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1.
Cancer Discov ; 9(10): 1343-1345, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31575563

RESUMO

In this issue of Cancer Discovery, Halbritter and colleagues utilize single-cell RNA sequencing to dissect the cellular hierarchy in Langerhans cell histiocytosis. They identified a remarkably consistent composition of 14 cellular subsets across all patients with a range of clinical spectrums consistent with a shared developmental hierarchy driven by key transcriptional regulators.See related article by Halbritter et al., p. 1406.


Assuntos
Epigenômica , Histiocitose de Células de Langerhans , Humanos , Análise de Sequência de RNA
2.
Arch Virol ; 164(11): 2829-2836, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31486908

RESUMO

The complete sequence of the medium (M) and small (S) RNA genome segments were determined for twelve isolates of impatiens necrotic spot virus from eight plant species. The M- and S-RNAs of these isolates shared 97-99% and 93-98% nucleotide sequence identity, respectively, with the corresponding full-length sequences available in public databases. Phylogenetic analysis based on the M- or S-RNA sequences showed incongruence in the phylogenetic position of some isolates, suggesting intraspecies segment reassortment. The lack of phylogenetic discordance in individual and concatenated sequences of individual genes encoded by M- or S-RNAs suggests that segment reassortment rather than recombination is driving evolution of these INSV isolates.


Assuntos
RNA Viral/genética , Vírus Reordenados/genética , Tospovirus/genética , Sequência de Bases , Genoma Viral/genética , Plantas/virologia , Análise de Sequência de RNA , Tospovirus/isolamento & purificação
3.
BMC Plant Biol ; 19(1): 337, 2019 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375064

RESUMO

BACKGROUND: Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. RESULTS: In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. CONCLUSIONS: RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.


Assuntos
Flores/metabolismo , Genes de Plantas/genética , Odorantes , Orchidaceae/genética , Acetatos/metabolismo , Ciclopentanos/metabolismo , Farneseno Álcool/metabolismo , Flores/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas/fisiologia , Orchidaceae/metabolismo , Oxilipinas/metabolismo , Filogenia , Análise de Sequência de RNA , Sesquiterpenos/metabolismo , Terpenos/metabolismo
4.
J Forensic Leg Med ; 67: 37-48, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31419763

RESUMO

Previous studies have begun to characterize the microbial community dynamics of the skin, soil, gut, and oral cavities of decomposing remains. One area that has yet to be explored in great detail is the microbiome of the fly larval mass, the community of immature flies that plays a significant role in decomposition. The current study aimed to characterize the microbiology and chemistry of larval masses established on pig (Sus scrofa domesticus) carcasses and to determine if these characteristics have potential as temporal evidence. Carcasses (n = 3) were decomposed on the soil surface of a tropical habitat on Oahu, Hawaii, USA and sampled over three days at 74 h, 80 h, 98 h, 104 h, 122 h, and 128 h (∼85-142 Accumulated Degree Days) postmortem. Larval masses were analyzed via high-throughput 16S rRNA sequencing and in situ chemical measurements (pH, temperature, oxidation-reduction potential). A trend was observed that resulted in three distinct microbial communities (pre-98 h, 98 h, and post-98 h). The oxidation-reduction potential (Eh) of larval masses apparently regulated microbial community structure with the most negative Eh being associated with the least rich and diverse microbial communities. Overall, a significant interaction between time and taxa was observed, particularly with bacterial phyla Firmicutes and Proteobacteria. The current results provide new insight into the microbial community and chemical parameters of larval masses and indicate a temporal shift that could be further studied as a PMI estimator.


Assuntos
Comportamento Alimentar , Larva/química , Larva/microbiologia , Microbiota , Mudanças Depois da Morte , Animais , Bactérias/genética , Entomologia , Patologia Legal , Hawaii , Concentração de Íons de Hidrogênio , Modelos Animais , Oxirredução , RNA Ribossômico 16S , Análise de Sequência de RNA , Suínos
5.
BMC Plant Biol ; 19(1): 367, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31429697

RESUMO

BACKGROUND: Adaptation to abiotic stresses is crucial for the survival of perennial plants in a natural environment. However, very little is known about the underlying mechanisms. Here, we adopted a liquid culture system to investigate plant adaptation to repeated salt stress in Populus trees. RESULTS: We first evaluated phenotypic responses and found that plants exhibit better stress tolerance after pre-treatment of salt stress. Time-course RNA sequencing (RNA-seq) was then performed to profile changes in gene expression over 12 h of salt treatments. Analysis of differentially expressed genes (DEGs) indicated that significant transcriptional reprogramming and adaptation to repeated salt treatment occurred. Clustering analysis identified two modules of co-expressed genes that were potentially critical for repeated salt stress adaptation, and one key module for salt stress response in general. Gene Ontology (GO) enrichment analysis identified pathways including hormone signaling, cell wall biosynthesis and modification, negative regulation of growth, and epigenetic regulation to be highly enriched in these gene modules. CONCLUSIONS: This study illustrates phenotypic and transcriptional adaptation of Populus trees to salt stress, revealing novel gene modules which are potentially critical for responding and adapting to salt stress.


Assuntos
Adaptação Fisiológica/genética , Regulação da Expressão Gênica de Plantas , Populus/genética , Estresse Salino/genética , Transcrição Genética , Ontologia Genética , Redes Reguladoras de Genes , Genoma de Planta , Fenótipo , Populus/fisiologia , RNA de Plantas , Análise de Sequência de RNA , Transcriptoma , Árvores/genética , Árvores/fisiologia
6.
BMC Plant Biol ; 19(1): 369, 2019 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-31438855

RESUMO

BACKGROUND: Cucumis melo is a suitable study material for investigation of fruit ripening owing to its climacteric nature. Long non-coding RNAs have been linked to many important biological processes, such as fruit ripening, flowering time regulation, and abiotic stress responses in plants. However, knowledge of the regulatory roles of lncRNAs underlying the ripening process in C. melo are largely unknown. In this study the complete transcriptome of Cucumis melo L. cv. Hetao fruit at four developmental stages was sequenced and analyzed. The potential role of lncRNAs was predicted based on the function of differentially expressed target genes and correlated genes. RESULTS: In total, 3857 lncRNAs were assembled and annotated, of which 1601 were differentially expressed between developmental stages. The target genes of these lncRNAs and the regulatory relationship (cis- or trans-acting) were predicted. The target genes were enriched with GO terms for biological process, such as response to auxin stimulus and hormone biosynthetic process. Enriched KEGG pathways included plant hormone signal transduction and carotenoid biosynthesis. Co-expression network construction showed that LNC_002345 and LNC_000154, which were highly expressed, might co-regulate with mutiple genes associated with auxin signal transduction and acted in the same pathways. We identified lncRNAs (LNC_000987, LNC_000693, LNC_001323, LNC_003610, LNC_001263 and LNC_003380) that were correlated with fruit ripening and the climacteric, and may participate in the regulation of ethylene biosynthesis and metabolism and the ABA signaling pathway. A number of crucial transcription factors, such as ERFs, WRKY70, NAC56, and NAC72, may also play important roles in the regulation of fruit ripening in C. melo. CONCLUSIONS: Our results predict the regulatory functions of the lncRNAs during melon fruit development and ripening, and 142 highly expressed lncRNAs (average FPKM > 100) were identified. These lncRNAs participate in the regulation of auxin signal transduction, ethylene, sucrose biosynthesis and metabolism, the ABA signaling pathway, and transcription factors, thus regulating fruit development and ripening.


Assuntos
Cucumis melo/genética , Frutas/genética , RNA Longo não Codificante/fisiologia , RNA de Plantas/fisiologia , Mapeamento Cromossômico , Climatério , Cucumis melo/crescimento & desenvolvimento , Frutas/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Genoma de Planta , Fenótipo , Reguladores de Crescimento de Planta/metabolismo , Análise de Sequência de RNA , Transdução de Sinais , Transcriptoma
7.
Gene ; 717: 143998, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31381951

RESUMO

Eid1 is a member of the EID protein family, which regulates differentiation, transcription and acetyltransferase activity. Accumulating evidence suggests that Eid1 is relevant to neurological disorder, but the main function of Eid1 is still unclear, especially in the brain. To better understand this issue, we generated Eid1-knockout (Eid1-KO) mice and profiled its gene expression changes in the brain by RNA sequencing. This study identified 2531 genes differentially expressed in Eid1-KO mice compared with the wild-type, then qRT-PCR verification demonstrated that the transcriptomic data are reliable. By protein-protein interaction cluster analysis, 'regulation of cell proliferation' were unexpectedly discovered as important Eid1 functions. We then isolated neural progenitor cells (NPCs) and showed that the number of neurospheres and the proliferation rate of Eid1-KO NPCs were obviously lower than that in the control group, furthermore, CCK-8 and immunofluorescence assay clearly demonstrated that the Eid1-KO NPCs showed significantly less cell proliferation than the control group. To the best of our knowledge, this is the first comprehensive report of the Eid1-KO transcriptome of mice brain. Our analysis and experimental data provide a foundation for further studies on understanding function of Eid1 in the brain.


Assuntos
Encéfalo/citologia , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Animais , Encéfalo/embriologia , Encéfalo/fisiologia , Proliferação de Células/genética , Feminino , Perfilação da Expressão Gênica , Camundongos Endogâmicos C57BL , Camundongos Knockout , Células-Tronco Neurais/citologia , Células-Tronco Neurais/fisiologia , Gravidez , Mapas de Interação de Proteínas , Análise de Sequência de RNA
8.
Arch Virol ; 164(11): 2853-2857, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31377887

RESUMO

A double-stranded RNA (dsRNA) segment was extracted from the ectomycorrhizal fungus Geopora sumneriana (Cooke) M. Torre, and its full-length cDNA sequence, comprising 3146 nucleotides, was determined. Sequence analysis revealed the presence of a large open reading frame (ORF) on the positive strand of this dsRNA segment when the mold mitochondrial genetic code was applied. The ORF encodes a putative RNA-dependent RNA polymerase (RdRp), which shares the highest degree of similarity with Tuber excavatum mitovirus, with 37.52% identity. This dsRNA segment represents the genome replication intermediate of a novel mitovirus that was tentatively designated as "Geopora sumneriana mitovirus 1" (GsMV1). Phylogenetic analysis further suggested that GsMV1 is a member of the family Narnaviridae. This is the first study reporting on a mitovirus genome sequence in the ectomycorrhizal fungus G. sumneriana.


Assuntos
Colletotrichum/virologia , Micovírus/classificação , Micovírus/genética , Genoma Viral/genética , Sequência de Aminoácidos , Sequência de Bases , Micovírus/isolamento & purificação , Fases de Leitura Aberta/genética , RNA Replicase/genética , RNA Viral/genética , Análise de Sequência de RNA , Sequenciamento Completo do Genoma
9.
Medicine (Baltimore) ; 98(34): e16916, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31441872

RESUMO

BACKGROUND: Colorectal Cancer (CRC) is a highly heterogeneous disease. RNA profiles of bulk tumors have enabled transcriptional classification of CRC. However, such ways of sequencing can only target a cell colony and obscure the signatures of distinct cell populations. Alternatively, single-cell RNA sequencing (scRNA-seq), which can provide unbiased analysis of all cell types, opens the possibility to map cellular heterogeneity of CRC unbiasedly. METHODS: In this study, we utilized scRNA-seq to profile cells from cancer tissue of a CRC patient. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to understand the roles of genes within the clusters. RESULTS AND CONCLUSION: The 2824 cells were analyzed and categorized into 5 distinct clusters by scRNA-seq. For every cluster, specific cell markers can be applied, indicating each 1 of them different from another. We discovered that the tumor of CRC displayed a clear sign of heterogenicity, while genes within each cluster serve different functions. GO term analysis also stated that different cluster's relatedness towards the tumor of CRC differs. Three clusters participate in peripheral works in cells, including, energy transport, extracellular matrix generation, etc; Genes in other 2 clusters participate more in immunology processes. Lastly, trajectory plot analysis also supports the viewpoint, in that some clusters present in different states and pseudo-time, while others present in a single state or pseudo time. Our analysis provides more insight into the heterogeneity of CRC, which can provide assistance to further researches on this topic.


Assuntos
Neoplasias Colorretais/genética , Perfilação da Expressão Gênica/métodos , Heterogeneidade Genética , Análise de Sequência de RNA/métodos , Idoso , Biomarcadores Tumorais/genética , Feminino , Humanos
10.
Biol Res ; 52(1): 48, 2019 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-31466525

RESUMO

BACKGROUND: Light exposure is a common stress factor in in vitro manipulation of embryos in the reproductive center. Many studies have shown the deleterious effects of high-intensity light exposure in different animal embryos. However, no transcriptomic studies have explored the light-induced injury and response in preimplantation embryos. RESULTS: Here, we adopt different time-courses and illumination intensities to treat mouse embryos at the 2-cell stage and evaluate their effects on blastulation. Meanwhile, single-cell transcriptomes from the 2-cell to blastocyst stage were analyzed after high-intensity light exposure. These data show that cells at each embryonic stage can be categorized into different light conditions. Further analyses of differentially expressed genes and GO terms revealed the light-induced injury as well as the potential repair response after high-intensity lighting. Maternal-to-zygote transition is also affected by the failure to remove maternal RNAs and deactivate zygotic genome expression. CONCLUSION: Our work revealed an integrated response to high-intensity lighting, involving morphological changes, long-lasting injury effects, and intracellular damage repair mechanisms.


Assuntos
Técnicas de Cultura Embrionária , Desenvolvimento Embrionário , Luz/efeitos adversos , Análise de Sequência de RNA , Análise de Célula Única , Animais , Blastocisto , Feminino , Camundongos , Camundongos Endogâmicos C57BL
11.
BMC Plant Biol ; 19(1): 352, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31412781

RESUMO

BACKGROUND: Rice plants show yellowing, stunting, withering, reduced tillering and utimately low productivity in susceptible varieties under low temperature stress. Comparative transcriptome analysis was performed to identify novel transcripts, gain new insights into different gene expression and pathways involved in cold tolerance in rice. RESULTS: Comparative transcriptome analyses of 5 treatments based on chilling stress exposure revealed more down regulated genes in susceptible and higher up regulated genes in tolerant genotypes. A total of 13930 and 10599 differentially expressed genes (DEGs) were detected in cold susceptible variety (CSV) and cold tolerant variety (CTV), respectively. A continuous increase in DEGs at 6, 12, 24 and 48 h exposure of cold stress was detected in both the genotypes. Gene ontology (GO) analysis revealed 18 CSV and 28 CTV term significantly involved in molecular function, cellular component and biological process. GO classification showed a significant role of transcription regulation, oxygen, lipid binding, catalytic and hydrolase activity for tolerance response. Absence of photosynthesis related genes, storage products like starch and synthesis of other classes of molecules like fatty acids and terpenes during the stress were noticed in susceptible genotype. However, biological regulations, generation of precursor metabolites, signal transduction, photosynthesis, regulation of cellular process, energy and carbohydrate metabolism were seen in tolerant genotype during the stress. KEGG pathway annotation revealed more number of genes regulating different pathways resulting in more tolerant. During early response phase, 24 and 11 DEGs were enriched in CTV and CSV, respectively in energy metabolism pathways. Among the 1583 DEG transcription factors (TF) genes, 69 WRKY, 46 bZIP, 41 NAC, 40 ERF, 31/14 MYB/MYB-related, 22 bHLH, 17 Nin-like 7 HSF and 4C3H were involved during early response phase. Late response phase showed 30 bHLH, 65 NAC, 30 ERF, 26/20 MYB/MYB-related, 11 C3H, 12 HSF, 86 Nin-like, 41 AP2/ERF, 55 bZIP and 98 WRKY members TF genes. The recovery phase included 18 bHLH, 50 NAC, 31 ERF, 24/13 MYB/MYB-related, 4 C3H, 4 HSF, 14 Nin-like, 31 bZIP and 114 WRKY TF genes. CONCLUSIONS: Transcriptome analysis of contrasting genotypes for cold tolerance detected the genes, pathways and transcription factors involved in the stress tolerance.


Assuntos
Resposta ao Choque Frio/genética , Oryza/genética , Proteínas de Plantas/fisiologia , Fatores de Transcrição/fisiologia , Metabolismo Energético , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genótipo , Oryza/metabolismo , Oryza/fisiologia , Fotossíntese , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Análise de Sequência de RNA , Transdução de Sinais , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
12.
BMC Bioinformatics ; 20(1): 421, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409274

RESUMO

BACKGROUND: Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing or differential gene expression analysis, without including a non-essential transcript quantification step. RESULTS: In this paper, we introduce a transcriptome segmentation approach to decouple these two tasks. We propose an efficient algorithm to generate maximal disjoint segments given a transcriptome reference library on which ultra-fast pseudo-alignment can be used to produce per-sample segment counts. We show how to apply these maximally unambiguous count statistics in two specific expression analyses - alternative splicing and gene differential expression - without the need of a transcript quantification step. Our experiments based on simulated and experimental data showed that the use of segment counts, like other methods that rely on local coverage statistics, provides an advantage over approaches that rely on transcript quantification in detecting and correctly estimating local splicing in the case of incomplete transcript annotations. CONCLUSIONS: The transcriptome segmentation approach implemented in Yanagi exploits the computational and space efficiency of pseudo-alignment approaches. It significantly expands their applicability and interpretability in a variety of RNA-seq analyses by providing the means to model and capture local coverage variation in these analyses.


Assuntos
Algoritmos , Transcriptoma , Processamento Alternativo , Animais , Área Sob a Curva , Drosophila/genética , Humanos , RNA/química , RNA/metabolismo , Curva ROC , Análise de Sequência de RNA
13.
BMC Bioinformatics ; 20(1): 418, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409293

RESUMO

BACKGROUND: Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling. Preparation of hundreds or more samples for a large study often requires multiple library pools. However, sometimes correlation between expression profiles among the libraries is low and batch effect biases make integration of data between library pools difficult. RESULTS: We investigated 166 technical replicates in 14 RNAseq libraries made using the STRT method. The patterns of the library biases differed by genes, and uneven library yields were associated with library biases. The former bias was corrected using the NBGLM-LBC algorithm, which we present in the current study. The latter bias could not be corrected directly, but could be solved by omitting libraries with particularly low yields. A simulation experiment suggested that the library bias correction using NBGLM-LBC requires a consistent sample layout. The NBGLM-LBC correction method was applied to an expression profile for a cohort study of childhood acute respiratory illness, and the library biases were resolved. CONCLUSIONS: The R source code for the library bias correction named NBGLM-LBC is available at https://shka.github.io/NBGLM-LBC and https://shka.bitbucket.io/NBGLM-LBC . This method is applicable to correct the library biases in various studies that use highly multiplexed sequencing-based profiling methods with a consistent sample layout with samples to be compared (e.g., "cases" and "controls") equally distributed in each library.


Assuntos
Biblioteca Gênica , Análise de Sequência de RNA/métodos , Transcriptoma , Linhagem Celular , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Componente Principal , RNA/química , RNA/metabolismo , Interface Usuário-Computador
14.
Nat Commun ; 10(1): 3004, 2019 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-31285436

RESUMO

Identity determining transcription factors (TFs), or core regulatory (CR) TFs, are governed by cell-type specific super enhancers (SEs). Drugs to selectively inhibit CR circuitry are of high interest for cancer treatment. In alveolar rhabdomyosarcoma, PAX3-FOXO1 activates SEs to induce the expression of other CR TFs, providing a model system for studying cancer cell addiction to CR transcription. Using chemical genetics, the systematic screening of chemical matter for a biological outcome, here we report on a screen for epigenetic chemical probes able to distinguish between SE-driven transcription and constitutive transcription. We find that chemical probes along the acetylation-axis, and not the methylation-axis, selectively disrupt CR transcription. Additionally, we find that histone deacetylases (HDACs) are essential for CR TF transcription. We further dissect the contribution of HDAC isoforms using selective inhibitors, including the newly developed selective HDAC3 inhibitor LW3. We show HDAC1/2/3 are the co-essential isoforms that when co-inhibited halt CR transcription, making CR TF sites hyper-accessible and disrupting chromatin looping.


Assuntos
Elementos Facilitadores Genéticos/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Inibidores de Histona Desacetilases/farmacologia , Histona Desacetilases/metabolismo , Rabdomiossarcoma/genética , Acetilação/efeitos dos fármacos , Linhagem Celular Tumoral , Cromatina/efeitos dos fármacos , Cromatina/metabolismo , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Ensaios de Triagem em Larga Escala , Inibidores de Histona Desacetilases/química , Histona Desacetilases/química , Humanos , Simulação de Dinâmica Molecular , Sondas Moleculares/química , Sondas Moleculares/farmacologia , Proteínas de Fusão Oncogênica/genética , Fatores de Transcrição Box Pareados/genética , Cultura Primária de Células , Isoformas de Proteínas/antagonistas & inibidores , Isoformas de Proteínas/química , Isoformas de Proteínas/metabolismo , Rabdomiossarcoma/patologia , Análise de Sequência de RNA , Transcrição Genética/efeitos dos fármacos
15.
Plant Mol Biol ; 101(1-2): 129-148, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31267256

RESUMO

Iron and phosphorus are abundant elements in soils but poorly available for plant nutrition. The availability of these two nutrients represents a major constraint for fruit tree cultivation such as apple (Malus × domestica) leading very often to a decrease of fruit productivity and quality worsening. Aim of this study was to characterize common and specific features of plant response to Fe and P deficiencies by ionomic, transcriptomic and exudation profiling of apple roots. Under P deficiency, the root release of oxalate and flavonoids increased. Genes encoding for transcription factors and transporters involved in the synthesis and release of root exudates were upregulated by P-deficient roots, as well as those directly related to P acquisition. In Fe-deficiency, plants showed an over-accumulation of P, Zn, Cu and Mn and induced the transcription of those genes involved in the mechanisms for the release of Fe-chelating compounds and Fe mobilization inside the plants. The intriguing modulation in roots of some transcription factors, might indicate that, in this condition, Fe homeostasis is regulated by a FIT-independent pathway. In the present work common and specific features of apple response to Fe and P deficiency has been reported. In particular, data indicate similar modulation of a. 230 genes, suggesting the occurrence of a crosstalk between the two nutritional responses involving the transcriptional regulation, shikimate pathway, and the root release of exudates.


Assuntos
Ferro/deficiência , Malus/fisiologia , Fósforo/deficiência , Transcriptoma , Transporte Biológico , Perfilação da Expressão Gênica , Homeostase , Ferro/metabolismo , Malus/genética , Fósforo/metabolismo , Exsudatos de Plantas/metabolismo , Folhas de Planta/genética , Folhas de Planta/fisiologia , Raízes de Plantas/genética , Raízes de Plantas/fisiologia , Análise de Sequência de RNA
16.
Plant Mol Biol ; 101(1-2): 163-182, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31273589

RESUMO

KEY MESSAGE: Deeper insights into the resistance response of Cajanus platycarpus were obtained based on comparative transcriptomics under Helicoverpa armigera infestation. Devastation by pod borer, Helicoverpa armigera is one of the major factors for stagnated productivity in Pigeonpea. Despite possessing a multitude of desirable traits including pod borer resistance, wild relatives of Cajanus spp. have remained under-utilized due to linkage drag and cross-incompatibility. Discovery and deployment of genes from them can provide means to tackle key pests like H. armigera. Transcriptomic differences between Cajanus platycarpus and Cajanus cajan during different time points (0, 18, 38, 96 h) of pod borer infestation were elucidated in this study. For the first ever time, we demonstrated captivating variations in their response; C. platycarpus apparently being reasonably agile with effectual transcriptomic reprogramming to deter the insect. Deeper insights into the differential response were obtained by identification of significant GO-terms related to herbivory followed by combined KEGG and ontology analyses. C. platycarpus portrayed a multilevel response with cardinal involvement of SAR, redox homeostasis and reconfiguration of primary metabolites leading to a comprehensive defense response. The credibility of RNA-seq analyses was ascertained by transient expression of selected putative insect resistance genes from C. platycarpus viz., chitinase (CHI4), Alpha-amylase/subtilisin inhibitor (IAAS) and Flavonoid 3_5 hydroxylase (C75A1) in Nicotiana benthamiana followed by efficacy analysis against H. armigera. qPCR validated results of the study provided innovative insights and useful leads for development of durable pod borer resistance.


Assuntos
Cajanus/genética , Resistência à Doença/genética , Mariposas/fisiologia , Doenças das Plantas/imunologia , Transcriptoma , Animais , Cajanus/imunologia , Cajanus/parasitologia , Perfilação da Expressão Gênica , Genômica , Herbivoria , Sequenciamento de Nucleotídeos em Larga Escala , Doenças das Plantas/parasitologia , Análise de Sequência de RNA
17.
BMC Plant Biol ; 19(1): 313, 2019 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-31307374

RESUMO

BACKGROUND: Essential oils (EOs) of Lavandula angustifolia, mainly consist of monoterpenoids and sesquiterpenoids, are of great commercial value. The multi-flower spiciform thyrse of lavender not only determines the output of EOs but also reflects an environmental adaption strategy. With the flower development and blossom in turn, the fluctuation of the volatile terpenoids displayed a regular change at each axis. However, the molecular mechanism underlying the regulation of volatile terpenoids during the process of flowering is poorly understood in lavender. Here, we combine metabolite and RNA-Seq analyses of flowers of five developmental stages at first- and second-axis (FFDSFSA) and initial flower bud (FB0) to discover the active terpenoid biosynthesis as well as flowering-related genes. RESULTS: A total of 56 mono- and sesquiterpenoids were identified in the EOs of L. angustifolia 'JX-2'. FB0' EO consists of 55 compounds and the two highest compounds, ß-trans-ocimene (20.57%) and (+)-R-limonene (17.00%), can get rid of 74.71 and 78.41% aphids in Y-tube olfactometer experiments, respectively. With sequential and successive blossoms, temporally regulated volatiles were linked to pollinator attraction in field and olfaction bioassays. In three characteristic compounds of FFDSFSA' EOs, linalyl acetate (72.73%) and lavandulyl acetate (72.09%) attracted more bees than linalool (45.35%). Many transcripts related to flowering time and volatile terpenoid metabolism expressed differently during the flower development. Similar metabolic and transcriptomic profiles were observed when florets from the two axes were maintained at the same maturity grade. Besides both compounds and differentially expressed genes were rich in FB0, most volatile compounds were significantly correlated with FB0-specific gene module. Most key regulators related to flowering and terpenoid metabolism were interconnected in the subnetwork of FB0-specific module, suggesting the cross-talk between the two biological processes to some degree. CONCLUSIONS: Characteristic compounds and gene expression profile of FB0 exhibit ecological value in pest control. The precise control of each-axis flowering and regular emissions at transcriptional and metabolic level are important to pollinators attraction for lavender. Our study sheds new light on lavender maximizes its fitness from "gene-volatile terpenoid-insect" three layers.


Assuntos
Flores/genética , Redes Reguladoras de Genes , Lavandula/genética , Terpenos/metabolismo , Acetatos/metabolismo , Animais , Ecossistema , Flores/crescimento & desenvolvimento , Flores/metabolismo , Perfilação da Expressão Gênica , Insetos , Lavandula/crescimento & desenvolvimento , Lavandula/metabolismo , Monoterpenos/metabolismo , Odorantes , Óleos Voláteis/metabolismo , Óleos Vegetais/metabolismo , Polinização , RNA de Plantas , Análise de Sequência de RNA
18.
J Photochem Photobiol B ; 197: 111550, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31330424

RESUMO

The plant species of the genus Epimedium L. are well-known traditional Chinese medicinal herbs with special therapeutic effects on human beings and animals in invigorating sexuality and strengthening muscles and bones. In large-scale cultivating Epimedium that is a typical shade plant species, they are arbitrarily covered with black colored shade nets. However, their optimal growth conditions, especially light, are still less understood. During the investigation of different light qualities on the growth of Epimedium pseudowushanense, it was found that, all the values of plant growth characteristics (except shoot number) and photosynthetic characteristics were lower under red, yellow, or blue light treatment than under white light treatment. However, yellow light treatment had beneficial effects on shoot number, dry biomass (per plant) as well as net photosynthesis rate (Pn) and maximal apparent quantum efficiency (AQY) in E. pseudowushanense when compared with red or blue light treatment. More importantly, we found that E. pseudowushanense accumulated higher levels of bioactive flavonoids under yellow light treatment than under white, red, or blue light treatment. Furthermore, both RNAseq and qPCR analyses revealed that yellow light could highly up-regulate the expression levels of flavonoid biosynthetic genes, in particular CHS1, F3H1, PT_5, and raGT_5 that possibly contributed to the enhanced accumulation of bioactive flavonoids in E. pseudowushanense. Taken together, our study revealed that yellow light is the optimal light for the growth of E. pseudowushanense. Our results provided key information on how to improve the cultivation condition and concurrently enhance the accumulation of bioactive flavonoids in E. pseudowushanense.


Assuntos
Epimedium/metabolismo , Flavonoides/metabolismo , Luz , Biomassa , Cromatografia Líquida de Alta Pressão , Medicamentos de Ervas Chinesas , Epimedium/crescimento & desenvolvimento , Epimedium/efeitos da radiação , Flavonoides/análise , Fotossíntese/efeitos da radiação , Folhas de Planta/metabolismo , Folhas de Planta/efeitos da radiação , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Brotos de Planta/metabolismo , Brotos de Planta/efeitos da radiação , RNA de Plantas/genética , RNA de Plantas/metabolismo , Análise de Sequência de RNA , Transcriptoma/efeitos da radiação
19.
Plant Sci ; 286: 98-107, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31300147

RESUMO

Flax seeds have a high oil content and are rich in unsaturated fatty acids, which have advantageous effects in preventing chronic diseases, such as cardiovascular diseases. At present, flax seeds are mainly developed for oil. Therefore, it is of practical significance to identify the candidate genes of fatty acid metabolism in flax seeds for breeding flax seeds with high oil content. In the present study, a natural population of flax containing 224 samples planted in 3 different environments was studied. The genome-wide association analysis (GWAS) of seed fatty acid content was conducted based on specific length amplified fragment sequencing (SLAF-seq) data. Transcriptome sequencing (RNA-seq) of samples from 3 different periods (14 d, 21 d and 28 d after anthesis) during seed development of the low oil variety Shuangya 4 and the high oil variety NEW was performed. The candidate genes for seed fatty acid metabolism were identified by combined analysis of these 2 methods. GWAS detected 16 SNP loci significantly associated with seed fatty acid content, and RNA-seq analysis identified 11,802 differentially expressed genes between high and low oil samples. Pathway enrichment analysis revealed that some differentially expressed genes were classified into fatty acid-related pathways. After comparison of these differentially expressed genes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 20 genes homologous to other species were obtained. After analysis, 10 candidate genes were screened by GWAS and RNA-seq screening. Of these 10 genes, qRT-PCR assays using flax seeds in 5 different developmental stages showed that the expression levels of 6 candidate genes were significantly correlated with 5 fatty acid contents in seeds of the high oil variety NEW. Through metabolic pathway analysis found that 6 genes were involved in important fatty acid metabolic pathways, and some of them also have upstream and downstream regulation relations. The present study combined GWAS and RNA-seq methods to identify candidate genes for fatty acid metabolism in flax seeds, which provided reference for screening of candidate genes with complex traits.


Assuntos
Ácidos Graxos/metabolismo , Linho/genética , Genes de Plantas , Estudo de Associação Genômica Ampla , Transcriptoma , Linho/metabolismo , Regulação da Expressão Gênica de Plantas , Sementes/metabolismo , Análise de Sequência de RNA
20.
BMC Bioinformatics ; 20(1): 369, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262249

RESUMO

BACKGROUND: Single cell RNA sequencing (scRNA-seq) brings unprecedented opportunities for mapping the heterogeneity of complex cellular environments such as bone marrow, and provides insight into many cellular processes. Single cell RNA-seq has a far larger fraction of missing data reported as zeros (dropouts) than traditional bulk RNA-seq, and unsupervised clustering combined with Principal Component Analysis (PCA) can be used to overcome this limitation. After clustering, however, one has to interpret the average expression of markers on each cluster to identify the corresponding cell types, and this is normally done by hand by an expert curator. RESULTS: We present a computational tool for processing single cell RNA-seq data that uses a voting algorithm to automatically identify cells based on approval votes received by known molecular markers. Using a stochastic procedure that accounts for imbalances in the number of known molecular signatures for different cell types, the method computes the statistical significance of the final approval score and automatically assigns a cell type to clusters without an expert curator. We demonstrate the utility of the tool in the analysis of eight samples of bone marrow from the Human Cell Atlas. The tool provides a systematic identification of cell types in bone marrow based on a list of markers of immune cell types, and incorporates a suite of visualization tools that can be overlaid on a t-SNE representation. The software is freely available as a Python package at https://github.com/sdomanskyi/DigitalCellSorter . CONCLUSIONS: This methodology assures that extensive marker to cell type matching information is taken into account in a systematic way when assigning cell clusters to cell types. Moreover, the method allows for a high throughput processing of multiple scRNA-seq datasets, since it does not involve an expert curator, and it can be applied recursively to obtain cell sub-types. The software is designed to allow the user to substitute the marker to cell type matching information and apply the methodology to different cellular environments.


Assuntos
Células da Medula Óssea/citologia , Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Software , Algoritmos , Células da Medula Óssea/metabolismo , Análise por Conglomerados , Humanos , Análise de Componente Principal , Análise de Célula Única
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