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1.
Nucleic Acids Res ; 47(18): 9480-9494, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504786

RESUMO

Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.


Assuntos
Biologia Computacional/métodos , Motivos de Nucleotídeos/genética , RNA Catalítico/genética , Análise de Sequência de RNA/métodos , Catálise , Modelos Moleculares , Conformação de Ácido Nucleico , RNA Catalítico/química , RNA Catalítico/isolamento & purificação
2.
BMC Plant Biol ; 19(1): 191, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072335

RESUMO

BACKGROUND: BRASSINAZOLE-RESISTANT (BZR) family genes encode plant-specific transcription factors (TFs) that participate in brassinosteroid signal transduction. BZR TFs have vital roles in plant growth, including cell elongation. However, little is known about BZR genes in sugar beet (Beta vulgaris L.). RESULTS: Therefore, we performed a genome-wide investigation of BvBZR genes in sugar beet. Through an analysis of the BES1_N conserved domain, six BvBZR gene family members were identified in the sugar beet genome, which clustered into three subgroups according to a phylogenetic analysis. Each clade was well defined by the conserved motifs, implying that close genetic relationships could be identified among the members of each subfamily. According to chromosomal distribution mapping, 2, 1, 1, 1, and 1 genes were located on chromosomes 1, 4, 5, 6, and 8, respectively. The cis-acting elements related to taproot growth were randomly distributed in the promoter sequences of the BvBZR genes. Tissue-specific expression analyses indicated that all BvBZR genes were expressed in all three major tissue types (roots, stems, and leaves), with significantly higher expression in leaves. Subcellular localization analysis revealed that Bv1_fxre and Bv6_nyuw are localized in the nuclei, consistent with the prediction of Wolf PSORT. CONCLUSION: These findings offer a basis to predict the functions of BZR genes in sugar beet, and lay a foundation for further research of the biological functions of BZR genes in sugar beet.


Assuntos
Beta vulgaris/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Fatores de Transcrição/genética , Motivos de Aminoácidos , Beta vulgaris/efeitos dos fármacos , Cromossomos de Plantas/genética , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas , Proteínas de Fluorescência Verde/metabolismo , Motivos de Nucleotídeos/genética , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Regiões Promotoras Genéticas , Fatores de Transcrição/metabolismo
3.
BMC Res Notes ; 12(1): 257, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072404

RESUMO

OBJECTIVE: Use next-generation sequencing to develop microsatellite loci that will provide the variability necessary for studies of genetic diversity and population connectivity of two New World vulture species. RESULTS: We characterized 11 microsatellite loci for black vultures (Coragyps atratus) and 14 loci for turkey vultures (Cathartes aura). These microsatellite loci were grouped into 3 multiplex panels for each species. The number of alleles among black vulture samples ranged from 2 to 11, and 3 to 48 among turkey vulture samples.


Assuntos
Aves/genética , Repetições de Microssatélites/genética , Animais , Motivos de Nucleotídeos/genética , Reação em Cadeia da Polimerase
4.
BMC Plant Biol ; 19(1): 150, 2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30995906

RESUMO

BACKGROUND: Powdery mildew (PM) is a widespread fungal disease of plants in temperate climates, causing significant economic losses in agricultural settings. Specific homologs of the MLO gene family are PM susceptibility factors, as their loss-of function results in durable PM resistance (mlo resistance) in several plant species. The role of MLO susceptibility genes in plant-pathogen interactions is still elusive, however it is known that they are strongly upregulated following PM infection. RESULTS: In this study, we investigated the structure of 414 Putative Promoter Regions (PPRs) of MLO genes and highlighted motif and regulatory element patterns related to genomic relationships among species and phylogenetic distance among homologs. A TC box-like motif and a thymine-rich motif were found to be overrepresented in MLO genes transcriptionally upregulated upon infection with PM fungi. As proof of concept, we showed that the expression of a melon (Cucumis melo L.) gene enriched for the motifs above mentioned was strongly upregulated upon infection with the PM fungus Podosphaera xanthii. CONCLUSION: While identifying a candidate MLO susceptibility gene in melon, this study provides insight on the transcriptional control of MLO genes and indicates diagnostic features useful to identify MLO susceptibility genes across species affected by the PM disease.


Assuntos
Sequência Conservada/genética , Evolução Molecular , Genes de Plantas , Regiões Promotoras Genéticas , Ascomicetos/fisiologia , Sequência de Bases , Biologia Computacional , Cucurbitaceae/genética , Cucurbitaceae/microbiologia , Regulação da Expressão Gênica de Plantas , Motivos de Nucleotídeos/genética , Filogenia , Doenças das Plantas/microbiologia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transcrição Genética , Regulação para Cima/genética
5.
Genome Res ; 29(5): 711-722, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30962178

RESUMO

The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonrandomness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated. Finally, coregulated exons encoding amino acids with similar physicochemical properties correspond to specific protein features. In conclusion, the regulation of an exon by a splicing factor that relies on the affinity of this factor for specific nucleotide(s) is tightly interconnected with the exon-encoded physicochemical properties. We therefore uncover an unanticipated bidirectional interplay between the splicing regulatory process and its biological functional outcome.


Assuntos
Processamento Alternativo , Éxons/genética , Sítios de Splice de RNA/genética , Fatores de Processamento de RNA/metabolismo , Aminoácidos/química , Composição de Bases/genética , Linhagem Celular , Código Genético , Ribonucleoproteínas Nucleares Heterogêneas/metabolismo , Humanos , Íntrons/genética , Motivos de Nucleotídeos/genética , Análise de Sequência de Proteína , Análise de Sequência de RNA , Fatores de Processamento de Serina-Arginina/metabolismo
7.
Plant Mol Biol ; 100(1-2): 83-93, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30847712

RESUMO

KEY MESSAGE: The novel AP2/ERF transcription factor SmERF128 positively regulates diterpenoid tanshinone biosynthesis by activating the expression of SmCPS1, SmKSL1, and SmCYP76AH1 in Salvia miltiorrhiza. Certain members of the APETALA2/ethylene-responsive factor (AP2/ERF) family regulate plant secondary metabolism. Although it is clearly documented that AP2/ERF transcription factors (TFs) are involved in sesquiterpenoid biosynthesis, the regulation of diterpenoid biosynthesis by AP2/ERF TFs remains elusive. Here, we report that the novel AP2/ERF TF SmERF128 positively regulates diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza. Overexpression of SmERF128 increased the expression levels of copalyl diphosphate synthase 1 (SmCPS1), kaurene synthase-like 1 (SmKSL1) and cytochrome P450 monooxygenase 76AH1 (SmCYP76AH1), whereas their expression levels were decreased when SmERF128 was silenced. Accordingly, the content of tanshinone was reduced in SmERF128 RNA interference (RNAi) hairy roots and dramatically increased in SmERF128 overexpression hairy roots, as demonstrated through Ultra Performance Liquid Chromatography (UPLC) and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. Furthermore, SmERF128 activated the expression of SmCPS1, SmKSL1, and SmCYP76AH1 by binding to the GCC box, and to the CRTDREHVCBF2 (CBF2) and RAV1AAT (RAA) motifs within their promoters during in vivo and in vitro assays. Our findings not only reveal the molecular basis of how the AP2/ERF transcription factor SmERF128 regulates diterpenoid biosynthesis, but also provide useful information for improving tanshinone production through genetic engineering.


Assuntos
Diterpenos/metabolismo , Proteínas de Plantas/metabolismo , Salvia miltiorrhiza/metabolismo , Fatores de Transcrição/metabolismo , Diterpenos/isolamento & purificação , Diterpenos de Abietano/biossíntese , Regulação da Expressão Gênica de Plantas , Inativação Gênica , Genes de Plantas , Motivos de Nucleotídeos/genética , Proteínas de Plantas/genética , Raízes de Plantas/genética , Plantas Geneticamente Modificadas , Regiões Promotoras Genéticas/genética , Ligação Proteica , Transporte Proteico , Interferência de RNA , Salvia miltiorrhiza/genética , Fatores de Transcrição/isolamento & purificação
8.
Int J Mol Med ; 43(5): 1927-1938, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30896855

RESUMO

The farnesoid X receptor (FXR) is known to regulate the gene expression of SR­BI, which mediates plasma high­density lipoprotein (HDL)­cholesterol uptake. Our previous study demonstrated that the activation of FXR by obeticholic acid (OCA) lowered plasma HDL­cholesterol levels and increased the hepatic mRNA and protein expression levels of SR­BI in hypercholesterolemic hamsters, but not in normolipidemic hamsters, suggesting that dietary cholesterol may be involved in the OCA­induced transcription of SR­BI. In the present study, a functional 90­base­pair regulatory region was identified in the first intron of the SR­BI gene of hamster and mouse that contains a FXR response element (IR­1) and an adjacent liver X receptor (LXR) response element (LXRE). By in vitro DNA binding and luciferase reporter gene assays, it was demonstrated that FXR and LXR bind to their recognition sequences within this intronic region and transactivate the SR­BI reporter gene in a synergistic manner. It was also shown that mutations at either the IR­1 site or the LXRE site eliminated OCA­mediated gene transcription. Utilizing chow­fed hamsters as an in vivo model, it was demonstrated that treating normolipidemic hamsters with OCA or GW3965 alone did not effectively induce levels of SR­BI, whereas their combined treatment significantly increased the mRNA and protein levels of SR­BI in the liver. The study further investigated effects of FXR and LXR coactivation on the gene expression of SR­BI in human liver cells. The intronic FXRE and LXRE regulatory region was not conserved in the human SR­BI genomic sequence, however, higher mRNA expression levels of SR­BI were observed in human primary hepatocytes and HepG2 cells exposed to combined treatments of FXR and LXR agonists, compared with those in cells exposed to individual ligand treatment. Therefore, these results suggest that human SR­BI gene transcription may also be subject to concerted activation by FXR and LXR, mediated via currently unidentified regulatory sequences.


Assuntos
Antígenos CD36/genética , Ácido Quenodesoxicólico/análogos & derivados , Regulação da Expressão Gênica/efeitos dos fármacos , Receptores X do Fígado/metabolismo , Fígado/metabolismo , Receptores Citoplasmáticos e Nucleares/metabolismo , Transcrição Genética/efeitos dos fármacos , Animais , Sequência de Bases , Benzoatos/farmacologia , Benzilaminas/farmacologia , Antígenos CD36/metabolismo , Ácido Quenodesoxicólico/farmacologia , Genes Reporter , Células Hep G2 , Humanos , Íntrons/genética , Fígado/efeitos dos fármacos , Masculino , Mesocricetus , Motivos de Nucleotídeos/genética , Elementos de Resposta/genética
9.
Mol Cell ; 74(2): 245-253.e6, 2019 04 18.
Artigo em Inglês | MEDLINE | ID: mdl-30826165

RESUMO

Transcription factors (TFs) control gene expression by binding DNA recognition sites in genomic regulatory regions. Although most forkhead TFs recognize a canonical forkhead (FKH) motif, RYAAAYA, some forkheads recognize a completely different (FHL) motif, GACGC. Bispecific forkhead proteins recognize both motifs, but the molecular basis for bispecific DNA recognition is not understood. We present co-crystal structures of the FoxN3 DNA binding domain bound to the FKH and FHL sites, respectively. FoxN3 adopts a similar conformation to recognize both motifs, making contacts with different DNA bases using the same amino acids. However, the DNA structure is different in the two complexes. These structures reveal how a single TF binds two unrelated DNA sequences and the importance of DNA shape in the mechanism of bispecific recognition.


Assuntos
Proteínas de Ciclo Celular/química , Proteínas de Ligação a DNA/química , DNA/química , Conformação de Ácido Nucleico , Proteínas Repressoras/química , Sequência de Aminoácidos/genética , Sequência de Bases/genética , Sítios de Ligação/genética , Proteínas de Ciclo Celular/genética , Cristalografia por Raios X , DNA/genética , Proteínas de Ligação a DNA/genética , Regulação da Expressão Gênica/genética , Humanos , Complexos Multiproteicos/química , Complexos Multiproteicos/genética , Motivos de Nucleotídeos/genética , Sequências Reguladoras de Ácido Nucleico/genética , Proteínas Repressoras/genética
10.
Dev Cell ; 48(6): 793-810.e6, 2019 03 25.
Artigo em Inglês | MEDLINE | ID: mdl-30713076

RESUMO

Piwi-interacting RNAs (piRNAs) are important for genome regulation across metazoans, but their biogenesis evolves rapidly. In Caenorhabditis elegans, piRNA loci are clustered within two 3-Mb regions on chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce an ∼28 nt primary transcript. We used comparative epigenomics across nematodes to gain insight into the origin, evolution, and mechanism of nematode piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription. We describe two alternative modes of piRNA organization in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, while in other species, typified by Pristionchus pacificus, piRNAs are found within introns of active genes. Additionally, we discover that piRNA production depends on sequence signals associated with RNA polymerase II pausing. We show that pausing signals synergize with chromatin to control piRNA transcription.


Assuntos
Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Cromatina/metabolismo , Epigenômica , RNA Polimerase II/metabolismo , RNA Interferente Pequeno/biossíntese , Animais , Sequência de Bases , Evolução Molecular , Loci Gênicos , Motivos de Nucleotídeos/genética , RNA Interferente Pequeno/genética , Transcrição Genética
11.
Proc Natl Acad Sci U S A ; 116(9): 3668-3677, 2019 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-30755522

RESUMO

Histones are modified by enzymes that act in a locus, cell-type, and developmental stage-specific manner. The recruitment of enzymes to chromatin is regulated at multiple levels, including interaction with sequence-specific DNA-binding factors. However, the DNA-binding specificity of the regulatory factors that orchestrate specific histone modifications has not been broadly mapped. We have analyzed 6 histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3, K3H9me3, H3K36me3) across 121 human cell types and tissues from the NIH Roadmap Epigenomics Project as well as 8 histone marks (with addition of H3K4me2 and H3K9ac) from the mouse ENCODE Consortium. We have identified 361 and 369 DNA motifs in human and mouse, respectively, that are the most predictive of each histone mark. Interestingly, 107 human motifs are conserved between the two species. In human embryonic cell line H1, we mutated only the found DNA motifs at particular loci and the significant reduction of H3K27ac levels validated the regulatory roles of the perturbed motifs. The functionality of these motifs was also supported by the evidence that histone-associated motifs, especially H3K4me3 motifs, significantly overlap with the expression of quantitative trait loci SNPs in cancer patients more than the known and random motifs. Furthermore, we observed possible feedbacks to control chromatin dynamics as the found motifs appear in the promoters or enhancers associated with various histone modification enzymes. These results pave the way toward revealing the molecular mechanisms of epigenetic events, such as histone modification dynamics and epigenetic priming.


Assuntos
Metilação de DNA/genética , Código das Histonas/genética , Motivos de Nucleotídeos/genética , Sequências Reguladoras de Ácido Nucleico/genética , Animais , Cromatina/genética , Proteínas de Ligação a DNA/genética , Epigenômica , Humanos , Camundongos , Regiões Promotoras Genéticas , Processamento de Proteína Pós-Traducional/genética
12.
PLoS Biol ; 17(2): e3000094, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30742611

RESUMO

The repeatability or predictability of evolution is a central question in evolutionary biology and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage-compensation male-specific lethal (MSL) complex to study the mutational paths that have led to the acquisition of hundreds of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the D. melanica and D. robusta species groups by genome sequencing and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve hundreds of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element (TE) insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes and appears to be contingent on genomic properties of that species, such as simple repeat or TE density. This establishes the "genomic environment" as an important determinant in predicting the outcome of evolutionary adaptations.


Assuntos
Compensação de Dosagem (Genética) , Drosophila melanogaster/genética , Evolução Molecular , Redes Reguladoras de Genes , Animais , Sequência de Bases , Sítios de Ligação , Cromatina/metabolismo , Sequência Conservada/genética , Proteínas de Drosophila/metabolismo , Feminino , Masculino , Anotação de Sequência Molecular , Mutação/genética , Motivos de Nucleotídeos/genética , Filogenia , Cromossomos Sexuais/genética
13.
Biometals ; 32(2): 273-291, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30810877

RESUMO

Heme may represent a major iron-source for bacteria. In the symbiotic nitrogen-fixing bacterium Ensifer meliloti 1021, iron acquisition from heme depends on the outer-membrane heme-receptor ShmR. Expression of shmR gene is repressed by iron in a RirA dependent manner while under iron-limitation its expression requires the small protein HmuP. In this work, we identified highly conserved nucleotide motifs present upstream the shmR gene. These motifs are widely distributed among Alpha and Beta Proteobacteria, and correlate with the presence of HmuP coding sequences in bacterial genomes. According to data presented in this work, we named these new motifs as HmuP-responsive elements (HPREs). In the analyzed genomes, the HPREs were always present upstream of genes encoding putative heme-receptors. Moreover, in those Alpha and Beta Proteobacteria where transcriptional start sites for shmR homologs are known, HPREs were located in the 5'UTR region. In this work we show that in E. meliloti 1021, HPREs are involved in HmuP-dependent shmR expression. Moreover, we show that changes in sequence composition of the HPREs correlate with changes in a predicted RNA secondary structure element and affect shmR gene expression.


Assuntos
Regiões 5' não Traduzidas/genética , Proteínas da Membrana Bacteriana Externa/genética , Proteínas de Bactérias/genética , Sequência Conservada/genética , Motivos de Nucleotídeos/genética , Receptores de Superfície Celular/genética , Sinorhizobium meliloti/genética , Reação em Cadeia da Polimerase em Tempo Real , Sinorhizobium meliloti/crescimento & desenvolvimento
14.
Nucleic Acids Res ; 47(7): 3728-3738, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-30753696

RESUMO

Members of the pentatricopeptide repeat (PPR) protein family are sequence-specific RNA-binding proteins that play crucial roles in organelle RNA metabolism. Each PPR protein consists of a tandem array of PPR motifs, each of which aligns to one nucleotide of the RNA target. The di-residues in the PPR motif, which are referred to as the PPR codes, determine nucleotide specificity. Numerous PPR codes are distributed among the vast number of PPR motifs, but the correlation between PPR codes and RNA bases is poorly understood, which hinders target RNA prediction and functional investigation of PPR proteins. To address this issue, we developed a modular assembly method for high-throughput construction of designer PPRs, and by using this method, 62 designer PPR proteins containing various PPR codes were assembled. Then, the correlation between these PPR codes and RNA bases was systematically explored and delineated. Based on this correlation, the web server PPRCODE (http://yinlab.hzau.edu.cn/pprcode) was developed. Our study will not only serve as a platform for facilitating target RNA prediction and functional investigation of the large number of PPR family proteins but also provide an alternative strategy for the assembly of custom PPRs that can potentially be used for plant organelle RNA manipulation.


Assuntos
Proteínas de Arabidopsis/genética , Motivos de Nucleotídeos/genética , Proteínas de Ligação a RNA/genética , RNA/genética , Sequência de Aminoácidos/genética , Arabidopsis/genética , Modelos Moleculares , Organelas/genética
15.
Brain ; 142(2): 276-294, 2019 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-30649277

RESUMO

Spinal muscular atrophy is a motor neuron disorder caused by mutations in SMN1. The reasons for the selective vulnerability of motor neurons linked to SMN (encoded by SMN1) reduction remain unclear. Therefore, we performed deep RNA sequencing on human spinal muscular atrophy motor neurons to detect specific altered gene splicing/expression and to identify the presence of a common sequence motif in these genes. Many deregulated genes, such as the neurexin and synaptotagmin families, are implicated in critical motor neuron functions. Motif-enrichment analyses of differentially expressed/spliced genes, including neurexin2 (NRXN2), revealed a common motif, motif 7, which is a target of SYNCRIP. Interestingly, SYNCRIP interacts only with full-length SMN, binding and modulating several motor neuron transcripts, including SMN itself. SYNCRIP overexpression rescued spinal muscular atrophy motor neurons, due to the subsequent increase in SMN and their downstream target NRXN2 through a positive loop mechanism and ameliorated SMN-loss-related pathological phenotypes in Caenorhabditis elegans and mouse models. SMN/SYNCRIP complex through motif 7 may account for selective motor neuron degeneration and represent a potential therapeutic target.


Assuntos
Ribonucleoproteínas Nucleares Heterogêneas/genética , Neurônios Motores/fisiologia , Atrofia Muscular Espinal/genética , Motivos de Nucleotídeos/genética , Análise de Sequência de RNA/métodos , Proteína 1 de Sobrevivência do Neurônio Motor/genética , Animais , Caenorhabditis elegans , Linhagem Celular Tumoral , Sobrevivência Celular/fisiologia , Humanos , Células-Tronco Pluripotentes Induzidas/patologia , Células-Tronco Pluripotentes Induzidas/fisiologia , Camundongos , Camundongos Transgênicos , Neurônios Motores/patologia , Atrofia Muscular Espinal/patologia , RNA/genética
16.
Mol Biol Rep ; 46(1): 777-791, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30535894

RESUMO

E2 (ubiquitin conjugating enzymes) is an important part of the ubiquitin-proteasome pathway. These enzymes have a significant role to play during plant growth and development, which can response to various stresses. To date, the E2 family has been reported in some high plants, but the genome-wide characterization of this gene family in potato remains unknown. In the present study, 57 putative StUBCs were identified, which were clustered into eight subgroups based on phylogeny. The introns varied in numbers 0 to 9. The highest numbers of introns were 5, which accounted for 31.57%. The analysis of gene duplication showed that 22 StUBC genes were involved in 13 segmental duplication events, while no tandem duplication was found in StUBC genes. According to gene ontology analysis (GO), StUBC family major function is protein binding and ion binding. The RNA sequencing data revealed that 15 StUBC genes were highly expressed in different organs and tubers. 27 StUBC genes were up-regulated under 50 µM ABA treatments. Moreover, the RNA-seq data and qRT-PCR analysis indicated that 17 StUBC genes responded to heat stress. 8 StUBC genes responded to salt stress according to qRT-PCR analysis, and StUBC2, StUBC12, StUBC30 and StUBC13 were predominant expression. The result of this research could provide valuable information to insight into potato E2 family and establish a foundation for further to elucidate function of E2 genes.


Assuntos
Regulação da Expressão Gênica de Plantas , Genoma de Planta , Família Multigênica , Solanum tuberosum/genética , Arabidopsis/genética , Cromossomos de Plantas/genética , Sequência Conservada , Éxons/genética , Duplicação Gênica , Perfilação da Expressão Gênica , Ontologia Genética , Genes de Plantas , Íntrons/genética , Motivos de Nucleotídeos/genética , Especificidade de Órgãos/genética , Filogenia , Regiões Promotoras Genéticas/genética , Solanum tuberosum/fisiologia , Estresse Fisiológico/genética , Sintenia/genética
17.
Nucleic Acids Res ; 47(4): 1628-1636, 2019 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-30590725

RESUMO

Bound by transcription factors, DNA motifs (i.e. transcription factor binding sites) are prevalent and important for gene regulation in different tissues at different developmental stages of eukaryotes. Although considerable efforts have been made on elucidating monomeric DNA motif patterns, our knowledge on heterodimeric DNA motifs are still far from complete. Therefore, we propose to develop a computational approach to synthesize a heterodimeric DNA motif from two monomeric DNA motifs. The approach is sequentially divided into two components (Phases A and B). In Phase A, we propose to develop the inference models on how two DNA monomeric motifs can be oriented and overlapped with each other at nucleotide level. In Phase B, given the two monomeric DNA motifs oriented, we further propose to develop DNA-binding family-specific input-output hidden Markov models (IOHMMs) to synthesize a heterodimeric DNA motif. To validate the approach, we execute and cross-validate it with the experimentally verified 618 heterodimeric DNA motifs across 49 DNA-binding family combinations. We observe that our approach can even "rescue" the existing heterodimeric DNA motif pattern (i.e. HOXB2_EOMES) previously published on Nature. Lastly, we apply the proposed approach to infer previously uncharacterized heterodimeric motifs. Their motif instances are supported by DNase accessibility, gene ontology, protein-protein interactions, in vivo ChIP-seq peaks, and even structural data from PDB. A public web-server is built for open accessibility and scientific impact. Its address is listed as follows: http://motif.cs.cityu.edu.hk/custom/MotifKirin.


Assuntos
Biologia Computacional , Genômica/métodos , Motivos de Nucleotídeos/genética , Fatores de Transcrição/genética , Algoritmos , Sítios de Ligação/genética , Replicação do DNA/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Humanos , Cadeias de Markov , Elementos Reguladores de Transcrição/genética , Análise de Sequência de DNA/métodos , Software , Fatores de Transcrição/química
18.
Int J Mol Sci ; 19(12)2018 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-30544665

RESUMO

In plants, the HAK (high-affinity K⁺)/KUP (K⁺ uptake)/KT (K⁺ transporter) family represents a large group of potassium transporters that play important roles in plant growth and environmental adaptation. Although HAK/KUP/KT genes have been extensively investigated in many plant species, they remain uncharacterized in wheat, especially those involved in the response to environmental stresses. In this study, 56 wheat HAK/KUP/KT (hereafter called TaHAKs) genes were identified by a genome-wide search using recently released wheat genomic data. Phylogenetic analysis grouped these genes into four clusters (Ι, II, III, IV), containing 22, 19, 7 and 8 genes, respectively. Chromosomal distribution, gene structure, and conserved motif analyses of the 56 TaHAK genes were subsequently performed. In silico RNA-seq data analysis revealed that TaHAKs from clusters II and III are constitutively expressed in various wheat tissues, while most genes from clusters I and IV have very low expression levels in the examined tissues at different developmental stages. qRT-PCR analysis showed that expression levels of TaHAK genes in wheat seedlings were significantly up- or downregulated when seedlings were exposed to K⁺ deficiency, high salinity, or dehydration. Furthermore, we functionally characterized TaHAK1b-2BL and showed that it facilitates K⁺ transport in yeast. Collectively, these results provide valuable information for further functional studies of TaHAKs, and contribute to a better understanding of the molecular basis of wheat development and stress tolerance.


Assuntos
Proteínas de Transporte de Cátions/genética , Genoma de Planta , Família Multigênica , Proteínas de Plantas/genética , Triticum/genética , Proteínas de Transporte de Cátions/metabolismo , Cromossomos de Plantas/genética , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas , Motivos de Nucleotídeos/genética , Filogenia , Proteínas de Plantas/metabolismo , Saccharomyces cerevisiae/metabolismo , Cloreto de Sódio/farmacologia , Estresse Fisiológico/efeitos dos fármacos , Estresse Fisiológico/genética , Triticum/efeitos dos fármacos , Triticum/fisiologia
19.
Cell Rep ; 25(13): 3591-3602.e5, 2018 12 26.
Artigo em Inglês | MEDLINE | ID: mdl-30590035

RESUMO

Human primordial germ cells (hPGCs) are the first embryonic progenitors in the germ cell lineage, yet the molecular mechanisms required for hPGC formation are not well characterized. To identify regulatory regions in hPGC development, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to systematically characterize regions of open chromatin in hPGCs and hPGC-like cells (hPGCLCs) differentiated from human embryonic stem cells (hESCs). We discovered regions of open chromatin unique to hPGCs and hPGCLCs that significantly overlap with TFAP2C-bound enhancers identified in the naive ground state of pluripotency. Using CRISPR/Cas9, we show that deleting the TFAP2C-bound naive enhancer at the OCT4 locus (also called POU5F1) results in impaired OCT4 expression and a negative effect on hPGCLC identity.


Assuntos
Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica no Desenvolvimento , Células Germinativas/metabolismo , Fator 3 de Transcrição de Octâmero/genética , Fator de Transcrição AP-2/metabolismo , Cromatina/metabolismo , Feminino , Células Germinativas/citologia , Humanos , Fatores de Transcrição Kruppel-Like/metabolismo , Masculino , Motivos de Nucleotídeos/genética , Células-Tronco Pluripotentes/metabolismo , Transcriptoma/genética
20.
Plant Physiol Biochem ; 132: 104-119, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30179736

RESUMO

Studies have shown that basic helix-loop-helix (bHLH) transcription factors play important roles in plant growth and survival, and response to various biotic/abiotic stresses. We identified a total of 448 bHLH genes. These genes were classified into 21 bHLH subfamilies, and most genes in a given subfamily had similar gene structures and conserved motifs. We identified 176 homologous pairs in the three species. We calculated Ka, Ks, and Ka/Ks to analyze the replication relationships among the three species. Multiple sequence analysis revealed that the PebHLH genes had the distinct bHLH structure. The gene ontology annotation analysis showed that the PebHLH genes had many molecular functions. Promoter cis-element analysis revealed that most of the PebHLH genes contained cis-elements that can respond to various biotic/abiotic stress-related events. The tissue expression patterns of the PebHLH genes indicated that most members were expressed in leaves, roots, and stems. Quantitative real-time PCR analysis showed that 21 selected PebHLH genes were differentially regulated after abscisic acid, drought, and methyl jasmonate treatments. This study has laid the basis for studying the functions of AtbHLH, OsbHLH, and PebHLH genes, and will contribute to future studies of the functions of bHLH genes in other plant species.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Família Multigênica , Filogenia , Poaceae/genética , Arabidopsis/genética , Sequência Conservada/genética , Perfilação da Expressão Gênica , Ontologia Genética , Genes de Plantas , Anotação de Sequência Molecular , Motivos de Nucleotídeos/genética , Oryza/genética , Regiões Promotoras Genéticas , Estresse Fisiológico/genética
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