Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 7 de 7
Filtrar
1.
Bioinformatics ; 32(13): 2024-5, 2016 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-27153680

RESUMEN

UNLABELLED: Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. AVAILABILITY AND IMPLEMENTATION: TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html CONTACT: : jeffery.shen@unlv.nevada.edu.


Asunto(s)
Biología Computacional/métodos , Dominios Proteicos , Programas Informáticos , Internet , Análisis de Secuencia de Proteína
2.
Plant Cell Environ ; 40(9): 2004-2016, 2017 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-28626890

RESUMEN

Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA-induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA sequencing was performed on aleurone cells of rice seeds treated with 20 µM ABA. Gibbs sampling was used to identify enriched elements, and particle bombardment-mediated transient expression studies were performed to verify the function. Gene ontology analysis was performed to predict the roles of genes containing the novel ABREs. This study revealed 2443 ABA-inducible genes and a novel ABRE, designated as ABREN, which was experimentally verified to mediate ABA signalling in rice aleurone cells. Many of the ABREN-containing genes are predicted to be involved in stress responses and transcription. Analysis of other species suggests that the ABREN may be monocot specific. This study also revealed interesting expression patterns of genes involved in ABA metabolism and signalling. Collectively, this study advanced our understanding of diverse cis-regulatory sequences and the transcriptomes underlying ABA responses in rice aleurone cells.


Asunto(s)
Ácido Abscísico/metabolismo , Perfilación de la Expresión Génica , Oryza/citología , Oryza/genética , Proteínas de Plantas/metabolismo , Elementos de Respuesta/genética , Regiones no Traducidas 5'/genética , Arabidopsis/genética , Emparejamiento Base/genética , Codón/genética , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Ontología de Genes , Genes de Plantas , Solanum lycopersicum/genética , Mutación/genética , Motivos de Nucleótidos/genética , Oryza/efectos de los fármacos , Regiones Promotoras Genéticas , Análisis de Secuencia de ARN , Transducción de Señal/efectos de los fármacos , Sorghum/genética , Estrés Fisiológico/efectos de los fármacos , Estrés Fisiológico/genética , Transcripción Genética/efectos de los fármacos
3.
Genomics ; 103(1): 122-34, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24200500

RESUMEN

The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germination growth. Herein, we report transcriptomes of aleurone cells treated with the hormones abscisic acid, gibberellic acid, or both. Using a comprehensive approach, we identified hundreds of novel genes. To minimize the number of false positives, only transcripts that did not overlap with existing annotations, had a high level of expression, and showed a high level of uniqueness within the rice genome were considered to be novel genes. This approach led to the identification of 553 novel genes that encode proteins and/or microRNAs. The transcriptome data reported here will help to further improve the annotation of the rice genome.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Genes de Plantas , MicroARNs/genética , Oryza/genética , Semillas/genética , Ácido Abscísico/farmacología , Algoritmos , Giberelinas/farmacología , Secuenciación de Nucleótidos de Alto Rendimiento , MicroARNs/metabolismo , Oryza/efectos de los fármacos , Reguladores del Crecimiento de las Plantas/farmacología , Semillas/efectos de los fármacos , Análisis de Secuencia de ARN , Transcriptoma
4.
Nat Commun ; 9(1): 2286, 2018 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-29875356

RESUMEN

In the originally published version of this Article, the GAPDH loading control blot in Fig. 1a was inadvertently replaced with a duplicate of the DNMT2 blot in the same panel during assembly of the figure. This has now been corrected in both the PDF and HTML versions of the Article.

5.
Nat Commun ; 9(1): 1163, 2018 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-29563491

RESUMEN

The roles of RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) in lineage-associated chromatin organization and drug response/resistance are unclear. Here we demonstrate that the RCMTs, namely NSUN3 and DNMT2, directly bind hnRNPK, a conserved RNA-binding protein. hnRNPK interacts with the lineage-determining transcription factors (TFs), GATA1 and SPI1/PU.1, and with CDK9/P-TEFb to recruit RNA-polymerase-II at nascent RNA, leading to formation of 5-Azacitidine (5-AZA)-sensitive chromatin structure. In contrast, NSUN1 binds BRD4 and RNA-polymerase-II to form an active chromatin structure that is insensitive to 5-AZA, but hypersensitive to the BRD4 inhibitor JQ1 and to the downregulation of NSUN1 by siRNAs. Both 5-AZA-resistant leukaemia cell lines and clinically 5-AZA-resistant myelodysplastic syndrome and acute myeloid leukaemia specimens have a significant increase in RNA:m5C and NSUN1-/BRD4-associated active chromatin. This study reveals novel RNA:m5C/RCMT-mediated chromatin structures that modulate 5-AZA response/resistance in leukaemia cells, and hence provides a new insight into treatment of leukaemia.


Asunto(s)
Antineoplásicos/farmacología , Azacitidina/farmacología , Resistencia a Antineoplásicos/genética , Regulación Leucémica de la Expresión Génica , Leucemia Mieloide Aguda/genética , Síndromes Mielodisplásicos/genética , ARN Neoplásico/genética , Médula Ósea/efectos de los fármacos , Médula Ósea/metabolismo , Médula Ósea/patología , Proteínas de Ciclo Celular , Línea Celular Tumoral , Cromatina/química , Cromatina/efectos de los fármacos , Cromatina/metabolismo , Ensamble y Desensamble de Cromatina , Quinasa 9 Dependiente de la Ciclina/genética , Quinasa 9 Dependiente de la Ciclina/metabolismo , Citosina/metabolismo , ADN (Citosina-5-)-Metiltransferasas/genética , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Factor de Transcripción GATA1/genética , Factor de Transcripción GATA1/metabolismo , Ribonucleoproteína Heterogénea-Nuclear Grupo K/genética , Ribonucleoproteína Heterogénea-Nuclear Grupo K/metabolismo , Humanos , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/metabolismo , Leucemia Mieloide Aguda/patología , Metilación , Metiltransferasas/genética , Metiltransferasas/metabolismo , Síndromes Mielodisplásicos/tratamiento farmacológico , Síndromes Mielodisplásicos/metabolismo , Síndromes Mielodisplásicos/patología , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Unión Proteica , Proteínas Proto-Oncogénicas/genética , Proteínas Proto-Oncogénicas/metabolismo , ARN Neoplásico/metabolismo , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/metabolismo , Transducción de Señal , Transactivadores/genética , Transactivadores/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
6.
DNA Res ; 23(4): 311-23, 2016 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-27345721

RESUMEN

The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara.


Asunto(s)
Oryza/genética , Proteínas de Plantas/genética , Factores de Transcripción/genética , Sequías , Regulación de la Expresión Génica de las Plantas , Oryza/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Estrés Fisiológico , Factores de Transcripción/química , Factores de Transcripción/metabolismo , Dedos de Zinc
7.
DNA Res ; 22(5): 319-29, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26341416

RESUMEN

Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation.


Asunto(s)
Anotación de Secuencia Molecular/métodos , Oryza/genética , Programas Informáticos , ADN Complementario/genética , Perfilación de la Expresión Génica/métodos , Genoma de Planta , Sistemas de Lectura Abierta , Análisis de Secuencia de ARN , Regiones Terminadoras Genéticas , Sitio de Iniciación de la Transcripción , Transcriptoma
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA