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1.
Nan Fang Yi Ke Da Xue Xue Bao ; 41(4): 567-573, 2021 Apr 20.
Artículo en Chino | MEDLINE | ID: mdl-33963717

RESUMEN

OBJECTIVE: To construct a corpus cavemosum smooth muscle cell (CCSMCs) line with TEAD1 knockout from diabetic rats with erectile dysfunction (ED) using CRISPR/Cas9 technology and explore the role of TEAD1 in phenotypic modulation of CCSMCs in diabetic rats with ED. OBJECTIVE: Models of diabetic ED were established in male Sprague-Dawley rats by intraperitoneal injection of streptozotocin. CCSMCs from the rat models were primarily cultured and identified with immunofluorescence assay. Three sgRNAs (sgRNA-1, sgRNA-2 and sgRNA-3) were transfected via lentiviral vectors into 293T cells to prepare the sgRNA-Cas9 lentivirus. CCSMCs from diabetic rats with ED were infected by the lentivirus, and the cellular expression of TEAD1 protein was detected using Western blotting. In CCSMCs infected with the sgRNA-Cas9 lentivirus (CCSMCs-sgRNA-2), or the empty lentiviral vector (CCSMCs-sgRNA-NC) and the blank control cells (CCSMCs-CK), the expressions of cellular phenotypic markers SMMHC, calponin and PCNA at the mRNA and protein levels were detected using real-time fluorescence quantitative RT-PCR (qRT-PCR) and Western blotting, respectively. OBJECTIVE: The primarily cultured CCSMCs from diabetic rats with ED showed a high α-SMA-positive rate of over 95%. The recombinant lentivirus of TEAD1-sgRNA was successfully packaged, and stable TEAD1-deficient CCSMC lines derived from diabetic rat with ED were obtained. Western blotting confirmed that the protein expression of TEAD1 in TEAD1-sgRNA-2 group was the lowest (P < 0.05), and this cell line was used in subsequent experiment. The results of qRT-PCR and Western blotting showed significantly up-regulated expressions of SMMHC and calponin (all P < 0.05) and down-regulated expression of PCNA (all P < 0.05) at both the mRNA and protein levels in TEAD1-deficient CCSMCs from diabetic rats with ED. OBJECTIVE: We successfully constructed a stable CCSMCs line with CRISPR/Cas9-mediated TEAD1 knockout from diabetic rats with ED. TEAD1 gene knockout can induce phenotype transformation of the CCSMCs from diabetic rats with ED from the synthetic to the contractile type.


Asunto(s)
Diabetes Mellitus Experimental , Disfunción Eréctil , Animales , Sistemas CRISPR-Cas , Proteínas de Unión al ADN/genética , Diabetes Mellitus Experimental/complicaciones , Disfunción Eréctil/genética , Humanos , Masculino , Miocitos del Músculo Liso , Proteínas Nucleares , Pene , Fenotipo , Ratas , Ratas Sprague-Dawley , Factores de Transcripción/genética
2.
Nat Commun ; 12(1): 2378, 2021 04 22.
Artículo en Inglés | MEDLINE | ID: mdl-33888716

RESUMEN

Structural variation in plant genomes is a significant driver of phenotypic variability in traits important for the domestication and productivity of crop species. Among these are traits that depend on functional meristems, populations of stem cells maintained by the CLAVATA-WUSCHEL (CLV-WUS) negative feedback-loop that controls the expression of the WUS homeobox transcription factor. WUS function and impact on maize development and yield remain largely unexplored. Here we show that the maize dominant Barren inflorescence3 (Bif3) mutant harbors a tandem duplicated copy of the ZmWUS1 gene, ZmWUS1-B, whose novel promoter enhances transcription in a ring-like pattern. Overexpression of ZmWUS1-B is due to multimerized binding sites for type-B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. Hypersensitivity to cytokinin causes stem cell overproliferation and major rearrangements of Bif3 inflorescence meristems, leading to the formation of ball-shaped ears and severely affecting productivity. These findings establish ZmWUS1 as an essential meristem size regulator in maize and highlight the striking effect of cis-regulatory variation on a key developmental program.


Asunto(s)
Proteínas de Homeodominio/genética , Inflorescencia/crecimiento & desarrollo , Proteínas de Plantas/genética , Factores de Transcripción/metabolismo , Zea mays/crecimiento & desarrollo , Productos Agrícolas/genética , Productos Agrícolas/crecimiento & desarrollo , Citocininas/metabolismo , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Proteínas de Homeodominio/metabolismo , Inflorescencia/citología , Meristema/crecimiento & desarrollo , Mutagénesis , Mutación , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente , Sitios de Carácter Cuantitativo , RNA-Seq , Transducción de Señal/genética , Células Madre , Factores de Transcripción/genética , Zea mays/genética
3.
Int J Mol Sci ; 22(5)2021 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-33800795

RESUMEN

Plant growth and development are challenged by biotic and abiotic stresses including salinity and heat stresses. For Populus simonii × P. nigra as an important greening and economic tree species in China, increasing soil salinization and global warming have become major environmental challenges. We aim to unravel the molecular mechanisms underlying tree tolerance to salt stress and high temprerature (HT) stress conditions. Transcriptomics revealed that a PsnNAC036 transcription factor (TF) was significantly induced by salt stress in P. simonii × P. nigra. This study focuses on addressing the biological functions of PsnNAC036. The gene was cloned, and its temporal and spatial expression was analyzed under different stresses. PsnNAC036 was significantly upregulated under 150 mM NaCl and 37 °C for 12 h. The result is consistent with the presence of stress responsive cis-elements in the PsnNAC036 promoter. Subcellular localization analysis showed that PsnNAC036 was targeted to the nucleus. Additionally, PsnNAC036 was highly expressed in the leaves and roots. To investigate the core activation region of PsnNAC036 protein and its potential regulatory factors and targets, we conducted trans-activation analysis and the result indicates that the C-terminal region of 191-343 amino acids of the PsnNAC036 was a potent activation domain. Furthermore, overexpression of PsnNAC036 stimulated plant growth and enhanced salinity and HT tolerance. Moreover, 14 stress-related genes upregulated in the transgenic plants under high salt and HT conditions may be potential targets of the PsnNAC036. All the results demonstrate that PsnNAC036 plays an important role in salt and HT stress tolerance.


Asunto(s)
Genes de Plantas , Respuesta al Choque Térmico/genética , Proteínas de Plantas/fisiología , Populus/genética , Estrés Salino/genética , Plantas Tolerantes a la Sal/genética , Factores de Transcripción/fisiología , Secuencia de Aminoácidos , Clorofila/biosíntesis , Cruzamientos Genéticos , Regulación de la Expresión Génica de las Plantas , Calor , Proteínas Nucleares/genética , Proteínas Nucleares/fisiología , Hojas de la Planta/metabolismo , Proteínas de Plantas/genética , Raíces de Plantas/metabolismo , Plantas Modificadas Genéticamente , Populus/fisiología , Regiones Promotoras Genéticas/genética , Salinidad , Plantas Tolerantes a la Sal/crecimiento & desarrollo , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Especificidad de la Especie , Fracciones Subcelulares/metabolismo , Tabaco/genética , Tabaco/metabolismo , Factores de Transcripción/genética , Activación Transcripcional
4.
Int J Mol Sci ; 22(5)2021 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-33800929

RESUMEN

The main restraint obstructing the wider adoption of lupins as protein crops is the presence of bitter and toxic quinolizidine alkaloids (QAs), whose contents might increase under exposure to stressful environmental conditions. A poor understanding of how QAs accumulate hinders the breeding of sweet varieties. Here, we characterize the expression profiles of QA-related genes, along with the alkaloid content, in various organs of sweet and bitter narrow-leafed lupin (NLL, Lupinus angustifolius L.). Special attention is paid to the RAP2-7 transcription factor, a candidate regulator of the QA pathway. We demonstrate the upregulation of RAP2-7 and other QA-related genes, across the aerial organs of a bitter cultivar and the significant correlations between their expression levels, thus supporting the role of RAP2-7 as an important regulatory gene in NLL. Moreover, we showed that the initial steps of QA synthesis might occur independently in all aerial plant organs sharing common regulatory mechanisms. Nonetheless, other regulatory steps might be involved in RAP2-7-triggered QA accumulation, given its expression pattern in leaves. Finally, the examination of QA-related gene expression in plants infected with Colletotrichum lupini evidenced no connection between QA synthesis and anthracnose resistance, in contrast to the important role of polyamines during plant-pathogen interactions.


Asunto(s)
Colletotrichum/fisiología , Regulación de la Expresión Génica de las Plantas , Lupinus/genética , Enfermedades de las Plantas/genética , Quinolizidinas/metabolismo , Cromatografía de Gases , Lupinus/metabolismo , Lupinus/microbiología , Especificidad de Órganos , Fitomejoramiento , Enfermedades de las Plantas/microbiología , Proteínas de Plantas/biosíntesis , Proteínas de Plantas/genética , Estructuras de las Plantas/metabolismo , Estructuras de las Plantas/microbiología , Poliaminas/metabolismo , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Factores de Transcripción/biosíntesis , Factores de Transcripción/genética
5.
Int J Mol Sci ; 22(6)2021 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-33803949

RESUMEN

Invasive urothelial carcinomas of the bladder (UCB) characteristically show a loss of differentiation markers. The transcription factor Grainyhead-like 3 (GRHL3) plays an important role in the development and differentiation of normal urothelium. The contribution to UCB progression is still elusive. Differential expression of GRHL3 was assessed in normal human urothelium and in non-invasive and invasive bladder cancer cell lines. The contribution of GRHL3 to cell proliferation, viability and invasion in UCB cell lines was determined by gain- and loss-of-function assays in vitro and in an organ culture model using de-epithelialized porcine bladders. GRHL3 expression was detectable in normal human urothelial cells and showed significantly higher mRNA and protein levels in well-differentiated, non-invasive RT4 urothelial carcinoma cells compared to moderately differentiated RT112 cells. GRHL3 expression was absent in anaplastic and invasive T24 cells. Ectopic de novo expression of GRHL3 in T24 cells significantly impaired their migration and invasion properties in vitro and in organ culture. Its downregulation improved the invasive capacity of RT4 cells. The results indicate that GRHL3 may play a role in progression and metastasis in UCB. In addition, this work demonstrates that de-epithelialized porcine bladder organ culture can be a useful, standardized tool to assess the invasive capacity of cancer cells.


Asunto(s)
Carcinoma/genética , Proteínas de Unión al ADN/genética , Factores de Transcripción/genética , Neoplasias de la Vejiga Urinaria/genética , Urotelio/metabolismo , Animales , Carcinoma/patología , Carcinoma de Células Transicionales , Diferenciación Celular/genética , Movimiento Celular/genética , Proliferación Celular/genética , Regulación Neoplásica de la Expresión Génica/genética , Humanos , Invasividad Neoplásica/genética , Invasividad Neoplásica/patología , Metástasis de la Neoplasia , Técnicas de Cultivo de Órganos , Porcinos , Neoplasias de la Vejiga Urinaria/patología , Urotelio/patología
6.
Mol Cell ; 81(8): 1591-1593, 2021 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-33861946

RESUMEN

Two recent papers, Rao et al. (2021), in this issue, and Sönmezer et al. (2021), investigate transcription factor cooperativity at cis-regulatory elements. Using data from nuclease- and methyltransferase-footprinting experiments, they demonstrate that factor co-occupancy at regulatory elements commonly occurs in vivo and is conserved from fly to mouse.


Asunto(s)
Cromatina , Factores de Transcripción , Animales , Cromatina/genética , Regulación de la Expresión Génica , Ratones , Unión Proteica , Secuencias Reguladoras de Ácidos Nucleicos , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
7.
Plant Physiol Biochem ; 162: 706-715, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33799182

RESUMEN

AINTEGUMENTA-like (AIL) proteins are members of the APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain family of transcription factors involved in plant growth, development, and abiotic stress responses. However, the biological functions of AIL members in pumpkin (Cucurbita moschata Duch.) remain unknown. In this study, we identified 12 AIL genes in the pumpkin genome encoding proteins predicted to be localized in the nucleus. Phylogenetic analysis showed that the AIL gene family could be classified into six major subfamilies, with each member encoding two AP2/ERF domains separated by a linker region. CmoAIL genes were expressed at varying levels in the examined tissues, and CmoANT genes showed different expression patterns under auxin (IAA), 1-naphthylphthalamic acid (NPA), and abscisic acid (ABA) treatments. Ectopic overexpression of CmoANT1.2 in Arabidopsis increased organ size and promoted growth of grafted plants by accelerating graft union formation. However, there was no significant difference at the graft junction for WT/WT and WT/ANT under IAA or NPA treatments. Taken together, the results of this study provide critical information about CmoAIL genes and their encoded proteins, and suggest future work should investigate the functions of CmoANT1.2 in the grafting process in pumpkin.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Cucurbita , Arabidopsis/genética , Arabidopsis/metabolismo , Cucurbita/genética , Cucurbita/metabolismo , Regulación de la Expresión Génica de las Plantas , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
8.
Nat Genet ; 53(4): 455-466, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33795864

RESUMEN

Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.


Asunto(s)
Cromatina/química , Diabetes Mellitus Tipo 2/genética , Células Secretoras de Glucagón/metabolismo , Células Secretoras de Insulina/metabolismo , Canal de Potasio KCNQ1/genética , Células Secretoras de Polipéptido Pancreático/metabolismo , Células Secretoras de Somatostatina/metabolismo , Glucemia/metabolismo , Diferenciación Celular , Cromatina/metabolismo , Diabetes Mellitus Tipo 2/metabolismo , Diabetes Mellitus Tipo 2/patología , Epigenómica , Ayuno , Perfilación de la Expresión Génica , Estudio de Asociación del Genoma Completo , Células Secretoras de Glucagón/patología , Secuenciación de Nucleótidos de Alto Rendimiento , Células Madre Embrionarias Humanas/citología , Humanos , Células Secretoras de Insulina/patología , Canal de Potasio KCNQ1/metabolismo , Familia de Multigenes , Células Secretoras de Polipéptido Pancreático/patología , Polimorfismo Genético , Análisis de la Célula Individual , Células Secretoras de Somatostatina/patología , Factores de Transcripción/clasificación , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
9.
Nat Genet ; 53(4): 477-486, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33795867

RESUMEN

Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly within multicellular developing organisms. In the present study, we employ Hi-M, a single-cell spatial genomics approach, to detect CRM-promoter looping interactions within topologically associating domains (TADs) during early Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses reveal that multiple CRMs spatially coalesce to form hubs. Loops and CRM hubs are established early during development, before the emergence of TADs. Moreover, CRM hubs are formed, in part, via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach provides insight into the role of CRM-promoter interactions in defining transcriptional states, as well as distinct cell types.


Asunto(s)
Linaje de la Célula/genética , Cromatina/química , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Regulación del Desarrollo de la Expresión Génica , Proteínas Nucleares/genética , Factores de Transcripción/genética , Animales , Diferenciación Celular , Cromatina/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/citología , Drosophila melanogaster/crecimiento & desarrollo , Drosophila melanogaster/metabolismo , Embrión no Mamífero , Elementos de Facilitación Genéticos , Perfilación de la Expresión Génica , Genómica , Proteínas Nucleares/metabolismo , Regiones Promotoras Genéticas , Análisis de la Célula Individual , Factores de Transcripción/clasificación , Factores de Transcripción/metabolismo , Transcripción Genética
10.
Int J Mol Sci ; 22(6)2021 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-33802225

RESUMEN

The AP2/ERF transcription factor family members play crucial roles in controlling plant growth and development, as well as responses to various abiotic stresses. Genome-wide identification and characterization of AP2/ERF genes has not yet been carried out in the oil palm genome. In the present work, we reported the occurrence of 172 EgAP2/ERFs (AP2, ERF, RAV & Soloist members) through genome-wide identification. Phylogenetic analysis was used to divide them into four groups, including: 34 AP2, 131 ERF, 5 RAV, and 2 Soloist gene family members. All 172 AP2/ERF members were unevenly distributed across 16 chromosomes of oil palm. Gene duplication analysis elucidated the tandem duplication of AP2/ERFs on chromosome blocks of the oil palm genome during evolution. Gene structure as well as conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements-related to hormone, stress, and defense responses-were identified in the promoter regions of AP2/ERFs. Tissue-specific expression of 172 AP2/ERFs in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Finally, abiotic stress (salinity, cold & drought)-responsive AP2/ERFs in the oil palm genome were validated through qPCR analysis. Our study provided valuable information on oil palm AP2/ERF superfamily members and dissected their role in abiotic stress conditions.


Asunto(s)
Arecaceae , Regulación de la Expresión Génica de las Plantas , Familia de Multigenes , Proteínas de Plantas , Estrés Fisiológico , Factores de Transcripción , Arecaceae/genética , Arecaceae/metabolismo , Estudio de Asociación del Genoma Completo , Proteínas de Plantas/biosíntesis , Proteínas de Plantas/genética , Factores de Transcripción/biosíntesis , Factores de Transcripción/genética
11.
Int J Mol Sci ; 22(5)2021 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-33807548

RESUMEN

About 8% of the human genome is covered with candidate cis-regulatory elements (cCREs). Disruptions of CREs, described as "cis-ruptions" have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator (CFTR) regulatory elements were identified, but the regulatory mechanisms of the CFTR gene have yet to be fully elucidated. The aim of this work is to improve our knowledge of the CFTR gene regulation, and to identity factors that could impact the CFTR gene expression, and potentially account for the variability of the clinical presentation of cystic fibrosis as well as CFTR-related disorders. Here, we apply the robust GWAS3D score to determine which of the CFTR introns could be involved in gene regulation. This approach highlights four particular CFTR introns of interest. Using reporter gene constructs in intestinal cells, we show that two new introns display strong cooperative effects in intestinal cells. Chromatin immunoprecipitation analyses further demonstrate fixation of transcription factors network. These results provide new insights into our understanding of the CFTR gene regulation and allow us to suggest a 3D CFTR locus structure in intestinal cells. A better understand of regulation mechanisms of the CFTR gene could elucidate cases of patients where the phenotype is not yet explained by the genotype. This would thus help in better diagnosis and therefore better management. These cis-acting regions may be a therapeutic challenge that could lead to the development of specific molecules capable of modulating gene expression in the future.


Asunto(s)
Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Intestinos/fisiología , Células CACO-2 , Línea Celular Tumoral , Inmunoprecipitación de Cromatina/métodos , Fibrosis Quística/genética , Regulación de la Expresión Génica/genética , Genes Reporteros/genética , Humanos , Intrones/genética , Factores de Transcripción/genética
12.
Int J Mol Sci ; 22(5)2021 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-33807564

RESUMEN

Ginkgo (Ginkgo biloba L.) is a deciduous tree species with high timber, medicinal, ecological, ornamental, and scientific values, and is widely cultivated worldwide. However, for such an important tree species, the regulatory mechanisms involved in the photosynthesis of developing leaves remain largely unknown. Here, we observed variations in light response curves (LRCs) and photosynthetic parameters (photosynthetic capacity (Pnmax) and dark respiration rate (Rd)) of leaves across different developmental stages. We found the divergence in the abundance of compounds (such as 3-phospho-d-glyceroyl phosphate, sedoheptulose-1,7-bisphosphate, and malate) involved in photosynthetic carbon metabolism. Additionally, a co-expression network was constructed to reveal 242 correlations between transcription factors (TFs) and photosynthesis-related genes (p < 0.05, |r| > 0.8). We found that the genes involved in the photosynthetic light reaction pathway were regulated by multiple TFs, such as bHLH, WRKY, ARF, IDD, and TFIIIA. Our analysis allowed the identification of candidate genes that most likely regulate photosynthesis, primary carbon metabolism, and plant development and as such, provide a theoretical basis for improving the photosynthetic capacity and yield of ginkgo trees.


Asunto(s)
Ginkgo biloba/genética , Metaboloma/genética , Fotosíntesis/genética , Transcriptoma/genética , Perfilación de la Expresión Génica/métodos , Hojas de la Planta/genética , Proteínas de Plantas/genética , Factores de Transcripción/genética
13.
Int J Mol Sci ; 22(6)2021 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-33809411

RESUMEN

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive diseases of banana. Methods to control the disease are still inadequate. The present investigation targeted expression of defense-related genes in tissue cultured banana plantlets of Fusarium resistant and susceptible cultivars after infection with biological control agents (BCAs) and Fusarium (Foc race 1). In total 3034 differentially expressed genes were identified which annotated to 58 transcriptional families (TF). TF families such as MYB, bHLH and NAC TFs were mostly up-regulated in response to pathogen stress, whereas AP2/EREBP were mostly down-regulated. Most genes were associated with plant-pathogen response, plant hormone signal transduction, starch and sucrose metabolism, cysteine and methionine metabolism, flavonoid biosynthesis, selenocompound metabolism, phenylpropanoid biosynthesis, mRNA surveillance pathway, mannose type O-glycan biosynthesis, amino acid and nucleotide sugar metabolism, cyanoamino acid metabolism, and hormone signal transduction. Our results showed that the defense mechanisms of resistant and susceptible banana cultivars treated with BCAs, were regulated by differentially expressed genes in various categories of defense pathways. Furthermore, the association with different resistant levels might serve as a strong foundation for the control of Fusarium wilt of banana.


Asunto(s)
Resistencia a la Enfermedad/genética , Fusarium/fisiología , Perfilación de la Expresión Génica , Musa/genética , Musa/microbiología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Transcriptoma/genética , Regulación de la Expresión Génica de las Plantas , Ontología de Genes , Redes Reguladoras de Genes , Anotación de Secuencia Molecular , Polimorfismo Genético , Mapas de Interacción de Proteínas/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Reproducibilidad de los Resultados , Estrés Fisiológico/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
14.
Science ; 372(6540): 385-393, 2021 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-33888637

RESUMEN

Motor and sensory functions of the spinal cord are mediated by populations of cardinal neurons arising from separate progenitor lineages. However, each cardinal class is composed of multiple neuronal types with distinct molecular, anatomical, and physiological features, and there is not a unifying logic that systematically accounts for this diversity. We reasoned that the expansion of new neuronal types occurred in a stepwise manner analogous to animal speciation, and we explored this by defining transcriptomic relationships using a top-down approach. We uncovered orderly genetic tiers that sequentially divide groups of neurons by their motor-sensory, local-long range, and excitatory-inhibitory features. The genetic signatures defining neuronal projections were tied to neuronal birth date and conserved across cardinal classes. Thus, the intersection of cardinal class with projection markers provides a unifying taxonomic solution for systematically identifying distinct functional subsets.


Asunto(s)
Vías Nerviosas , Neuronas/fisiología , Médula Espinal/citología , Transcriptoma , Animales , Médula Cervical/citología , Femenino , Masculino , Ratones , Neuronas Motoras/fisiología , Propiocepción , RNA-Seq , Células Receptoras Sensoriales/fisiología , Análisis de la Célula Individual , Análisis Espacial , Médula Espinal/embriología , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
15.
BMC Bioinformatics ; 22(1): 200, 2021 Apr 19.
Artículo en Inglés | MEDLINE | ID: mdl-33874910

RESUMEN

BACKGROUND: Transcriptional regulation is complex, requiring multiple cis (local) and trans acting mechanisms working in concert to drive gene expression, with disruption of these processes linked to multiple diseases. Previous computational attempts to understand the influence of regulatory mechanisms on gene expression have used prediction models containing input features derived from cis regulatory factors. However, local chromatin looping and trans-acting mechanisms are known to also influence transcriptional regulation, and their inclusion may improve model accuracy and interpretation. In this study, we create a general model of transcription factor influence on gene expression by incorporating both cis and trans gene regulatory features. RESULTS: We describe a computational framework to model gene expression for GM12878 and K562 cell lines. This framework weights the impact of transcription factor-based regulatory data using multi-omics gene regulatory networks to account for both cis and trans acting mechanisms, and measures of the local chromatin context. These prediction models perform significantly better compared to models containing cis-regulatory features alone. Models that additionally integrate long distance chromatin interactions (or chromatin looping) between distal transcription factor binding regions and gene promoters also show improved accuracy. As a demonstration of their utility, effect estimates from these models were used to weight cis-regulatory rare variants for sequence kernel association test analyses of gene expression. CONCLUSIONS: Our models generate refined effect estimates for the influence of individual transcription factors on gene expression, allowing characterization of their roles across the genome. This work also provides a framework for integrating multiple data types into a single model of transcriptional regulation.


Asunto(s)
Regulación de la Expresión Génica , Redes Reguladoras de Genes , Cromatina/genética , Almacenamiento y Recuperación de la Información , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
16.
Int J Mol Sci ; 22(7)2021 Mar 24.
Artículo en Inglés | MEDLINE | ID: mdl-33804889

RESUMEN

In chronic kidney disease, hyperphosphatemia upregulates the Ca2+ channel ORAI and its activating Ca2+ sensor STIM in megakaryocytes and platelets. ORAI1 and STIM1 accomplish store-operated Ca2+ entry (SOCE) and play a key role in platelet activation. Signaling linking phosphate to upregulation of ORAI1 and STIM1 includes transcription factor NFAT5 and serum and glucocorticoid-inducible kinase SGK1. In vascular smooth muscle cells, the effect of hyperphosphatemia on ORAI1/STIM1 expression and SOCE is suppressed by Mg2+ and the calcium-sensing receptor (CaSR) agonist Gd3+. The present study explored whether sustained exposure to Mg2+ or Gd3+ interferes with the phosphate-induced upregulation of NFAT5, SGK1, ORAI1,2,3, STIM1,2 and SOCE in megakaryocytes. To this end, human megakaryocytic Meg-01 cells were treated with 2 mM ß-glycerophosphate for 24 h in the absence and presence of either 1.5 mM MgCl2 or 50 µM GdCl3. Transcript levels were estimated utilizing q-RT-PCR, protein abundance by Western blotting, cytosolic Ca2+ concentration ([Ca2+]i) by Fura-2 fluorescence and SOCE from the increase in [Ca2+]i following re-addition of extracellular Ca2+ after store depletion with thapsigargin (1 µM). As a result, Mg2+ and Gd3+ upregulated CaSR and blunted or virtually abolished the phosphate-induced upregulation of NFAT5, SGK1, ORAI1,2,3, STIM1,2 and SOCE in megakaryocytes. In conclusion, Mg2+ and the CaSR agonist Gd3+ interfere with phosphate-induced dysregulation of [Ca2+]i in megakaryocytes.


Asunto(s)
Señalización del Calcio , Gadolinio/farmacología , Cloruro de Magnesio/farmacología , Megacariocitos/efectos de los fármacos , Proteína ORAI1/metabolismo , Células Cultivadas , Humanos , Proteínas Inmediatas-Precoces/genética , Proteínas Inmediatas-Precoces/metabolismo , Megacariocitos/metabolismo , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Proteína ORAI1/genética , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Molécula de Interacción Estromal 1/genética , Molécula de Interacción Estromal 1/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
17.
Int J Mol Sci ; 22(6)2021 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-33809237

RESUMEN

Recent developments in tissue clearing methods have significantly advanced the three-dimensional analysis of biological structures in whole, intact tissue, providing a greater understanding of spatial relationships and biological circuits. Nonetheless, studies have reported issues with maintaining structural integrity and preventing tissue disintegration, limiting the wide application of these techniques to fragile tissues such as developing embryos. Here, we present an optimized passive tissue clearing technique (PACT)-based embryo clearing method, initial embedding PACT (IMPACT)-Basic, that improves tissue rigidity without compromising optical transparency. We also present IMPACT-Advance, which is specifically optimized for thin slices of mouse embryos past E13.5. We demonstrate proof-of-concept by investigating the expression of two relatively understudied PR domain (PRDM) proteins, PRDM10 and PRDM13, in intact cleared mouse embryos at various stages of development. We observed strong PRDM10 and PRDM13 expression in the developing nervous system and skeletal cartilage, suggesting a functional role for these proteins in these tissues throughout embryogenesis.


Asunto(s)
Desarrollo Embrionario/genética , N-Metiltransferasa de Histona-Lisina/genética , Imagenología Tridimensional/métodos , Factores de Transcripción/genética , Animales , Embrión de Mamíferos , Regulación del Desarrollo de la Expresión Génica/genética , Ratones
18.
Science ; 372(6538): 150-156, 2021 04 09.
Artículo en Inglés | MEDLINE | ID: mdl-33833117

RESUMEN

In most vertebrates, camera-style eyes contain retinal ganglion cell neurons that project to visual centers on both sides of the brain. However, in fish, ganglion cells were thought to innervate only the contralateral side, suggesting that bilateral visual projections appeared in tetrapods. Here we show that bilateral visual projections exist in non-teleost fishes and that the appearance of ipsilateral projections does not correlate with terrestrial transition or predatory behavior. We also report that the developmental program that specifies visual system laterality differs between fishes and mammals, as the Zic2 transcription factor, which specifies ipsilateral retinal ganglion cells in tetrapods, appears to be absent from fish ganglion cells. However, overexpression of human ZIC2 induces ipsilateral visual projections in zebrafish. Therefore, the existence of bilateral visual projections likely preceded the emergence of binocular vision in tetrapods.


Asunto(s)
Evolución Biológica , Encéfalo/anatomía & histología , Peces/anatomía & histología , Peces/genética , Células Ganglionares de la Retina/citología , Vías Visuales , Animales , Diferenciación Celular , Ojo/anatomía & histología , Proteínas de Peces/genética , Proteínas de Peces/metabolismo , Peces/metabolismo , Lateralidad Funcional , Humanos , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Retina/embriología , Retina/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Visión Binocular , Pez Cebra/anatomía & histología , Pez Cebra/genética
19.
Int J Mol Sci ; 22(5)2021 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-33806406

RESUMEN

The NAC (NAM, ATAF1/2, and CUC2) transcription factors comprise one of the largest transcription factor families in plants and play important roles in stress responses. However, little is known about the functions of potato NAC family members. Here we report the cloning of a potato NAC transcription factor gene StNAC053, which was significantly upregulated after salt, drought, and abscisic acid treatments. Furthermore, the StNAC053-GFP fusion protein was found to be located in the nucleus and had a C-terminal transactivation domain, implying that StNAC053 may function as a transcriptional activator in potato. Notably, Arabidopsis plants overexpressing StNAC053 displayed lower seed germination rates compared to wild-type under exogenous ABA treatment. In addition, the StNAC053 overexpression Arabidopsis lines displayed significantly increased tolerance to salt and drought stress treatments. Moreover, the StNAC053-OE lines were found to have higher activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) under multiple stress treatments. Interestingly, the expression levels of several stress-related genes including COR15A,DREB1A, ERD11, RAB18, ERF5, and KAT2, were significantly upregulated in these StNAC053-overexpressing lines. Taken together, overexpression of the stress-inducible StNAC053 gene could enhance the tolerances to both salt and drought stress treatments in Arabidopsis, likely by upregulating stress-related genes.


Asunto(s)
Proteínas de Plantas/genética , Plantas Modificadas Genéticamente/genética , Solanum tuberosum/genética , Estrés Fisiológico/genética , Factores de Transcripción/genética , Ácido Abscísico/farmacología , Arabidopsis/efectos de los fármacos , Arabidopsis/genética , Catalasa/genética , Núcleo Celular/genética , Sequías , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Regulación de la Expresión Génica de las Plantas/genética , Peroxidasa/genética , Plantas Modificadas Genéticamente/efectos de los fármacos , Cloruro de Sodio/administración & dosificación , Cloruro de Sodio/farmacología , Solanum tuberosum/efectos de los fármacos , Superóxido Dismutasa/genética , Regulación hacia Arriba/genética
20.
Int J Mol Sci ; 22(6)2021 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-33799566

RESUMEN

Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Enfermedades de las Plantas/genética , Inmunidad de la Planta/genética , Potexvirus/genética , Solanum tuberosum/genética , Factores de Transcripción/genética , Transcriptoma , Arabidopsis/genética , Arabidopsis/inmunología , Arabidopsis/virología , Perfilación de la Expresión Génica , Redes Reguladoras de Genes , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/inmunología , Patrón Molecular Asociado a Patógenos/inmunología , Patrón Molecular Asociado a Patógenos/metabolismo , Enfermedades de las Plantas/inmunología , Enfermedades de las Plantas/virología , Proteínas de Plantas/clasificación , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Potexvirus/crecimiento & desarrollo , Potexvirus/patogenicidad , Transducción de Señal , Solanum tuberosum/inmunología , Solanum tuberosum/virología , Factores de Transcripción/clasificación , Factores de Transcripción/metabolismo , Transcripción Genética , Respuesta de Proteína Desplegada
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