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1.
Plant Cell ; 29(8): 1836-1863, 2017 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-28705956

RESUMEN

Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5'-3' RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.


Asunto(s)
Arabidopsis/genética , Arabidopsis/efectos de la radiación , Regulación hacia Abajo/genética , Regulación de la Expresión Génica de las Plantas/efectos de la radiación , Genes de Plantas , Luz , Estrés Fisiológico/genética , Arabidopsis/fisiología , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Metilación de ADN/genética , Perfilación de la Expresión Génica , Silenciador del Gen , Sitios Genéticos , Semivida , Dinámicas no Lineales , Biosíntesis de Proteínas , Estabilidad del ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN Interferente Pequeño/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , Análisis de Secuencia de ARN , Estrés Fisiológico/efectos de la radiación , Factores de Tiempo , Transcripción Genética/efectos de la radiación , Transcriptoma/genética
2.
BMC Bioinformatics ; 20(1): 253, 2019 May 16.
Artículo en Inglés | MEDLINE | ID: mdl-31096906

RESUMEN

BACKGROUND: The development of whole genome bisulfite sequencing has made it possible to identify methylation differences at single base resolution throughout an entire genome. However, a persistent challenge in DNA methylome analysis is the accurate identification of differentially methylated regions (DMRs) between samples. Sensitive and specific identification of DMRs among different conditions requires accurate and efficient algorithms, and while various tools have been developed to tackle this problem, they frequently suffer from inaccurate DMR boundary identification and high false positive rate. RESULTS: We present a novel Histogram Of MEthylation (HOME) based method that takes into account the inherent difference in the distribution of methylation levels between DMRs and non-DMRs to discriminate between the two using a Support Vector Machine. We show that generated features used by HOME are dataset-independent such that a classifier trained on, for example, a mouse methylome training set of regions of differentially accessible chromatin, can be applied to any other organism's dataset and identify accurate DMRs. We demonstrate that DMRs identified by HOME exhibit higher association with biologically relevant genes, processes, and regulatory events compared to the existing methods. Moreover, HOME provides additional functionalities lacking in most of the current DMR finders such as DMR identification in non-CG context and time series analysis. HOME is freely available at https://github.com/ListerLab/HOME . CONCLUSION: HOME produces more accurate DMRs than the current state-of-the-art methods on both simulated and biological datasets. The broad applicability of HOME to identify accurate DMRs in genomic data from any organism will have a significant impact upon expanding our knowledge of how DNA methylation dynamics affect cell development and differentiation.


Asunto(s)
Algoritmos , Metilación de ADN/genética , Aprendizaje Automático , Animales , Simulación por Computador , Bases de Datos Genéticas , Ratones , Anotación de Secuencia Molecular , Factores de Tiempo
3.
Genome Res ; 26(11): 1520-1531, 2016 11.
Artículo en Inglés | MEDLINE | ID: mdl-27613611

RESUMEN

DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.


Asunto(s)
Brachypodium/genética , Metilación de ADN , Polimorfismo Genético , Elementos Transponibles de ADN/genética , Genoma de Planta , Mutación
4.
Plant Physiol ; 178(4): 1614-1630, 2018 12.
Artículo en Inglés | MEDLINE | ID: mdl-30301775

RESUMEN

In plants, the molecular function(s) of the nucleus-localized 5'-3' EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis of RNA ends, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3' read-through. This occurred at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis (Arabidopsis thaliana). Read-through is speculated to have a negative effect on transcript abundance; however, we did not observe this. Rather, we identified a strong association between read-through and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (less than 1,000 bp) and expression of the upstream gene. We observed read-through in the proximity of 903 genes up-regulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may account directly for up to 23% of genes up-regulated in sal1-8 Using APX2 and AT5G43770 as exemplars, we genetically uncoupled read-through loci from downstream genes to validate the principle of read-through-mediated mRNA regulation, providing one mechanism by which an ostensibly posttranscriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.


Asunto(s)
Adenosina Difosfato/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Monoéster Fosfórico Hidrolasas/genética , ARN Polimerasa II/metabolismo , Adenosina Difosfato/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Ascorbato Peroxidasas/genética , Ascorbato Peroxidasas/metabolismo , Exorribonucleasas/genética , Exorribonucleasas/metabolismo , Regulación de la Expresión Génica de las Plantas , Mutación , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Monoéster Fosfórico Hidrolasas/metabolismo , ARN Polimerasa II/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN no Traducido/metabolismo , Reproducibilidad de los Resultados , Transducción de Señal
5.
Proc Natl Acad Sci U S A ; 113(44): E6895-E6902, 2016 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-27791153

RESUMEN

Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24-nt siRNAs and altered patterns of DNA methylation that can affect gene expression. Driving the changes in methylation are the processes trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). In TCM/TCdM the methylation state of one allele is altered to resemble the other allele. We show that Pol IV-dependent sRNAs are required to establish TCM events. The changes in DNA methylation and the associated changes in sRNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome. The inheritance of these altered epigenetic states varies in F2 individuals, resulting in individuals with genetically identical loci displaying different epigenetic states and gene expression profiles. The change in methylation at these regions is associated with the presence of sRNAs. Loci without any sRNA activity can have altered methylation states, suggesting that a sRNA-independent mechanism may also contribute to the altered methylation state of the F1 and F2 generations.


Asunto(s)
Arabidopsis/genética , Cromosomas de las Plantas/genética , Metilación de ADN/genética , Nucleótidos/metabolismo , ARN de Planta/genética , ARN Interferente Pequeño/genética , Alelos , Proteínas de Arabidopsis/metabolismo , Cruzamientos Genéticos , ADN de Plantas/genética , ADN de Plantas/metabolismo , ARN Polimerasas Dirigidas por ADN/metabolismo , Epigénesis Genética , Regulación de la Expresión Génica de las Plantas , Sitios Genéticos , Vigor Híbrido , Hibridación Genética , Patrón de Herencia/genética , ARN Interferente Pequeño/metabolismo , Autofecundación/genética , Factores de Tiempo
6.
Plant Physiol ; 175(4): 1893-1912, 2017 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-28986422

RESUMEN

Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epi-alleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Arabidopsis/fisiología , Metilación de ADN , Regulación de la Expresión Génica de las Plantas/fisiología , Agua , Alelos , Proteínas de Arabidopsis/genética , ADN de Plantas , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN de Planta/genética , ARN de Planta/metabolismo , Estrés Fisiológico
7.
Plant Cell Environ ; 41(7): 1657-1672, 2018 07.
Artículo en Inglés | MEDLINE | ID: mdl-29707792

RESUMEN

The capacity for plant stress priming and memory and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light stress, can lead to robust programmable changes in newly developing leaf tissues. Although key signalling molecules and transcription factors are known to promote this priming signal, an untested question is the potential involvement of chromatin marks towards the maintenance of light stress acclimation, or memory. Thus, we systematically tested our previous hypothesis of a stress-resistant methylome using a recurring excess-light stress, then analysing new, emerging, and existing tissues. The DNA methylome showed negligible stress-associated variation, with the vast majority attributable to stochastic differences. Yet, photoacclimation was evident through enhanced photosystem II performance in exposed tissues, and nonphotochemical quenching and fluorescence decline ratio showed evidence of mitotic transmission. Thus, we have observed physiological acclimation in new and emerging tissues in the absence of substantive DNA methylome changes.


Asunto(s)
Metilación de ADN/efectos de la radiación , Arabidopsis/genética , Arabidopsis/metabolismo , Arabidopsis/fisiología , Arabidopsis/efectos de la radiación , Clorofila/metabolismo , Genoma de Planta/genética , Luz , Fotosíntesis/efectos de la radiación , Complejo de Proteína del Fotosistema II/efectos de la radiación , Análisis de Secuencia de ADN , Estrés Fisiológico , Xantófilas/metabolismo
8.
Plant Cell ; 26(12): 4602-16, 2014 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-25527708

RESUMEN

DNA methylation can play important roles in the regulation of transposable elements and genes. A collection of mutant alleles for 11 maize (Zea mays) genes predicted to play roles in controlling DNA methylation were isolated through forward- or reverse-genetic approaches. Low-coverage whole-genome bisulfite sequencing and high-coverage sequence-capture bisulfite sequencing were applied to mutant lines to determine context- and locus-specific effects of these mutations on DNA methylation profiles. Plants containing mutant alleles for components of the RNA-directed DNA methylation pathway exhibit loss of CHH methylation at many loci as well as CG and CHG methylation at a small number of loci. Plants containing loss-of-function alleles for chromomethylase (CMT) genes exhibit strong genome-wide reductions in CHG methylation and some locus-specific loss of CHH methylation. In an attempt to identify stocks with stronger reductions in DNA methylation levels than provided by single gene mutations, we performed crosses to create double mutants for the maize CMT3 orthologs, Zmet2 and Zmet5, and for the maize DDM1 orthologs, Chr101 and Chr106. While loss-of-function alleles are viable as single gene mutants, the double mutants were not recovered, suggesting that severe perturbations of the maize methylome may have stronger deleterious phenotypic effects than in Arabidopsis thaliana.


Asunto(s)
Metilación de ADN , Regulación de la Expresión Génica de las Plantas , Zea mays/genética , Alelos , Cruzamientos Genéticos , ADN (Citosina-5-)-Metiltransferasas/genética , Epigenómica , Genes de Plantas , Mutación
9.
Nucleic Acids Res ; 43(12): e81, 2015 Jul 13.
Artículo en Inglés | MEDLINE | ID: mdl-25813045

RESUMEN

We present a capture-based approach for bisulfite-converted DNA that allows interrogation of pre-defined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.


Asunto(s)
5-Metilcitosina/análisis , Citosina/análogos & derivados , Genoma de Planta , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Alelos , Animales , Línea Celular , Citosina/análisis , Metilación de ADN , Genómica/métodos , Humanos , Ratones , Polimorfismo de Nucleótido Simple , Sulfitos
10.
Plant Physiol ; 168(4): 1262-74, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-25869653

RESUMEN

DNA methylation is a stable modification of chromatin that can contribute to epigenetic variation through the regulation of genes or transposons. Profiling of DNA methylation in five maize (Zea mays) inbred lines found that while DNA methylation levels for more than 99% of the analyzed genomic regions are similar, there are still 5,000 to 20,000 context-specific differentially methylated regions (DMRs) between any two genotypes. The analysis of identical-by-state genomic regions that have limited genetic variation provided evidence that DMRs can occur without local sequence variation, but they are less common than in regions with genetic variation. Characterization of the sequence specificity of DMRs, location of DMRs relative to genes and transposons, and patterns of DNA methylation in regions flanking DMRs reveals a distinct subset of DMRs. Transcriptome profiling of the same tissue revealed that only approximately 20% of genes with qualitative (on-off) differences in gene expression are associated with DMRs, and there is little evidence for association of DMRs with genes that show quantitative differences in gene expression. We also identify a set of genes that may represent cryptic information that is silenced by DNA methylation in the reference B73 genome. Many of these genes exhibit natural variation in other genotypes, suggesting the potential for selection to act upon existing epigenetic natural variation. This study provides insights into the origin and influences of DMRs in a crop species with a complex genome organization.


Asunto(s)
Metilación de ADN , Epigénesis Genética , Variación Genética , Genoma de Planta/genética , Zea mays/genética , Cruzamiento , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genotipo
11.
Plant Cell ; 25(3): 780-93, 2013 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-23463775

RESUMEN

Trimethylation of histone H3 Lys-27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize (Zea mays) plants of two genetic backgrounds, B73 and Mo17. There were more substantial differences in the genome-wide profile of H3K27me3 between different tissues than between the two genotypes. The tissue-specific patterns of H3K27me3 were often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. A comparison of the H3K27me3 targets in rice (Oryza sativa), maize, and Arabidopsis thaliana provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole-genome duplication, suggesting the potential for subfunctionalization of chromatin regulation of paralogs. Genomic profiling of H3K27me3 in loss-of-function mutant lines for Maize Enhancer of zeste-like2 (Mez2) and Mez3, two of the three putative H3K27me3 methyltransferases present in the maize genome, suggested partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 required Mez2 and/or Mez3, and there was limited evidence for functional consequences of H3K27me3 at these targets.


Asunto(s)
Metilación de ADN , ADN de Plantas/metabolismo , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Heterocromatina/metabolismo , Histonas/metabolismo , Zea mays/metabolismo , Alelos , Arabidopsis/genética , Arabidopsis/metabolismo , Ensamble y Desensamble de Cromatina , ADN de Plantas/genética , Endospermo/genética , Endospermo/metabolismo , Duplicación de Gen , Impresión Genómica , Genotipo , Heterocromatina/genética , Familia de Multigenes , Mutación , Oryza/genética , Oryza/metabolismo , Especificidad de la Especie , Zea mays/genética
12.
Plant Cell ; 25(8): 2783-97, 2013 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-23922207

RESUMEN

DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, genetic changes such as transposon insertions can also lead to changes in DNA methylation. Genome-wide profiles of DNA methylation for 20 maize (Zea mays) inbred lines were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize or teosinte genotypes, resulting in the discovery of 1966 common DMRs and 1754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with single nucleotide polymorphisms found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the variation in DNA methylation. Analysis of gene expression in the same samples used for DNA methylation profiling identified over 300 genes with expression patterns that are significantly associated with DNA methylation variation. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic changes that are often stably inherited and can influence the expression of nearby genes.


Asunto(s)
Metilación de ADN/genética , Epigénesis Genética , Variación Genética , Zea mays/genética , Análisis por Conglomerados , Genotipo , Endogamia , Patrón de Herencia/genética , Modelos Genéticos , Recombinación Genética/genética , Reproducibilidad de los Resultados
13.
Proc Natl Acad Sci U S A ; 110(48): 19639-44, 2013 Nov 26.
Artículo en Inglés | MEDLINE | ID: mdl-24218619

RESUMEN

In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting between maize and rice have elevated nonsynonymous to synonymous substitution ratios compared with other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize.


Asunto(s)
Alelos , Evolución Molecular , Variación Genética , Impresión Genómica/genética , Oryza/genética , Zea mays/genética , Secuencia de Bases , Teorema de Bayes , Cruzamientos Genéticos , Genética de Población , Hibridación Genética , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Polimorfismo de Nucleótido Simple/genética , Análisis de Secuencia de ARN , Especificidad de la Especie
14.
Plant Physiol ; 165(3): 933-947, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-24872382

RESUMEN

Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histones, modifications of DNA or histones, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against generically equating chromatin and epigenetics; although many examples of epigenetics involve chromatin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes.

15.
PLoS Genet ; 8(12): e1003127, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-23271981

RESUMEN

Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some retrotransposon families exhibit enrichment of heterochromatic marks within 800-1,200 base pairs of insertion sites, while other families exhibit very little evidence for the spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the heterochromatin in low-copy DNA flanking retrotransposons often results from the spreading of silencing marks rather than insertion-site preferences. Genes located near TEs that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of retrotransposon families may act as controlling elements influencing neighboring sequences, while the majority of retrotransposons have little effect on flanking sequences.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Heterocromatina/genética , Retroelementos/genética , Zea mays/genética , Secuencia de Bases , Metilación de ADN/genética , Silenciador del Gen , Genoma de Planta , Histonas/genética , Histonas/metabolismo , Análisis de Secuencia de ADN , Zea mays/metabolismo
16.
Genome Res ; 20(12): 1689-99, 2010 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-21036921

RESUMEN

Individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. Array comparative genomic hybridization (CGH) was used to compare gene content and copy number variation among 19 diverse maize inbreds and 14 genotypes of the wild ancestor of maize, teosinte. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes present in B73, but missing from other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes, and the majority of events are observed in both maize and teosinte, suggesting that these variants predate domestication and that there is not strong selection acting against them. Many of the genes affected by CNV/PAV are either maize specific (thus possible annotation artifacts) or members of large gene families, suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.


Asunto(s)
Dosificación de Gen/genética , Genes de Plantas/genética , Variación Genética , Zea mays/genética , Mapeo Cromosómico , Hibridación Genómica Comparativa , Genotipo , Recombinación Genética/genética , Especificidad de la Especie
17.
Plant Physiol ; 156(4): 1679-90, 2011 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-21705654

RESUMEN

Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.


Asunto(s)
Variación Genética , Endogamia , Zea mays/genética , Centrómero/genética , Mapeo Cromosómico , Cromosomas Artificiales Bacterianos/genética , Variaciones en el Número de Copia de ADN/genética , Genética de Población , Genoma de Planta/genética , Heterocigoto , Hibridación Genética , Sitios de Carácter Cuantitativo/genética , Zea mays/anatomía & histología
18.
G3 (Bethesda) ; 10(5): 1629-1637, 2020 05 04.
Artículo en Inglés | MEDLINE | ID: mdl-32132166

RESUMEN

Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.


Asunto(s)
Brachypodium , Brachypodium/genética , Metilación de ADN , Epigénesis Genética , Epigenómica , Variación Genética , Genotipo , Humanos , Fenotipo
19.
G3 (Bethesda) ; 9(11): 3611-3621, 2019 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-31484672

RESUMEN

Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant's ability to respond to future events. A clear example of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes toward stress priming and, consequently, the potential contribution from DNA methylation - a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional 'dampening' in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.


Asunto(s)
Arabidopsis/efectos de la radiación , Metilación de ADN , Luz , Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas , Genotipo , Estrés Fisiológico/genética
20.
Genome Biol ; 19(1): 122, 2018 08 23.
Artículo en Inglés | MEDLINE | ID: mdl-30134966

RESUMEN

The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effects should have been B73, rather than Mo17, due to the original coding of biallele SNPs as "0s" and "1s". Going through the entire analysis procedure, it was determined that the mistake was made while tabulating the eQTL results from QTL Cartographer.

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