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Article ; Online: The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants

Camille Fonouni-Farde / Aurélie Christ / Thomas Blein / María Florencia Legascue / Lucía Ferrero / Michaël Moison / Leandro Lucero / Juan Sebastián Ramírez-Prado / David Latrasse / Daniel Gonzalez / Moussa Benhamed / Leandro Quadrana / Martin Crespi / Federico Ariel

Genome Biology, Vol 23, Iss 1, Pp 1-

2022 Volume 30

Abstract: Abstract Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene ... ...

Abstract	Abstract Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Results Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner. Conclusions Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
Keywords	Long noncoding RNA ; DNA methylation ; PRC1 ; Polycomb ; RdDM ; Thermomorphogenesis ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Subject code	570
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis.

Alonso J Pardal / Sophie J M Piquerez / Ana Dominguez-Ferreras / Lucas Frungillo / Emmanouil Mastorakis / Emma Reilly / David Latrasse / Lorenzo Concia / Selena Gimenez-Ibanez / Steven H Spoel / Moussa Benhamed / Vardis Ntoukakis

PLoS Pathogens, Vol 17, Iss 5, p e

2021 Volume 1009572

Abstract: Perception of microbes by plants leads to dynamic reprogramming of the transcriptome, which is essential for plant health. The appropriate amplitude of this transcriptional response can be regulated at multiple levels, including chromatin. However, the ... ...

Abstract	Perception of microbes by plants leads to dynamic reprogramming of the transcriptome, which is essential for plant health. The appropriate amplitude of this transcriptional response can be regulated at multiple levels, including chromatin. However, the mechanisms underlying the interplay between chromatin remodeling and transcription dynamics upon activation of plant immunity remain poorly understood. Here, we present evidence that activation of plant immunity by bacteria leads to nucleosome repositioning, which correlates with altered transcription. Nucleosome remodeling follows distinct patterns of nucleosome repositioning at different loci. Using a reverse genetic screen, we identify multiple chromatin remodeling ATPases with previously undescribed roles in immunity, including EMBRYO SAC DEVELOPMENT ARREST 16, EDA16. Functional characterization of the immune-inducible chromatin remodeling ATPase EDA16 revealed a mechanism to negatively regulate immunity activation and limit changes in redox homeostasis. Our transcriptomic data combined with MNase-seq data for EDA16 functional knock-out and over-expressor mutants show that EDA16 selectively regulates a defined subset of genes involved in redox signaling through nucleosome repositioning. Thus, collectively, chromatin remodeling ATPases fine-tune immune responses and provide a previously uncharacterized mechanism of immune regulation.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 16

Abstract: Cell division and expansion are carefully coordinated during organ growth. Here, the authors show that the SCL28 and SMOS1 transcription factors interact to regulate cyclin-dependent kinase inhibitors and promote cell size increase over division in ... ...

Abstract	Cell division and expansion are carefully coordinated during organ growth. Here, the authors show that the SCL28 and SMOS1 transcription factors interact to regulate cyclin-dependent kinase inhibitors and promote cell size increase over division in Arabidopsis.
Keywords	Science ; Q
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype

iScience, Vol 25, Iss 1, Pp 103696- (2022)

2022

Abstract: Summary: Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome ... ...

Abstract	Summary: Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits.
Keywords	genomics ; omics ; plant biology ; plant evolution ; Science ; Q
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development

Maria Victoria Gomez Roldan / Farhaj Izhaq / Marion Verdenaud / John Eleblu / Aimen Haraghi / Vivien Sommard / Pierre Chambrier / David Latrasse / Teddy Jégu / Moussa Benhamed / Judit Szécsi / Mohammed Bendahmane / Adnane Boualem / Abdelhafid Bendahmane

Communications Biology, Vol 3, Iss 1, Pp 1-

2020 Volume 12

Abstract: Maria V Gomez Roldan, Farhaj Izhaq et al. study the role of WIP transcription factors in Arabidopsis thaliana. Using an inducible system, they generate ChIP-seq and RNA-seq data that reveal how WIP proteins repress development and growth. Through ectopic ...

Abstract	Maria V Gomez Roldan, Farhaj Izhaq et al. study the role of WIP transcription factors in Arabidopsis thaliana. Using an inducible system, they generate ChIP-seq and RNA-seq data that reveal how WIP proteins repress development and growth. Through ectopic expression of WIP in Arabidopsis carpels, they obtain male flower, mimicking sex determination in melon.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Involvement of Arabidopsis BIG protein in cell death mediated by Myo-inositol homeostasis

Quentin Bruggeman / Florence Piron-Prunier / Frédérique Tellier / Jean-Denis Faure / David Latrasse / Deborah Manza-Mianza / Christelle Mazubert / Sylvie Citerne / Stéphanie Boutet-Mercey / Raphael Lugan / Catherine Bergounioux / Cécile Raynaud / Moussa Benhamed / Marianne Delarue

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 14

Abstract: Abstract Programmed cell death (PCD) is essential for several aspects of plant life. We previously identified the mips1 mutant of Arabidopsis thaliana, which is deficient for the enzyme catalysing myo-inositol synthesis, and that displays light-dependent ...

Abstract	Abstract Programmed cell death (PCD) is essential for several aspects of plant life. We previously identified the mips1 mutant of Arabidopsis thaliana, which is deficient for the enzyme catalysing myo-inositol synthesis, and that displays light-dependent formation of lesions on leaves due to Salicylic Acid (SA) over-accumulation. Rationale of this work was to identify novel regulators of plant PCD using a genetic approach. A screen for secondary mutations that abolish the mips1 PCD phenotype identified a mutation in the BIG gene, encoding a factor of unknown molecular function that was previously shown to play pleiotropic roles in plant development and defence. Physiological analyses showed that BIG is required for lesion formation in mips1 via SA-dependant signalling. big mutations partly rescued transcriptomic and metabolomics perturbations as stress-related phytohormones homeostasis. In addition, since loss of function of the ceramide synthase LOH2 was not able to abolish cell death induction in mips1, we show that PCD induction is not fully dependent of sphingolipid accumulation as previously suggested. Our results provide further insights into the role of the BIG protein in the control of MIPS1-dependent cell death and also into the impact of sphingolipid homeostasis in this pathway.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato

Maria Victoria Gomez Roldan / Claire Périlleux / Halima Morin / Samuel Huerga-Fernandez / David Latrasse / Moussa Benhamed / Abdelhafid Bendahmane

Scientific Reports, Vol 7, Iss 1, Pp 1-

2017 Volume 10

Abstract: Abstract Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit ... ...

Abstract	Abstract Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, jointless (j) and jointless-2 (j-2), controlling pedicel abscission zone formation have been documented but only j-2 has been extensively used in breeding. J was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, Solyc12g038510, associated with j-2 phenotype. Targeted knockout of Solyc12g038510, using CRISPR/Cas9 system, validated our hypothesis. Solyc12g038510 encodes the MADS-box protein SlMBP21. Molecular analysis of j-2 natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a Rider retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of J and J-2 in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that J is epistatic to J-2 and that the branched inflorescences and the leafy sepals observed in accessions harboring j-2 alleles are likely the consequences of linkage drags.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2017-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Ying Huang / Jing An / Sanchari Sircar / Clara Bergis / Chloé Dias Lopes / Xiaoning He / Barbara Da Costa / Feng-Quan Tan / Jeremie Bazin / Javier Antunez-Sanchez / Maria Florencia Mammarella / Ravi-sureshbhai Devani / Rim Brik-Chaouche / Abdelhafid Bendahmane / Florian Frugier / Chongjing Xia / Christophe Rothan / Aline V. Probst / Zouine Mohamed /

Catherine Bergounioux / Marianne Delarue / Yijing Zhang / Shaojian Zheng / Martin Crespi / Sotirios Fragkostefanakis / Magdy M. Mahfouz / Federico Ariel / Jose Gutierrez-Marcos / Cécile Raynaud / David Latrasse / Moussa Benhamed

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 15

Abstract: Here the authors show genome-wide chromatin changes and transcriptional reprogramming occur in response to heat stress in tomato, leading to the transient formation of promoter-enhancer contacts to drive the expression of heat-stress responsive genes. ... ...

Abstract	Here the authors show genome-wide chromatin changes and transcriptional reprogramming occur in response to heat stress in tomato, leading to the transient formation of promoter-enhancer contacts to drive the expression of heat-stress responsive genes. Furthermore, they show chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato.
Keywords	Science ; Q
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A new role for histone demethylases in the maintenance of plant genome integrity

Javier Antunez-Sanchez / Matthew Naish / Juan Sebastian Ramirez-Prado / Sho Ohno / Ying Huang / Alexander Dawson / Korawit Opassathian / Deborah Manza-Mianza / Federico Ariel / Cecile Raynaud / Anjar Wibowo / Josquin Daron / Minako Ueda / David Latrasse / R Keith Slotkin / Detlef Weigel / Moussa Benhamed / Jose Gutierrez-Marcos

eLife, Vol

2020 Volume 9

Abstract: Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is ... ...

Abstract	Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
Keywords	chromatin ; DNA methylation ; epimutation ; transposon ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

Ariel, Federico / AurÃ©lie Christ / David Latrasse / Martin Crespi / Moussa Benhamed / Natali Romero-Barrios / Teddy Jegu

Molecular cell. 2014 Aug. 07, v. 55

2014

Abstract: The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis ... ...

Abstract	The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxinÂ transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes.
Keywords	auxins ; chromatin ; DNA ; DNA methylation ; eukaryotic cells ; genes ; non-coding RNA ; plant development ; plant hormones ; topology ; transcription (genetics)
Language	English
Dates of publication	2014-0807
Size	p. 383-396.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2014.06.011
Database	NAL-Catalogue (AGRICOLA)

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