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1.
Nat Commun ; 12(1): 1781, 2021 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-33741908

RESUMO

Prostate cancer (PCa) risk-associated SNPs are enriched in noncoding cis-regulatory elements (rCREs), yet their modi operandi and clinical impact remain elusive. Here, we perform CRISPRi screens of 260 rCREs in PCa cell lines. We find that rCREs harboring high risk SNPs are more essential for cell proliferation and H3K27ac occupancy is a strong indicator of essentiality. We also show that cell-line-specific essential rCREs are enriched in the 8q24.21 region, with the rs11986220-containing rCRE regulating MYC and PVT1 expression, cell proliferation and tumorigenesis in a cell-line-specific manner, depending on DNA methylation-orchestrated occupancy of a CTCF binding site in between this rCRE and the MYC promoter. We demonstrate that CTCF deposition at this site as measured by DNA methylation level is highly variable in prostate specimens, and observe the MYC eQTL in the 8q24.21 locus in individuals with low CTCF binding. Together our findings highlight a causal mechanism synergistically driven by a risk SNP and DNA methylation-mediated 3D genome architecture, advocating for the integration of genetics and epigenetics in assessing risks conferred by genetic predispositions.


Assuntos
Sistemas CRISPR-Cas , Metilação de DNA , Edição de Genes/métodos , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla/métodos , Neoplasias da Próstata/genética , Animais , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , Carcinogênese/genética , Linhagem Celular Tumoral , Humanos , Masculino , Camundongos Endogâmicos NOD , Camundongos SCID , Polimorfismo de Nucleotídeo Único , Regiões Promotoras Genéticas/genética , Proteínas Proto-Oncogênicas c-myc/genética , Locos de Características Quantitativas/genética , Elementos Reguladores de Transcrição/genética , Fatores de Risco
2.
Science ; 371(6531)2021 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-33602827

RESUMO

Genes with novel cellular functions may evolve through exon shuffling, which can assemble novel protein architectures. Here, we show that DNA transposons provide a recurrent supply of materials to assemble protein-coding genes through exon shuffling. We find that transposase domains have been captured-primarily via alternative splicing-to form fusion proteins at least 94 times independently over the course of ~350 million years of tetrapod evolution. We find an excess of transposase DNA binding domains fused to host regulatory domains, especially the Krüppel-associated box (KRAB) domain, and identify four independently evolved KRAB-transposase fusion proteins repressing gene expression in a sequence-specific fashion. The bat-specific KRABINER fusion protein binds its cognate transposons genome-wide and controls a network of genes and cis-regulatory elements. These results illustrate how a transcription factor and its binding sites can emerge.


Assuntos
Elementos de DNA Transponíveis , Evolução Molecular , Regulação da Expressão Gênica , Fatores de Transcrição/genética , Transposases/genética , Vertebrados/genética , Processamento Alternativo , Animais , Sítios de Ligação , Quirópteros/genética , Redes Reguladoras de Genes , Domínios Proteicos , Elementos Reguladores de Transcrição , Fatores de Transcrição/metabolismo , Transposases/química , Transposases/metabolismo , Vertebrados/metabolismo
3.
Ecotoxicol Environ Saf ; 208: 111661, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-33396171

RESUMO

NRAMP family genes participate in the absorption and transport of heavy metals such as cadmium (Cd), zinc (Zn), copper (Cu), lead (Pb), iron (Fe) and manganese (Mn) and play an important role in the response to heavy metal stress. There is an abundance of research on these genes in bacteria, plants and fungi, although not in S. tuberosum. A total of 48 members(potato(5), Arabidopsis(7), Tomato(9), pepper(9), rice(12) and tobacco(6)) were identified from 6 species (potato (Solanum tuberosum), Arabidopsis thaliana, Tomato (Solanum lycopersicum), pepper (Capsicum annuum), rice (Oryza sativa) and tobacco (Nicotiana attenuate)) and were classified into four subgroups. Across NRAMP gene family members, there are 15 highly conserved motifs that have similar genetic structures and characteristics. In addition, a total of 16 pairs of colinear genes were found in eight species. Analysis of cis-elements indicated that, in response to abiotic stress, NRAMPs are mainly regulated by phytohormones and transcription factors. In addition, analysis of expression profiles indicated that StNRAMP4 is mainly expressed in the roots. According to a qRT-PCR-based analysis of the StNRAMP family, with the exception of Pb2+ stress, StNRAMPs positively responded to stress from Cu2+, Cd2+, Zn2+ and Ni2+ and The expression patterns is similar of StNRAMP2, under Pb2+, and Cu2+ treatment, the relative expression peaked at 24 h. the relative expression peaked at 12 h and was upregulated 428-fold in the roots under Ni2+ stress. Under Cd2+ stress, StNRAMP3 was upregulated 28-fold in the leaves. StNRAMP1, StNRAMP4 and StNRAMP5 showed significant upregulation under Cu2+, Cd2+ and Zn2+ stress, respectively. Expression of StNRAMPs could be specifically induced by heavy metals, implying their possible role in the transport and absorption of heavy metals. This research explains the colinear characteristics of NRAMPs in several food crop species, which is useful for providing important genetic resources for cultivating food crop that accumulate low amounts of heavy metals and for explaining the biological functions of NRAMPs in plants.


Assuntos
Metais Pesados/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Solanum tuberosum/fisiologia , Estresse Fisiológico/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta/genética , Família Multigênica , Elementos Reguladores de Transcrição , Solanum tuberosum/genética , Solanum tuberosum/metabolismo
4.
Nat Commun ; 11(1): 5656, 2020 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-33168808

RESUMO

Establishment of spermatogonia throughout the fetal and postnatal period is essential for production of spermatozoa and male fertility. Here, we establish a protocol for in vitro reconstitution of human prospermatogonial specification whereby human primordial germ cell (PGC)-like cells differentiated from human induced pluripotent stem cells are further induced into M-prospermatogonia-like cells and T1 prospermatogonia-like cells (T1LCs) using long-term cultured xenogeneic reconstituted testes. Single cell RNA-sequencing is used to delineate the lineage trajectory leading to T1LCs, which closely resemble human T1-prospermatogonia in vivo and exhibit gene expression related to spermatogenesis and diminished proliferation, a hallmark of quiescent T1 prospermatogonia. Notably, this system enables us to visualize the dynamic and stage-specific regulation of transposable elements during human prospermatogonial specification. Together, our findings pave the way for understanding and reconstructing human male germline development in vitro.


Assuntos
Células Germinativas Embrionárias/fisiologia , Células-Tronco Pluripotentes Induzidas/fisiologia , Espermatogênese/genética , Espermatogênese/fisiologia , Animais , Diferenciação Celular , Epigenômica , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Humanos , Masculino , Camundongos , Camundongos Endogâmicos ICR , Elementos Reguladores de Transcrição , Análise de Sequência de RNA , Espermatogônias/citologia , Espermatozoides , Testículo/citologia , Transcriptoma
5.
Nat Commun ; 11(1): 4928, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004791

RESUMO

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.


Assuntos
Aclimatação/genética , Cromatina/metabolismo , Grupos Étnicos/genética , Redes Reguladoras de Genes , Modelos Genéticos , Altitude , Doença da Altitude/etnologia , Doença da Altitude/genética , Doença da Altitude/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Hipóxia Celular/genética , Células Cultivadas , Cromatina/genética , Sequenciamento de Cromatina por Imunoprecipitação , Resistência à Doença/genética , Feminino , Regulação da Expressão Gênica , Células Endoteliais da Veia Umbilical Humana , Humanos , Hipóxia/genética , Hipóxia/metabolismo , Oxigênio/metabolismo , Polimorfismo de Nucleotídeo Único , Gravidez , Cultura Primária de Células , RNA-Seq , Elementos Reguladores de Transcrição/genética , Seleção Genética , Tibet/etnologia , Fatores de Transcrição/metabolismo , Sequenciamento Completo do Genoma
6.
Science ; 370(6513): 208-214, 2020 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-33033216

RESUMO

Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.


Assuntos
Adaptação Fisiológica/genética , Fator 9 de Crescimento de Fibroblastos/genética , Toupeiras/genética , Elementos Reguladores de Transcrição , Diferenciação Sexual/genética , Esteroide 17-alfa-Hidroxilase/genética , Animais , Inversão Cromossômica , Conjuntos de Dados como Assunto , Feminino , Regulação da Expressão Gênica , Genoma , Camundongos , Camundongos Transgênicos , Sequências de Repetição em Tandem , Testosterona/sangue , Testosterona/genética
7.
PLoS Genet ; 16(9): e1009023, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32925947

RESUMO

Lung cancer is the leading cause of cancer-related death and lung adenocarcinoma is its most common subtype. Although genetic alterations have been identified as drivers in subsets of lung adenocarcinoma, they do not fully explain tumor development. Epigenetic alterations have been implicated in the pathogenesis of tumors. To identify epigenetic alterations driving lung adenocarcinoma, we used an improved version of the Tracing Enhancer Networks using Epigenetic Traits method (TENET 2.0) in primary normal lung and lung adenocarcinoma cells. We found over 32,000 enhancers that appear differentially activated between normal lung and lung adenocarcinoma. Among the identified transcriptional regulators inactivated in lung adenocarcinoma vs. normal lung, NKX2-1 was linked to a large number of silenced enhancers. Among the activated transcriptional regulators identified, CENPA, FOXM1, and MYBL2 were linked to numerous cancer-specific enhancers. High expression of CENPA, FOXM1, and MYBL2 is particularly observed in a subgroup of lung adenocarcinomas and is associated with poor patient survival. Notably, CENPA, FOXM1, and MYBL2 are also key regulators of cancer-specific enhancers in breast adenocarcinoma of the basal subtype, but they are associated with distinct sets of activated enhancers. We identified individual lung adenocarcinoma enhancers linked to CENPA, FOXM1, or MYBL2 that were associated with poor patient survival. Knockdown experiments of FOXM1 and MYBL2 suggest that these factors regulate genes involved in controlling cell cycle progression and cell division. For example, we found that expression of TK1, a potential target gene of a MYBL2-linked enhancer, is associated with poor patient survival. Identification and characterization of key transcriptional regulators and associated enhancers in lung adenocarcinoma provides important insights into the deregulation of lung adenocarcinoma epigenomes, highlighting novel potential targets for clinical intervention.


Assuntos
Adenocarcinoma de Pulmão/genética , Epigênese Genética/genética , Elementos Reguladores de Transcrição/genética , Adenocarcinoma/genética , Adulto , Idoso , Proteínas de Ciclo Celular/genética , Epigenômica , Proteína Forkhead Box M1/genética , Regulação Neoplásica da Expressão Gênica/genética , Genes Homeobox , Humanos , Pulmão/metabolismo , Neoplasias Pulmonares/genética , Masculino , Pessoa de Meia-Idade , Sequências Reguladoras de Ácido Nucleico/genética
8.
Proc Natl Acad Sci U S A ; 117(34): 20636-20644, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32778581

RESUMO

The diversity of forms in multicellular organisms originates largely from the spatial redeployment of developmental genes [S. B. Carroll, Cell 134, 25-36 (2008)]. Several scenarios can explain the emergence of cis-regulatory elements that govern novel aspects of a gene expression pattern [M. Rebeiz, M. Tsiantis, Curr. Opin. Genet. Dev. 45, 115-123 (2017)]. One scenario, enhancer co-option, holds that a DNA sequence producing an ancestral regulatory activity also becomes the template for a new regulatory activity, sharing regulatory information. While enhancer co-option might fuel morphological diversification, it has rarely been documented [W. J. Glassford et al., Dev. Cell 34, 520-531 (2015)]. Moreover, if two regulatory activities are borne from the same sequence, their modularity, considered a defining feature of enhancers [J. Banerji, L. Olson, W. Schaffner, Cell 33, 729-740 (1983)], might be affected by pleiotropy. Sequence overlap may thereby play a determinant role in enhancer function and evolution. Here, we investigated this problem with two regulatory activities of the Drosophila gene yellow, the novel spot enhancer and the ancestral wing blade enhancer. We used precise and comprehensive quantification of each activity in Drosophila wings to systematically map their sequences along the locus. We show that the spot enhancer has co-opted the sequences of the wing blade enhancer. We also identified a pleiotropic site necessary for DNA accessibility of a shared regulatory region. While the evolutionary steps leading to the derived activity are still unknown, such pleiotropy suggests that enhancer accessibility could be one of the molecular mechanisms seeding evolutionary co-option.


Assuntos
Proteínas de Drosophila/genética , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Animais , Evolução Biológica , Cromatina/genética , Cromatina/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Evolução Molecular , Elementos Reguladores de Transcrição/genética , Asas de Animais/metabolismo
9.
Proc Natl Acad Sci U S A ; 117(35): 21364-21372, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32817564

RESUMO

A person's genome typically contains millions of variants which represent the differences between this personal genome and the reference human genome. The interpretation of these variants, i.e., the assessment of their potential impact on a person's phenotype, is currently of great interest in human genetics and medicine. We have developed a prioritization tool called OpenCausal which takes as inputs 1) a personal genome and 2) a reference context-specific TF expression profile and returns a list of noncoding variants prioritized according to their impact on chromatin accessibility for any given genomic region of interest. We applied OpenCausal to 6,430 samples across 18 tissues derived from the GTEx project and found that the variants prioritized by OpenCausal are highly enriched for eQTLs and caQTLs. We further propose a strategy to integrate the predicted open scores with genome-wide association studies (GWAS) data to prioritize putative causal variants and regulatory elements for a given risk locus (i.e., fine-mapping analysis). As an initial example, we applied this method to a GWAS dataset of human height and found that the prioritized putative variants and elements are correlated with the phenotype (i.e., heights of individuals) better than others.


Assuntos
Técnicas Genéticas , Variação Genética , Genoma Humano , Modelos Genéticos , Elementos Reguladores de Transcrição , Estatura/genética , Perfilação da Expressão Gênica , Estudo de Associação Genômica Ampla , Humanos , Locos de Características Quantitativas , Software , Fatores de Transcrição/metabolismo
10.
PLoS Biol ; 18(7): e3000799, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32730243

RESUMO

Epigenetic dynamics, such as DNA methylation and chromatin accessibility, have been extensively explored in human preimplantation embryos. However, the active demethylation process during this crucial period remains largely unexplored. In this study, we use single-cell chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to quantify the DNA 5-formylcytosine (5fC) levels of human preimplantation embryos. We find that 5-formylcytosine phosphate guanine (5fCpG) exhibits genomic element-specific distribution features and is enriched in L1 and endogenous retrovirus-K (ERVK), the subfamilies of repeat elements long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs), respectively. Unlike in mice, paired pronuclei in the same zygote present variable difference of 5fCpG levels, although the male pronuclei experience stronger global demethylation. The nucleosome-occupied regions show a higher 5fCpG level compared with nucleosome-depleted ones, suggesting the role of 5fC in organizing nucleosome position. Collectively, our work offers a valuable resource for ten-eleven translocation protein family (TET)-dependent active demethylation-related study during human early embryonic development.


Assuntos
Blastocisto/metabolismo , Citosina/análogos & derivados , Desmetilação do DNA , Citosina/metabolismo , Desenvolvimento Embrionário , Genoma Humano , Humanos , Elementos Reguladores de Transcrição , Análise de Célula Única
11.
Nat Commun ; 11(1): 3383, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32636391

RESUMO

The endogenous repair process can result in recovery after acute kidney injury (AKI) with adaptive proliferation of tubular epithelial cells, but repair can also lead to fibrosis and progressive kidney disease. There is currently limited knowledge about transcriptional regulators regulating these repair programs. Herein we establish the enhancer and super-enhancer landscape after AKI by ChIP-seq in uninjured and repairing kidneys on day two after ischemia reperfusion injury (IRI). We identify key transcription factors including HNF4A, GR, STAT3 and STAT5, which show specific binding at enhancer and super-enhancer sites, revealing enhancer dynamics and transcriptional changes during kidney repair. Loss of bromodomain-containing protein 4 function before IRI leads to impaired recovery after AKI and increased mortality. Our comprehensive analysis of epigenetic changes after kidney injury in vivo has the potential to identify targets for therapeutic intervention. Importantly, our data also call attention to potential caveats involved in use of BET inhibitors in patients at risk for AKI.


Assuntos
Lesão Renal Aguda/genética , Elementos Facilitadores Genéticos , Túbulos Renais/citologia , Lesão Renal Aguda/metabolismo , Motivos de Aminoácidos , Animais , Sítios de Ligação , Proliferação de Células , Epigênese Genética , Fibrose , Fator 4 Nuclear de Hepatócito/metabolismo , Rim/metabolismo , Rim/patologia , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Endogâmicos C57BL , Proteínas Nucleares , Receptores de Glucocorticoides/metabolismo , Elementos Reguladores de Transcrição , Traumatismo por Reperfusão/metabolismo , Fator de Transcrição STAT3/metabolismo , Fator de Transcrição STAT5/metabolismo , Transdução de Sinais , Fatores de Transcrição , Transcrição Genética
12.
J Insect Sci ; 20(3)2020 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-32556319

RESUMO

Bombyx mori vitellogenin (BmVg) is highly upregulated during pupation, and the 20-hydroxyecdysone and amino acids may regulate stage-specific BmVg expression. However, previous studies showed that other factors may also affect stage-specific BmVg expression. Here, we characterized effective BmVg transcription factors by identifying the corresponding cis-regulatory elements (CREs). We prepared transgenic B. mori, in which DsRed was driven by various lengths of BmVg promoter. qRT-PCR analysis showed that DsRed expression driven by a 1.0-kb BmVg promoter (VgP1.0K) was consistent with endogenous BmVg. VgP1.0K specificity was closer to the endogenous BmVg promoter than that of VgP0.8K. These results suggest that CREs affecting stage-specific BmVg expression were localized to the 1.0-kb BmVg promoter. We investigated the effects of certain CREs that could influence the stage specificity of BmVg promoter on BmVg expression in transgenic B. mori. The relative DsRed expression was significantly reduced in transgenic female B. mori and the peak in DsRed expression was delayed after E-box CRE mutation. These results demonstrate that the E-box element enhanced BmVg expression and also affected stage-specific BmVg expression. Moreover, the relative DsRed expression was significantly increased in transgenic female of B. mori after 3×BD CRE mutation in BmVg promoter. However, the stage specificity of the mutated promoter was consistent with that of the endogenous BmVg promoter. The 3×BD element downregulated BmVg but had no effect on stage-specific BmVg expression. The present study promoted the process of elucidating the regulatory network for stage-specific BmVg expression and furnished a theoretical basis for the application of BmVg promoter.


Assuntos
Bombyx/genética , Expressão Gênica/genética , Genes de Insetos , Proteínas de Insetos/genética , Elementos Reguladores de Transcrição/genética , Fatores de Transcrição/genética , Vitelogeninas/genética , Animais , Bombyx/metabolismo , Proteínas de Insetos/metabolismo , Larva/genética , Larva/crescimento & desenvolvimento , Fatores de Transcrição/metabolismo , Vitelogeninas/metabolismo
13.
PLoS One ; 15(5): e0231824, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32357166

RESUMO

MOTIVATION: Cellular identity and behavior is controlled by complex gene regulatory networks. Transcription factors (TFs) bind to specific DNA sequences to regulate the transcription of their target genes. On the basis of these TF motifs in cis-regulatory elements we can model the influence of TFs on gene expression. In such models of TF motif activity the data is usually modeled assuming a linear relationship between the motif activity and the gene expression level. A commonly used method to model motif influence is based on Ridge Regression. One important assumption of linear regression is the independence between samples. However, if samples are generated from the same cell line, tissue, or other biological source, this assumption may be invalid. This same assumption of independence is also applied to different yet similar experimental conditions, which may also be inappropriate. In theory, the independence assumption between samples could lead to loss in signal detection. Here we investigate whether a Bayesian model that allows for correlations results in more accurate inference of motif activities. RESULTS: We extend the Ridge Regression to a Bayesian Linear Mixed Model, which allows us to model dependence between different samples. In a simulation study, we investigate the differences between the two model assumptions. We show that our Bayesian Linear Mixed Model implementation outperforms Ridge Regression in a simulation scenario where the noise, which is the signal that can not be explained by TF motifs, is uncorrelated. However, we demonstrate that there is no such gain in performance if the noise has a similar covariance structure over samples as the signal that can be explained by motifs. We give a mathematical explanation to why this is the case. Using four representative real datasets we show that at most ∼â€<40% of the signal is explained by motifs using the linear model. With these data there is no advantage to using the Bayesian Linear Mixed Model, due to the similarity of the covariance structure. AVAILABILITY & IMPLEMENTATION: The project implementation is available at https://github.com/Sim19/SimGEXPwMotifs.


Assuntos
Motivos de Aminoácidos/genética , Teorema de Bayes , Regulação da Expressão Gênica/genética , Fatores de Transcrição/genética , Sequenciamento de Cromatina por Imunoprecipitação/métodos , Simulação por Computador , Redes Reguladoras de Genes , Modelos Lineares , Elementos Reguladores de Transcrição/genética , Fatores de Transcrição/química
14.
BMC Bioinformatics ; 21(1): 194, 2020 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-32429868

RESUMO

BACKGROUND: Finding combinations of homotypic or heterotypic genomic sites obeying a specific grammar in DNA sequences is a frequent task in bioinformatics. A typical case corresponds to the identification of cis-regulatory modules characterized by a combination of transcription factor binding sites in a defined window size. Although previous studies identified clusters of genomic sites in species with varying genome sizes, the availability of a dedicated and versatile tool to search for such clusters is lacking. RESULTS: We present fcScan, an R/Bioconductor package to search for clusters of genomic sites based on user defined criteria including cluster size, inter-cluster distances and sites order and orientation allowing users to adapt their search criteria to specific biological questions. It supports GRanges, data frame and VCF/BED files as input and returns data in GRanges format. By performing clustering on vectorized data, fcScan is adapted to search for genomic clusters in millions of sites as input in short time and is thus ideal to scan data generated by high throughput methods including next generation sequencing. CONCLUSIONS: fcScan is ideal for detecting cis-regulatory modules of transcription factor binding sites with a specific grammar as well as genomic loci enriched for mutations. The flexibility in input parameters allows users to perform searches targeting specific research questions. It is released under Artistic-2.0 License. The source code is freely available through Bioconductor (https://bioconductor.org/packages/fcScan) and GitHub (https://github.com/pkhoueiry/fcScan).


Assuntos
Genômica/métodos , Elementos Reguladores de Transcrição , Análise de Sequência de DNA/métodos , Software , Sítios de Ligação , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Fatores de Transcrição/metabolismo
15.
Nat Commun ; 11(1): 2606, 2020 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-32451376

RESUMO

Nucleoporin proteins (Nups) have been proposed to mediate spatial and temporal chromatin organization during gene regulation. Nevertheless, the molecular mechanisms in mammalian cells are not well understood. Here, we report that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin binding and differential gene expression - specifically at the bivalent developmental genes. To investigate the molecular mechanism, we utilize epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We find that NUP153 controls CTCF and cohesin binding at the cis-regulatory elements and POL II pausing during the basal state. Furthermore, efficient IEG transcription relies on NUP153. We propose that NUP153 links the nuclear pore complex (NPC) to chromatin architecture allowing genes that are poised to respond rapidly to developmental cues to be properly modulated.


Assuntos
Fator de Ligação a CCCTC/metabolismo , Proteínas de Ciclo Celular/metabolismo , Cromatina/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Complexo de Proteínas Formadoras de Poros Nucleares/metabolismo , Animais , Fator de Ligação a CCCTC/química , Proteínas de Ciclo Celular/química , Linhagem Celular , Cromatina/química , Cromatina/genética , Proteínas Cromossômicas não Histona/química , Genes Precoces , Células HeLa , Humanos , Camundongos , Células-Tronco Embrionárias Murinas/metabolismo , Poro Nuclear/metabolismo , Complexo de Proteínas Formadoras de Poros Nucleares/deficiência , Complexo de Proteínas Formadoras de Poros Nucleares/genética , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , RNA Polimerase II/metabolismo , Elementos Reguladores de Transcrição
16.
Nat Chem Biol ; 16(8): 857-865, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32424304

RESUMO

Agricultural biotechnology strategies often require the precise regulation of multiple genes to effectively modify complex plant traits. However, most efforts are hindered by a lack of characterized tools that allow for reliable and targeted expression of transgenes. We have successfully engineered a library of synthetic transcriptional regulators that modulate expression strength in planta. By leveraging orthogonal regulatory systems from Saccharomyces spp., we have developed a strategy for the design of synthetic activators, synthetic repressors, and synthetic promoters and have validated their use in Nicotiana benthamiana and Arabidopsis thaliana. This characterization of contributing genetic elements that dictate gene expression represents a foundation for the rational design of refined synthetic regulators. Our findings demonstrate that these tools provide variation in transcriptional output while enabling the concerted expression of multiple genes in a tissue-specific and environmentally responsive manner, providing a basis for generating complex genetic circuits that process endogenous and environmental stimuli.


Assuntos
Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Elementos Reguladores de Transcrição/genética , Arabidopsis/genética , Expressão Gênica/genética , Redes Reguladoras de Genes/genética , Regiões Promotoras Genéticas/genética , Saccharomyces/enzimologia , Saccharomyces/genética , Tabaco/genética , Fatores de Transcrição/metabolismo
17.
Nucleic Acids Res ; 48(W1): W193-W199, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32459338

RESUMO

A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM's activity and its estimated cell type-specific contribution to its target gene's expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https://epiregio.de/.


Assuntos
Elementos Reguladores de Transcrição , Software , Sequenciamento de Cromatina por Imunoprecipitação , Doença/genética , Regulação da Expressão Gênica , Humanos , Fatores de Transcrição/metabolismo
18.
Nat Commun ; 11(1): 2656, 2020 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-32461609

RESUMO

The earthworm is particularly fascinating to biologists because of its strong regenerative capacity. However, many aspects of its regeneration in nature remain elusive. Here we report chromosome-level genome, large-scale transcriptome and single-cell RNA-sequencing data during earthworm (Eisenia andrei) regeneration. We observe expansion of LINE2 transposable elements and gene families functionally related to regeneration (for example, EGFR, epidermal growth factor receptor) particularly for genes exhibiting differential expression during earthworm regeneration. Temporal gene expression trajectories identify transcriptional regulatory factors that are potentially crucial for initiating cell proliferation and differentiation during regeneration. Furthermore, early growth response genes related to regeneration are transcriptionally activated in both the earthworm and planarian. Meanwhile, single-cell RNA-sequencing provides insight into the regenerative process at a cellular level and finds that the largest proportion of cells present during regeneration are stem cells.


Assuntos
Perfilação da Expressão Gênica/métodos , Oligoquetos/genética , Regeneração/genética , Animais , Diferenciação Celular/genética , Proliferação de Células/genética , Oligoquetos/citologia , Oligoquetos/metabolismo , RNA-Seq/métodos , Regeneração/fisiologia , Elementos Reguladores de Transcrição/genética , Sequenciamento Completo do Exoma , Sequenciamento Completo do Genoma
19.
Arch Virol ; 165(8): 1899-1903, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32462284

RESUMO

Tacaribe virus (TCRV) is the prototype of the New World arenaviruses (also known as TCRV serocomplex viruses). While TCRV is not itself a human pathogen, many closely related members of this group cause hemorrhagic fever, and thus TCRV has long served as an important BSL2 system for research into diverse areas of arenavirus biology. Due to its widespread use, a coding-complete sequence for both the S and L segments of the bipartite genome has been publically available for almost 30 years. However, more recently, this sequence has been found to contain significant discrepancies compared to other samples of the same original strain (i.e., TRVL-11573). Further, it is incomplete with respect to the genome ends, which contain critical regulatory elements for RNA synthesis. In order to rectify these issues we now present the first complete genome sequence for this important prototype arenavirus. In addition to completing the S segment 5' end, we identified an apparent error in the L segment 3' end as well as substantial discrepancies in the S segment intergenic region likely to affect folding. Comparison of this sequence with existing partial sequences confirmed a 12-amino-acid deletion in GP, including putative glycosylation sites, and a 4-amino-acid exchange flanking the exonuclease domain of NP. Accounting for these corrections, the TRVL-11573 strain appears to be nearly identical to that isolated in Florida in 2012. The availability of this information provides a solid basis for future molecular and genetic work on this important prototype arenavirus.


Assuntos
Arenavirus do Novo Mundo/genética , Florida , Humanos , Elementos Reguladores de Transcrição/genética , Replicação Viral/genética , Sequenciamento Completo do Genoma/métodos
20.
Nucleic Acids Res ; 48(W1): W208-W217, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32324215

RESUMO

Transcription factors (TFs) regulate the expression of gene expression. The binding specificities of many TFs have been deciphered and summarized as position-weight matrices, also called TF motifs. Despite the availability of hundreds of known TF motifs in databases, it remains non-trivial to quickly query and visualize the enrichment of known TF motifs in genomic regions of interest. Towards this goal, we developed TFmotifView, a web server that allows to study the distribution of known TF motifs in genomic regions. Based on input genomic regions and selected TF motifs, TFmotifView performs an overlap of the genomic regions with TF motif occurrences identified using a dynamic P-value threshold. TFmotifView generates three different outputs: (i) an enrichment table and scatterplot calculating the significance of TF motif occurrences in genomic regions compared to control regions, (ii) a genomic view of the organisation of TF motifs in each genomic region and (iii) a metaplot summarizing the position of TF motifs relative to the center of the regions. TFmotifView will contribute to the integration of TF motif information with a wide range of genomic datasets towards the goal to better understand the regulation of gene expression by transcription factors. TFmotifView is freely available at http://bardet.u-strasbg.fr/tfmotifview/.


Assuntos
Elementos Reguladores de Transcrição , Software , Fatores de Transcrição/metabolismo , Animais , Composição de Bases , Sequenciamento de Cromatina por Imunoprecipitação , Gráficos por Computador , DNA/química , Genômica/métodos , Camundongos , Motivos de Nucleotídeos , Matrizes de Pontuação de Posição Específica
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