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Artikel ; Online: Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture.

Quadrana, Leandro / Silveira, Amanda Bortolini / Caillieux, Erwann / Colot, Vincent

Methods in molecular biology (Clifton, N.J.)

2021 Band 2250, Seite(n) 141–155

Abstract: Transposable elements (TEs) are repetitive DNA sequences that have the ability to mobilize in the genome and create major effect mutations. Despite the importance of transposition as a source of genetic novelty, we still know little about the rate, ... ...

Abstract	Transposable elements (TEs) are repetitive DNA sequences that have the ability to mobilize in the genome and create major effect mutations. Despite the importance of transposition as a source of genetic novelty, we still know little about the rate, landscape, and consequences of TE mobilization. This situation stems in large part from the repetitive nature of TEs, which complicates their analysis. Moreover, TE mobilization is typically rare and therefore new TE (i.e., non-reference) insertions tend to be missed in small-scale population studies. This chapter describes a TE-sequence capture approach designed to identify transposition events for most of the TE families that are potentially active in Arabidopsis thaliana. We show that our TE-sequence capture design provides an efficient means to detect with high sensitivity and specificity insertions that are present at a frequency as low as 1/1000 within a DNA sample.
Mesh-Begriff(e)	Arabidopsis/genetics ; DNA Transposable Elements ; DNA, Plant/analysis ; Evolution, Molecular ; Mutagenesis, Insertional ; Selection, Genetic ; Sequence Analysis, DNA/methods
Chemische Substanzen	DNA Transposable Elements ; DNA, Plant
Sprache	Englisch
Erscheinungsdatum	2021-04-26
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1134-0_14
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects.

Van Dooren, Tom J M / Silveira, Amanda Bortolini / Gilbault, Elodie / Jiménez-Gómez, José M / Martin, Antoine / Bach, Liên / Tisné, Sébastien / Quadrana, Leandro / Loudet, Olivier / Colot, Vincent

Journal of experimental botany

2020 Band 71, Heft 12, Seite(n) 3588–3602

Abstract: There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it ... ...

Abstract	There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.
Mesh-Begriff(e)	Arabidopsis/genetics ; DNA Methylation ; Droughts ; Epigenesis, Genetic ; Gene Expression ; Phenotype
Sprache	Englisch
Erscheinungsdatum	2020-03-09
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/eraa132
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies.

Silveira, Amanda Bortolini / Bidard, François-Clément / Kasperek, Amélie / Melaabi, Samia / Tanguy, Marie-Laure / Rodrigues, Manuel / Bataillon, Guillaume / Cabel, Luc / Buecher, Bruno / Pierga, Jean-Yves / Proudhon, Charlotte / Stern, Marc-Henri

Clinical chemistry

2020 Band 66, Heft 4, Seite(n) 606–613

Abstract: Background: Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, ... ...

Abstract	Background: Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool. Methods: We developed drop-off droplet-digital PCR (ddPCR) assays targeting BAT-26, activin A receptor type 2A (ACVR2A), and defensin beta 105A/B (DEFB105A/B) microsatellite markers. Performances of the assays were measured on reconstitution experiments of various mutant allelic fractions, on 185 tumor samples with known MSI status, and on 72 blood samples collected from 42 patients with advanced colorectal or endometrial cancers before and/or during therapy. Results: The 3 ddPCR assays reached analytical sensitivity <0.1% variant allelic frequency and could reliably detect and quantify MSI in both tumor and body fluid samples. High concordance between MSI status determination by the three-marker ddPCR test and the reference pentaplex method were observed (100% for colorectal tumors and 93% for other tumor types). Moreover, the 3 assays showed correlations with r ≥ 0.99 with other circulating tumor DNA markers and their dynamic during treatment correlated well with clinical response. Conclusions: This innovative approach for MSI detection provides a noninvasive, cost-effective, and fast diagnostic tool, well suited for large-scale screening of patients that may benefit from immunotherapy agents, as well as for monitoring treatment responses.
Mesh-Begriff(e)	Activin Receptors, Type II/genetics ; Biomarkers, Tumor ; Cell Line, Tumor ; Circulating Tumor DNA/blood ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Endometrial Neoplasms/drug therapy ; Endometrial Neoplasms/genetics ; Endometrial Neoplasms/pathology ; False Positive Reactions ; Female ; Genetic Markers ; Humans ; Limit of Detection ; Liquid Biopsy ; Microsatellite Instability ; Microsatellite Repeats ; Polymerase Chain Reaction/methods ; beta-Defensins/genetics
Chemische Substanzen	BAT26 microsatellite DNA ; Biomarkers, Tumor ; Circulating Tumor DNA ; DEFB105A protein, human ; Genetic Markers ; beta-Defensins ; Activin Receptors, Type II (EC 2.7.11.30) ; activin receptor type II-A (EC 2.7.11.30)
Sprache	Englisch
Erscheinungsdatum	2020-03-16
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1093/clinchem/hvaa013
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Microsatellite instability detection in breast cancer using drop-off droplet digital PCR.

Oncogene

2022 Band 41, Heft 49, Seite(n) 5289–5297

Abstract: The use of conventional methods (immunohistochemistry, pentaplex PCR) for detecting microsatellite instability (MSI), a predictive biomarker of immunotherapy efficacy, is debated for cancers with low MSI prevalence, such as breast cancer (BC). We ... ...

Abstract	The use of conventional methods (immunohistochemistry, pentaplex PCR) for detecting microsatellite instability (MSI), a predictive biomarker of immunotherapy efficacy, is debated for cancers with low MSI prevalence, such as breast cancer (BC). We developed two multiplex drop-off droplet digital PCR (ddPCR) assays targeting four microsatellites, initially identified from public BC whole-genome sequencing dataset. Performances of the assays were investigated and 352 tumor DNA and 28 circulating cell-free DNA from BC patients, with unknown MSI status were blindly screened. Cross-validation of ddPCR MSI status with other MSI detection methods was performed. We then monitored circulating tumor DNA (ctDNA) dynamics before and during pembrolizumab immunotherapy in one patient with MSI-high (MSI-H) metastatic BC. The assays showed high analytical specificity and sensitivity (limit of detection = 0.16%). Among N = 380 samples, seven (1.8%) were found as MSI-H by ddPCR with six of them confirmed by next-generation sequencing (NGS). Specificity was 100% in N = 133 microsatellite stable BC submitted to NGS. In the patient with MSI-H metastatic BC, ctDNA monitoring revealed an early decrease of microsatellite mutant allelic frequencies during immunotherapy. These results demonstrated MSI detection by ddPCR, a non-invasive, fast and cost-effective approach, allowing for large pre-screening of BC patients who may benefit from immunotherapy.
Mesh-Begriff(e)	Humans ; Female ; Microsatellite Instability ; Breast Neoplasms/diagnosis ; Breast Neoplasms/genetics ; Circulating Tumor DNA/genetics ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction ; Colorectal Neoplasms/genetics
Chemische Substanzen	Circulating Tumor DNA
Sprache	Englisch
Erscheinungsdatum	2022-11-03
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	639046-8
ISSN	1476-5594 ; 0950-9232
ISSN (online)	1476-5594
ISSN	0950-9232
DOI	10.1038/s41388-022-02504-6
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Extensive natural epigenetic variation at a de novo originated gene.

Silveira, Amanda Bortolini / Trontin, Charlotte / Cortijo, Sandra / Barau, Joan / Del Bem, Luiz Eduardo Vieira / Loudet, Olivier / Colot, Vincent / Vincentz, Michel

PLoS genetics

2013 Band 9, Heft 4, Seite(n) e1003437

Abstract: Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the ... ...

Abstract	Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.
Mesh-Begriff(e)	5' Untranslated Regions ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Base Sequence ; DNA Methylation/genetics ; Epigenesis, Genetic ; Gene Expression Regulation, Plant ; Genetic Variation ; Phenotype ; Starch/metabolism
Chemische Substanzen	5' Untranslated Regions ; Arabidopsis Proteins ; Starch (9005-25-8)
Sprache	Englisch
Erscheinungsdatum	2013-04-11
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1003437
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: The Arabidopsis bZIP gene AtbZIP63 is a sensitive integrator of transient abscisic acid and glucose signals.

Matiolli, Cleverson Carlos / Tomaz, Juarez Pires / Duarte, Gustavo Turqueto / Prado, Fernanda Manso / Del Bem, Luiz Eduardo Vieira / Silveira, Amanda Bortolini / Gauer, Luciane / Corrêa, Luiz Gustavo Guedes / Drumond, Rodrigo Duarte / Viana, Américo José Carvalho / Di Mascio, Paolo / Meyer, Christian / Vincentz, Michel

Plant physiology

2011 Band 157, Heft 2, Seite(n) 692–705

Abstract: Glucose modulates plant metabolism, growth, and development. In Arabidopsis (Arabidopsis thaliana), Hexokinase1 (HXK1) is a glucose sensor that may trigger abscisic acid (ABA) synthesis and sensitivity to mediate glucose-induced inhibition of seedling ... ...

Abstract	Glucose modulates plant metabolism, growth, and development. In Arabidopsis (Arabidopsis thaliana), Hexokinase1 (HXK1) is a glucose sensor that may trigger abscisic acid (ABA) synthesis and sensitivity to mediate glucose-induced inhibition of seedling development. Here, we show that the intensity of short-term responses to glucose can vary with ABA activity. We report that the transient (2 h/4 h) repression by 2% glucose of AtbZIP63, a gene encoding a basic-leucine zipper (bZIP) transcription factor partially involved in the Snf1-related kinase KIN10-induced responses to energy limitation, is independent of HXK1 and is not mediated by changes in ABA levels. However, high-concentration (6%) glucose-mediated repression appears to be modulated by ABA, since full repression of AtbZIP63 requires a functional ABA biosynthetic pathway. Furthermore, the combination of glucose and ABA was able to trigger a synergistic repression of AtbZIP63 and its homologue AtbZIP3, revealing a shared regulatory feature consisting of the modulation of glucose sensitivity by ABA. The synergistic regulation of AtbZIP63 was not reproduced by an AtbZIP63 promoter-5'-untranslated region::β-glucuronidase fusion, thus suggesting possible posttranscriptional control. A transcriptional inhibition assay with cordycepin provided further evidence for the regulation of mRNA decay in response to glucose plus ABA. Overall, these results indicate that AtbZIP63 is an important node of the glucose-ABA interaction network. The mechanisms by which AtbZIP63 may participate in the fine-tuning of ABA-mediated abiotic stress responses according to sugar availability (i.e., energy status) are discussed.
Mesh-Begriff(e)	5' Untranslated Regions ; Abscisic Acid/biosynthesis ; Abscisic Acid/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Basic-Leucine Zipper Transcription Factors/genetics ; Basic-Leucine Zipper Transcription Factors/metabolism ; Biosynthetic Pathways ; Gene Expression Regulation, Plant ; Glucose/metabolism ; Glucuronidase/genetics ; Glucuronidase/metabolism ; Hexokinase/metabolism ; Promoter Regions, Genetic ; Protein-Serine-Threonine Kinases/metabolism ; RNA Stability ; Signal Transduction ; Trans-Activators/metabolism
Chemische Substanzen	5' Untranslated Regions ; Arabidopsis Proteins ; Basic-Leucine Zipper Transcription Factors ; Sen1 protein, Arabidopsis ; Trans-Activators ; bZIP34 protein, Arabidopsis ; bZIP63 protein, Arabidopsis ; Abscisic Acid (72S9A8J5GW) ; SNF1-related protein kinases (EC 2.7.1.-) ; Hexokinase (EC 2.7.1.1) ; ATHXK1 protein, Arabidopsis (EC 2.7.1.1.) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; Glucuronidase (EC 3.2.1.31) ; Glucose (IY9XDZ35W2)
Sprache	Englisch
Erscheinungsdatum	2011-08-15
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1104/pp.111.181743
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: The Arabidopsis bZIP Gene AtbZIP63 Is a Sensitive Integrator of Transient Abscisic Acid and Glucose Signals

Plant physiology. 2011 Oct., v. 157, no. 2

2011

Abstract	Glucose modulates plant metabolism, growth, and development. In Arabidopsis (Arabidopsis thaliana), Hexokinase1 (HXK1) is a glucose sensor that may trigger abscisic acid (ABA) synthesis and sensitivity to mediate glucose-induced inhibition of seedling development. Here, we show that the intensity of short-term responses to glucose can vary with ABA activity. We report that the transient (2 h/4 h) repression by 2% glucose of AtbZIP63, a gene encoding a basic-leucine zipper (bZIP) transcription factor partially involved in the Snf1-related kinase KIN10-induced responses to energy limitation, is independent of HXK1 and is not mediated by changes in ABA levels. However, high-concentration (6%) glucose-mediated repression appears to be modulated by ABA, since full repression of AtbZIP63 requires a functional ABA biosynthetic pathway. Furthermore, the combination of glucose and ABA was able to trigger a synergistic repression of AtbZIP63 and its homologue AtbZIP3, revealing a shared regulatory feature consisting of the modulation of glucose sensitivity by ABA. The synergistic regulation of AtbZIP63 was not reproduced by an AtbZIP63 promoter-5'-untranslated region::β-glucuronidase fusion, thus suggesting possible posttranscriptional control. A transcriptional inhibition assay with cordycepin provided further evidence for the regulation of mRNA decay in response to glucose plus ABA. Overall, these results indicate that AtbZIP63 is an important node of the glucose-ABA interaction network. The mechanisms by which AtbZIP63 may participate in the fine-tuning of ABA-mediated abiotic stress responses according to sugar availability (i.e., energy status) are discussed.
Schlagwörter	Arabidopsis thaliana ; abiotic stress ; abscisic acid ; biochemical pathways ; energy ; genes ; glucose ; messenger RNA ; metabolism ; seedlings ; stress response ; transcription factors
Sprache	Englisch
Erscheinungsverlauf	2011-10
Umfang	p. 692-705.
Erscheinungsort	American Society of Plant Biologists
Dokumenttyp	Artikel
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel: Extensive natural epigenetic variation at a De Novo originated gene

Silveira, Amanda Bortolini / Trontin, Charlotte / Cortijo, Sandra / Barau, Joan / Vieira Del Bem, Luiz Eduardo / Loudet, Olivier / Colot, Vincent / Vincentz, Michel

Plos Genetics 4 (9), . (2013)

Abstract	Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.
Sprache	Englisch
Dokumenttyp	Artikel
Datenquelle	AGRIS - International Information System for the Agricultural Sciences and Technology

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Artikel: Extensive natural epigenetic variation at a De Novo originated gene

Silveira, Amanda Bortolini / Trontin, Charlotte / Cortijo, Sandra / Barau, Joan / Vieira Del Bem, Luiz Eduardo / Loudet, Olivier / Colot, Vincent / Vincentz, Michel

Plos Genetics 4 (9), . (2013)

Abstract	Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.
Sprache	Englisch
Dokumenttyp	Artikel
Datenquelle	AGRIS - International Information System for the Agricultural Sciences and Technology

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