain's structural characteristics, such as myelin content (345 lipids) and cell type composition (353 lipids), but also functional traits: functional connectivity (76 lipids) and information processing hierarchy (60 lipids). Combining lipid composition and mRNA expression data further enhances functional connectivity association. Biochemically, lipids linked with structural and functional brain features display distinct lipid class distribution, unsaturation extent, and prevalence of omega-3 and omega-6 fatty acid residues. We verified our conclusions by parallel analysis of three adult macaque brains, targeted analysis of 216 lipids, mass spectrometry imaging, and lipidome assessment of sorted murine neurons.


Asunto(s)
Encéfalo , Lipidómica , Lípidos , Humanos , Animales , Encéfalo/metabolismo , Ratones , Adulto , Lípidos/química , Lípidos/análisis , Masculino , Metabolismo de los Lípidos , Macaca , Neuronas/metabolismo , Femenino , Ácidos Grasos Omega-3/metabolismo , Ácidos Grasos Omega-6/metabolismo , Vaina de Mielina/metabolismo , Persona de Mediana Edad
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