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1.
Sci Adv ; 6(50)2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33298436

RESUMO

The lack of accessible noninvasive tools to examine the molecular alterations occurring in the brain limits our understanding of the causes and progression of Alzheimer's disease (AD), as well as the identification of effective therapeutic strategies. Here, we conducted a comprehensive profiling of circulating, cell-free messenger RNA (cf-mRNA) in plasma of 126 patients with AD and 116 healthy controls of similar age. We identified 2591 dysregulated genes in the cf-mRNA of patients with AD, which are enriched in biological processes well known to be associated with AD. Dysregulated genes included brain-specific genes and resembled those identified to be dysregulated in postmortem AD brain tissue. Furthermore, we identified disease-relevant circulating gene transcripts that correlated with the severity of cognitive impairment. These data highlight the potential of high-throughput cf-mRNA sequencing to evaluate AD-related pathophysiological alterations in the brain, leading to precision healthcare solutions that could improve AD patient management.

2.
Nat Commun ; 11(1): 400, 2020 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-31964864

RESUMO

Circulating cell-free mRNA (cf-mRNA) holds great promise as a non-invasive diagnostic biomarker. However, cf-mRNA composition and its potential clinical applications remain largely unexplored. Here we show, using Next Generation Sequencing-based profiling, that cf-mRNA is enriched in transcripts derived from the bone marrow compared to circulating cells. Further, longitudinal studies involving bone marrow ablation followed by hematopoietic stem cell transplantation in multiple myeloma and acute myeloid leukemia patients indicate that cf-mRNA levels reflect the transcriptional activity of bone marrow-resident hematopoietic lineages during bone marrow reconstitution. Mechanistically, stimulation of specific bone marrow cell populations in vivo using growth factor pharmacotherapy show that cf-mRNA reflects dynamic functional changes over time associated with cellular activity. Our results shed light on the biology of the circulating transcriptome and highlight the potential utility of cf-mRNA to non-invasively monitor bone marrow involved pathologies.


Assuntos
Biomarcadores Tumorais/isolamento & purificação , Medula Óssea/patologia , Ácidos Nucleicos Livres/isolamento & purificação , Leucemia Mieloide Aguda/diagnóstico , Mieloma Múltiplo/diagnóstico , RNA Mensageiro/isolamento & purificação , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/genética , Medula Óssea/efeitos dos fármacos , Ácidos Nucleicos Livres/sangue , Ácidos Nucleicos Livres/genética , Estudos de Viabilidade , Perfilação da Expressão Gênica/métodos , Fator Estimulador de Colônias de Granulócitos/administração & dosagem , Transplante de Células-Tronco Hematopoéticas/métodos , Células-Tronco Hematopoéticas/efeitos dos fármacos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Leucemia Mieloide Aguda/sangue , Leucemia Mieloide Aguda/patologia , Leucemia Mieloide Aguda/terapia , Estudos Longitudinais , Pessoa de Meia-Idade , Mieloma Múltiplo/sangue , Mieloma Múltiplo/patologia , Mieloma Múltiplo/terapia , RNA Mensageiro/sangue , RNA Mensageiro/genética , Análise de Sequência de RNA/métodos , Resultado do Tratamento , Adulto Jovem
3.
Pigment Cell Melanoma Res ; 31(1): 73-81, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28786531

RESUMO

To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.


Assuntos
Biomarcadores Tumorais/genética , Ácidos Nucleicos Livres/genética , Melanoma/diagnóstico , Mutação , Neoplasias Cutâneas/diagnóstico , Biomarcadores Tumorais/sangue , Ácidos Nucleicos Livres/sangue , Estudos de Viabilidade , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Melanoma/sangue , Melanoma/genética , Pessoa de Meia-Idade , Projetos Piloto , Neoplasias Cutâneas/sangue , Neoplasias Cutâneas/genética
4.
Clin Cancer Res ; 23(18): 5648-5656, 2017 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-28536309

RESUMO

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care.Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03).Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR.


Assuntos
Biomarcadores Tumorais , DNA Tumoral Circulante , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias/diagnóstico , Neoplasias/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Testes Genéticos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Neoplasias/mortalidade , Prognóstico , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
5.
BMC Genomics ; 17(1): 966, 2016 11 24.
Artigo em Inglês | MEDLINE | ID: mdl-27881084

RESUMO

BACKGROUND: Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. RESULTS: Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate measurements to be quantitative at an expression level greater than ~5-10 molecules. CONCLUSIONS: Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Técnicas de Amplificação de Ácido Nucleico , RNA/genética , Análise de Célula Única , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Análise de Sequência de RNA , Análise de Célula Única/métodos
6.
Science ; 352(6293): 1586-90, 2016 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-27339989

RESUMO

The human brain has enormously complex cellular diversity and connectivities fundamental to our neural functions, yet difficulties in interrogating individual neurons has impeded understanding of the underlying transcriptional landscape. We developed a scalable approach to sequence and quantify RNA molecules in isolated neuronal nuclei from a postmortem brain, generating 3227 sets of single-neuron data from six distinct regions of the cerebral cortex. Using an iterative clustering and classification approach, we identified 16 neuronal subtypes that were further annotated on the basis of known markers and cortical cytoarchitecture. These data demonstrate a robust and scalable method for identifying and categorizing single nuclear transcriptomes, revealing shared genes sufficient to distinguish previously unknown and orthologous neuronal subtypes as well as regional identity and transcriptomic heterogeneity within the human brain.


Assuntos
Transcriptoma , Núcleo Celular , Córtex Cerebral , Perfilação da Expressão Gênica , Humanos , Neurônios , Análise de Sequência de RNA
7.
Nat Commun ; 7: 10913, 2016 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-26941120

RESUMO

The breast cancer susceptibility gene BRCA1 is well known for its function in double-strand break (DSB) DNA repair. While BRCA1 is also implicated in transcriptional regulation, the physiological significance remains unclear. COBRA1 (also known as NELF-B) is a BRCA1-binding protein that regulates RNA polymerase II (RNAPII) pausing and transcription elongation. Here we interrogate functional interaction between BRCA1 and COBRA1 during mouse mammary gland development. Tissue-specific deletion of Cobra1 reduces mammary epithelial compartments and blocks ductal morphogenesis, alveologenesis and lactogenesis, demonstrating a pivotal role of COBRA1 in adult tissue development. Remarkably, these developmental deficiencies due to Cobra1 knockout are largely rescued by additional loss of full-length Brca1. Furthermore, Brca1/Cobra1 double knockout restores developmental transcription at puberty, alters luminal epithelial homoeostasis, yet remains deficient in homologous recombination-based DSB repair. Thus our genetic suppression analysis uncovers a previously unappreciated, DNA repair-independent function of BRCA1 in antagonizing COBRA1-dependent transcription programme during mammary gland development.


Assuntos
Reparo do DNA/fisiologia , Glândulas Mamárias Animais/crescimento & desenvolvimento , Proteínas Nucleares/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Envelhecimento , Animais , Proteína BRCA1 , Quebras de DNA de Cadeia Dupla , Células Epiteliais , Estrogênios/metabolismo , Feminino , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Homeostase , Camundongos , Camundongos Knockout , Proteínas Nucleares/genética , Progestinas/metabolismo , Proteínas de Ligação a RNA , Maturidade Sexual , Transcriptoma , Proteínas Supressoras de Tumor/genética
8.
Nat Methods ; 13(3): 241-4, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26780092

RESUMO

The transcriptional state of a cell reflects a variety of biological factors, from cell-type-specific features to transient processes such as the cell cycle, all of which may be of interest. However, identifying such aspects from noisy single-cell RNA-seq data remains challenging. We developed pathway and gene set overdispersion analysis (PAGODA) to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.


Assuntos
Perfilação da Expressão Gênica/métodos , Proteoma/metabolismo , Análise de Sequência de RNA/métodos , Transdução de Sinais/fisiologia , Transcrição Genética/fisiologia , Transcriptoma/fisiologia , Animais , Células Cultivadas , Simulação por Computador , Camundongos , Modelos Biológicos , Modelos Estatísticos , Neurônios/fisiologia , Proteoma/química
9.
J Invest Dermatol ; 133(3): 812-821, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23096717

RESUMO

Skin wounds comprise a serious medical issue for which few pharmacological interventions are available. Moreover, the inflammatory, angiogenic, and proliferative facets of a typical response to a wound each have broader relevance in other pathological conditions. Here we describe a genomics-driven approach to identify secreted proteins that modulate wound healing in a mouse ear punch model. We show that adiponectin, when injected into the wound edge, accelerates wound healing. Notably, adiponectin injection causes upregulation of keratin gene transcripts within hours of treatment, and subsequently promotes collagen organization, formation of pilosebaceous units, and proliferation of cells in the basal epithelial cell layer and pilosebaceous units of healing tissue. The globular domain of adiponectin is sufficient to mediate accelerated dorsal skin wound closure, and the effects are lost in mice that are homozygous null for the adiponectin receptor 1 gene. These findings extend recent observations of a protective role of adiponectin in other tissue injury settings, suggest modulation of AdipoR1 for the clinical management of wounds, and demonstrate a new approach to the identification of regulators of a wound healing response.


Assuntos
Adiponectina/fisiologia , Pele/lesões , Pele/fisiopatologia , Cicatrização/fisiologia , Adiponectina/farmacologia , Animais , Colágeno/metabolismo , Queratinas/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Modelos Animais , Receptores de Adiponectina/deficiência , Receptores de Adiponectina/genética , Receptores de Adiponectina/fisiologia , Pele/metabolismo , Regulação para Cima/efeitos dos fármacos , Cicatrização/efeitos dos fármacos
10.
Proc Natl Acad Sci U S A ; 105(8): 2969-74, 2008 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-18287064

RESUMO

HSP90 is a protein chaperone particularly important in the maturation of a diverse set of proteins that regulate key steps in a multitude of biological processes. Alterations in HSP90 function produce altered phenotypes at low penetrance in natural populations. Previous work has shown that at least some of these phenotypes are due to genetic variation that remains phenotypically cryptic until it is revealed by the impairment of HSP90 function. Exposure of such "buffered" genetic polymorphisms can also be accomplished by environmental stress, linking the appearance of new phenotypes to defects in protein homeostasis. Should such polymorphisms be widespread, natural selection may be more effective at producing phenotypic change in suboptimal environments. In evaluating this hypothesis, a key unknown factor is the frequency with which HSP90-buffered polymorphisms occur in natural populations. Here, we present Arabidopsis thaliana populations suitable for genetic mapping that have constitutively reduced HSP90 levels. We employ quantitative genetic techniques to examine the HSP90-dependent polymorphisms affecting a host of plastic plant life-history traits. Our results demonstrate that HSP90-dependent natural variation is present at high frequencies in A. thaliana, with an expectation that at least one HSP90-dependent polymorphism will affect nearly every quantitative trait in progeny of two different wild lines. Hence, HSP90 is likely to occupy a central position in the translation of genotypic variation into phenotypic differences.


Assuntos
Arabidopsis/genética , Evolução Biológica , Variação Genética , Proteínas de Choque Térmico HSP90/genética , Fenótipo , Locos de Características Quantitativas/genética , Mapeamento Cromossômico
11.
Proc Natl Acad Sci U S A ; 105(8): 2963-8, 2008 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-18287065

RESUMO

Modulation of the activity of the molecular chaperone HSP90 has been extensively discussed as a means to alter phenotype in many traits and organisms. Such changes can be due to the exposure of cryptic genetic variation, which in some instances may also be accomplished by mild environmental alteration. Should such polymorphisms be widespread, natural selection may be more effective at producing phenotypic change in suboptimal environments. However, the frequency and identity of buffered polymorphisms in natural populations are unknown. Here, we employ quantitative genetic dissection of an Arabidopsis thaliana developmental response, hypocotyl elongation in the dark, to detail the underpinnings of genetic variation responsive to HSP90 modulation. We demonstrate that HSP90-dependent alleles occur in continuously distributed, environmentally responsive traits and are amenable to quantitative genetic mapping techniques. Furthermore, such alleles are frequent in natural populations and can have significant effects on natural phenotypic variation. We also find that HSP90 modulation has both general and allele-specific effects on developmental stability; that is, developmental stability is a phenotypic trait that can be affected by natural variation. However, effects of revealed variation on trait means outweigh effects of decreased developmental stability, and the HSP90-dependent trait alterations could be acted on by natural selection. Thus, HSP90 may centrally influence canalization, assimilation, and the rapid evolutionary alteration of phenotype through the concealment and exposure of cryptic genetic variation.


Assuntos
Arabidopsis/genética , Variação Genética , Proteínas de Choque Térmico HSP90/genética , Fenótipo , Locos de Características Quantitativas , Arabidopsis/crescimento & desenvolvimento , Hipocótilo/crescimento & desenvolvimento , Raízes de Plantas/crescimento & desenvolvimento
12.
Plant J ; 51(4): 727-37, 2007 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-17645438

RESUMO

Natural variation and induced mutations are important resources for gene discovery and the elucidation of genetic circuits. Mapping such polymorphisms requires rapid and cost-efficient methods for genome-wide genotyping. Here we report the development of a microarray-based method that assesses 240 unique markers in a single hybridization experiment at a cost of less than US$50 in materials per line. Our genotyping array is built with 70-mer oligonucleotide elements representing insertion/deletion (indel) polymorphisms between the Arabidopsis thaliana accessions Columbia-0 (Col) and Landsberg erecta (Ler). These indel polymorphisms are recognized with great precision by comparative genomic hybridization, eliminating the need for array replicates and complex statistical analysis. Markers are present genome-wide, with an average spacing of approximately 500 kb. PCR primer information is provided for all array indels, allowing rapid single-locus inquiries. Multi-well chips allow groups of 16 lines to be genotyped in a single experiment. We demonstrate the utility of the array for accurately mapping recessive mutations, RIL populations and mixed genetic backgrounds from accessions other than Col and Ler. Given the ease of use of shotgun sequencing to generate partial genomic sequences of unsequenced species, this approach is readily transferable to non-model organisms.


Assuntos
Deleção de Genes , Mutagênese Insercional , Polimorfismo Genético/genética , Arabidopsis/genética , Marcadores Genéticos/genética , Genoma de Planta , Genótipo , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Especificidade da Espécie
13.
J Biosci ; 32(3): 457-63, 2007 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-17536165

RESUMO

The Hsp90 chaperone machine facilitates the maturation of a diverse set of 'client' proteins. Many of these Hsp90 clients are essential nodes in signal transduction pathways and regulatory circuits,accounting for the important role Hsp90 plays in organismal development and responses to the environment. Recent findings suggest a broader impact of the chaperone on phenotype: fully functional Hsp90 canalizes wild-type phenotypes by suppressing underlying genetic and epigenetic variation. This variation can be expressed upon challenging the Hsp90 machinery by environmental stress, genetic or pharmaceutical targeting of Hsp90. The existence of Hsp90-buffered genetic and epigenetic variation together with plausible release mechanisms has wide-ranging implication for phenotype and possibly evolutionary processes. Here,we discuss the role of Hsp90 in canalization and organismal plasticity,and highlight important questions for future experimental inquiry.


Assuntos
Regulação da Expressão Gênica/fisiologia , Proteínas de Choque Térmico HSP90/metabolismo , Animais , Arabidopsis , Drosophila melanogaster , Epigênese Genética , Genótipo , Proteínas de Choque Térmico HSP90/genética , Fenótipo
14.
Theor Appl Genet ; 114(4): 683-92, 2007 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-17165080

RESUMO

Circadian rhythms regulate many aspects of plant growth, fitness and vigour. The components and detailed mechanism of circadian regulation to date have been dissected in the reference species Arabidopsis thaliana. To determine the genetic basis and range of natural allelic variation for intrinsic circadian period in the closest crop relatives, we used an accurate and high throughput data capture system to record rhythmic cotyledon movement in two immortal segregating populations of Brassica oleracea, derived from parent lines representing different crop types. Periods varied between 24.4 and 26.1 h between the parent lines, with transgressive segregation between extreme recombinant lines in both populations of approximately 3.5 h. The additive effect of individual QTL identified in each population varied from 0.17 to 0.36 h. QTL detected in one doubled haploid population were verified and the mapping intervals further resolved by determining circadian period in genomic substitution lines derived from the parental lines. Comparative genomic analysis based on collinearity between Brassica and Arabidopsis also allowed identification of candidate orthologous genes known to regulate period in Arabidopsis, that may account for the additive circadian effects of specific QTL. The distinct QTL positions detected in the two populations, and the extent of transgressive segregation suggest that there is likely to be considerable scope for modulating the range of available circadian periods in natural populations and crop species of Brassica. This may provide adaptive advantage for optimising growth and development in different latitudes, seasons or climate conditions.


Assuntos
Brassica/genética , Cruzamento/métodos , Ritmo Circadiano/genética , Locos de Características Quantitativas , Brassica/fisiologia , Mapeamento Cromossômico , Ritmo Circadiano/fisiologia , Cotilédone/crescimento & desenvolvimento , Cruzamentos Genéticos , Genômica/métodos , Fatores de Tempo
15.
BMC Plant Biol ; 6: 10, 2006 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-16737527

RESUMO

BACKGROUND: The circadian system drives pervasive biological rhythms in plants. Circadian clocks integrate endogenous timing information with environmental signals, in order to match rhythmic outputs to the local day/night cycle. Multiple signaling pathways affect the circadian system, in ways that are likely to be adaptively significant. Our previous studies of natural genetic variation in Arabidopsis thaliana accessions implicated FLOWERING LOCUS C (FLC) as a circadian-clock regulator. The MADS-box transcription factor FLC is best known as a regulator of flowering time. Its activity is regulated by many regulatory genes in the "autonomous" and vernalization-dependent flowering pathways. We tested whether these same pathways affect the circadian system. RESULTS: Genes in the autonomous flowering pathway, including FLC, were found to regulate circadian period in Arabidopsis. The mechanisms involved are similar, but not identical, to the control of flowering time. By mutant analyses, we demonstrate a graded effect of FLC expression upon circadian period. Related MADS-box genes had less effect on clock function. We also reveal an unexpected vernalization-dependent alteration of periodicity. CONCLUSION: This study has aided in the understanding of FLC's role in the clock, as it reveals that the network affecting circadian timing is partially overlapping with the floral-regulatory network. We also show a link between vernalization and circadian period. This finding may be of ecological relevance for developmental programming in other plant species.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiologia , Relógios Biológicos/fisiologia , Ritmo Circadiano/fisiologia , Flores/fisiologia , Proteínas de Domínio MADS/metabolismo , Proteínas de Arabidopsis/genética , Dosagem de Genes , Proteínas de Domínio MADS/deficiência , Proteínas de Domínio MADS/genética , Mutação/genética , Estações do Ano
16.
Plant Cell ; 18(3): 639-50, 2006 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-16473970

RESUMO

Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation.


Assuntos
Proteínas de Arabidopsis/fisiologia , Arabidopsis/genética , Ritmo Circadiano/genética , Regulação da Expressão Gênica de Plantas , Temperatura Alta , Proteínas de Domínio MADS/fisiologia , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Análise por Conglomerados , Análise de Fourier , Perfilação da Expressão Gênica , Genes de Plantas , Genômica/métodos , Genótipo , Proteínas de Domínio MADS/genética , Modelos Genéticos , Proteínas Nucleares/metabolismo , Locos de Características Quantitativas , Fatores de Transcrição/metabolismo
17.
Science ; 309(5734): 630-3, 2005 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-16040710

RESUMO

Circadian clocks are believed to confer an advantage to plants, but the nature of that advantage has been unknown. We show that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle. In wild type and in long- and short-circadian period mutants of Arabidopsis thaliana, plants with a clock period matched to the environment contain more chlorophyll, fix more carbon, grow faster, and survive better than plants with circadian periods differing from their environment. This explains why plants gain advantage from circadian control.


Assuntos
Arabidopsis/crescimento & desenvolvimento , Arabidopsis/fisiologia , Relógios Biológicos/fisiologia , Ritmo Circadiano/fisiologia , Fotossíntese , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Biomassa , Dióxido de Carbono/metabolismo , Clorofila/metabolismo , Escuridão , Regulação da Expressão Gênica de Plantas , Genótipo , Luz , Mutação , Folhas de Planta/metabolismo , Sementes/crescimento & desenvolvimento , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
18.
Genes Dev ; 17(2): 256-68, 2003 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-12533513

RESUMO

Plants possess several photoreceptors to sense the light environment. In Arabidopsis cryptochromes and phytochromes play roles in photomorphogenesis and in the light input pathways that synchronize the circadian clock with the external world. We have identified SRR1 (sensitivity to red light reduced), a gene that plays an important role in phytochrome B (phyB)-mediated light signaling. The recessive srr1 null allele and phyB mutants display a number of similar phenotypes indicating that SRR1 is required for normal phyB signaling. Genetic analysis suggests that SRR1 works both in the phyB pathway but also independently of phyB. srr1 mutants are affected in multiple outputs of the circadian clock in continuous light conditions, including leaf movement and expression of the clock components, CCA1 and TOC1. Clock-regulated gene expression is also impaired during day-night cycles and in constant darkness. The circadian phenotypes of srr1 mutants in all three conditions suggest that SRR1 activity is required for normal oscillator function. The SRR1 gene was identified and shown to code for a protein conserved in numerous eukaryotes including mammals and flies, implicating a conserved role for this protein in both the animal and plant kingdoms.


Assuntos
Proteínas de Arabidopsis/fisiologia , Arabidopsis/genética , Arabidopsis/fisiologia , Ritmo Circadiano/genética , Ritmo Circadiano/fisiologia , Genes de Plantas , Células Fotorreceptoras , Fitocromo/fisiologia , Sequência de Aminoácidos , Arabidopsis/efeitos da radiação , Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Dados de Sequência Molecular , Mutação , Filogenia , Fitocromo/genética , Fitocromo B , Homologia de Sequência de Aminoácidos , Transdução de Sinais , Fatores de Transcrição/genética , Fatores de Transcrição/fisiologia
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