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Article ; Online: DNA methylation in plants: mechanisms and tools for targeted manipulation.

Gallego-Bartolomé, Javier

2020 Volume 227, Issue 1, Page(s) 38–44

Abstract: DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of this mark in plants, although their genome-wide effect ... ...

Abstract	DNA methylation is an epigenetic mark that regulates multiple processes, such as gene expression and genome stability. Mutants and pharmacological treatments have been instrumental in the study of this mark in plants, although their genome-wide effect complicates the direct association between changes in methylation and a particular phenotype. A variety of tools that allow locus-specific manipulation of DNA methylation can be used to assess its direct role in specific processes, as well as to create novel epialleles. Recently, new tools that recruit the methylation machinery directly to target loci through programmable DNA-binding proteins have expanded the tool kit available to researchers. This review provides an overview of DNA methylation in plants and discusses the tools that have recently been developed for its manipulation.
MeSH term(s)	DNA Methylation/genetics ; Plants/genetics
Language	English
Publishing date	2020-04-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.16529
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Article ; Online: Mind the gap: Epigenetic regulation of chromatin accessibility in plants.

Candela-Ferre, Joan / Diego-Martin, Borja / Pérez-Alemany, Jaime / Gallego-Bartolomé, Javier

Plant physiology

2024 Volume 194, Issue 4, Page(s) 1998–2016

Abstract: Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by ... ...

Abstract	Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
MeSH term(s)	Chromatin/genetics ; Histones/genetics ; Histones/metabolism ; Nucleosomes/genetics ; Epigenesis, Genetic ; DNA/metabolism ; Chromatin Assembly and Disassembly/genetics ; Plants/genetics ; Plants/metabolism
Chemical Substances	Chromatin ; Histones ; Nucleosomes ; DNA (9007-49-2)
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiae024
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Article: Selective Growth of MAPbBr

Bartolomé, Javier / Vila, María / Redondo-Obispo, Carlos / de Andrés, Alicia / Coya, Carmen

Nanomaterials (Basel, Switzerland)

2023 Volume 13, Issue 18

Abstract: The synergistic combination of hybrid perovskites with graphene-related materials is leading to optoelectronic devices with enhanced performance and stability. Still, taking advantage of the solution processing of perovskite onto graphene is especially ... ...

Abstract	The synergistic combination of hybrid perovskites with graphene-related materials is leading to optoelectronic devices with enhanced performance and stability. Still, taking advantage of the solution processing of perovskite onto graphene is especially challenging. Here, MAPbBr
Language	English
Publishing date	2023-09-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano13182513
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Article: Epidermal GIGANTEA adjusts the response to shade at dusk by directly impinging on PHYTOCHROME INTERACTING FACTOR 7 function.

Martínez-Vasallo, Carlos / Cole, Benjamin / Gallego-Bartolomé, Javier / Chory, Joanne / Kay, Steve A / Nohales, Maria A

bioRxiv : the preprint server for biology

2023

Abstract: For plants adapted to bright light, a decrease in the amount of light received can be detrimental to their growth and survival. Consequently, in response to shade from surrounding vegetation, they initiate a suite of molecular and morphological changes ... ...

Abstract	For plants adapted to bright light, a decrease in the amount of light received can be detrimental to their growth and survival. Consequently, in response to shade from surrounding vegetation, they initiate a suite of molecular and morphological changes known as the shade avoidance response (SAR) through which stems and petioles elongate in search for light. Under sunlight-night cycles, the plant's responsiveness to shade varies across the day, being maximal at dusk time. While a role for the circadian clock in this regulation has long been proposed, mechanistic understanding of how it is achieved is incomplete. Here we show that the clock component GIGANTEA (GI) directly interacts with the transcriptional regulator PHYTOCHROME INTERACTING FACTOR 7 (PIF7), a key player in the response to shade. GI represses PIF7 transcriptional activity and the expression of its target genes in response to shade, thereby fine-tuning the magnitude of the response to limiting light conditions. We find that, under light/dark cycles, this function of GI is required to adequately modulate the gating of the response to shade at dusk. Importantly, we also show that GI expression in epidermal cells is sufficient for proper SAR regulation.
Language	English
Publishing date	2023-03-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.21.533699
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Article ; Online: The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide.

Blanco-Touriñán, Noel / Pérez-Alemany, Jaime / Bourbousse, Clara / Latrasse, David / Ait-Mohamed, Ouardia / Benhamed, Moussa / Barneche, Fredy / Blázquez, Miguel A / Gallego-Bartolomé, Javier / Alabadí, David

Plant physiology

2024 Volume 195, Issue 1, Page(s) 640–651

Abstract: The evolutionarily conserved POLYMERASE-ASSOCIATED FACTOR1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNA POLYMERASE II (RNAPII) progression through chromatin. We examined the genomic ... ...

Abstract	The evolutionarily conserved POLYMERASE-ASSOCIATED FACTOR1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNA POLYMERASE II (RNAPII) progression through chromatin. We examined the genomic distribution of the EARLY FLOWERING7 (ELF7) and VERNALIZATION INDEPENDENCE3 subunits of Paf1C in Arabidopsis (Arabidopsis thaliana). The occupancy of both subunits was confined to thousands of gene bodies and positively associated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome wide in elf7 seedlings. Genome-wide profiling of RNAPII revealed that in elf7 mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest a direct functional link between Paf1C activity, monoubiquitination of histone H2B, and the transition of RNAPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stable than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.
MeSH term(s)	Histones/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Ubiquitination ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; RNA Polymerase II/metabolism ; RNA Polymerase II/genetics ; Transcription, Genetic ; Gene Expression Regulation, Plant ; Genome, Plant ; Transcription Factors/metabolism ; Transcription Factors/genetics
Chemical Substances	Histones ; Arabidopsis Proteins ; RNA Polymerase II (EC 2.7.7.-) ; Transcription Factors
Language	English
Publishing date	2024-01-29
Publishing country	United States
Document type	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	10.1093/plphys/kiae041
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Article ; Online: Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems.

Papikian, Ashot / Liu, Wanlu / Gallego-Bartolomé, Javier / Jacobsen, Steven E

Nature communications

2019 Volume 10, Issue 1, Page(s) 729

Abstract: Understanding genomic functions requires site-specific manipulation of loci via efficient protein effector targeting systems. However, few approaches for targeted manipulation of the epigenome are available in plants. Here, we adapt the dCas9-SunTag ... ...

Abstract	Understanding genomic functions requires site-specific manipulation of loci via efficient protein effector targeting systems. However, few approaches for targeted manipulation of the epigenome are available in plants. Here, we adapt the dCas9-SunTag system to engineer targeted gene activation and DNA methylation in Arabidopsis. We demonstrate that a dCas9-SunTag system utilizing the transcriptional activator VP64 drives robust and specific activation of several loci, including protein coding genes and transposable elements, in diverse chromatin contexts. In addition, we present a CRISPR-based methylation targeting system for plants, utilizing a SunTag system with the catalytic domain of the Nicotiana tabacum DRM methyltransferase, which efficiently targets DNA methylation to specific loci, including the FWA promoter, triggering a developmental phenotype, and the SUPERMAN promoter. These SunTag systems represent valuable tools for the site-specific manipulation of plant epigenomes.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Binding Sites/genetics ; CRISPR-Cas Systems ; Chromatin/genetics ; Chromatin/metabolism ; DNA Methylation ; Epigenesis, Genetic ; Gene Editing/methods ; Gene Expression Regulation, Plant ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Arabidopsis Proteins ; Chromatin ; FWA protein, Arabidopsis ; Homeodomain Proteins ; Transcription Factors
Language	English
Publishing date	2019-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-08736-7
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Article ; Online: The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation.

Li, Zheng / Wang, Ming / Zhong, Zhenhui / Gallego-Bartolomé, Javier / Feng, Suhua / Jami-Alahmadi, Yasaman / Wang, Xinyi / Wohlschlegel, James / Bischof, Sylvain / Long, Jeff A / Jacobsen, Steven E

Nature communications

2023 Volume 14, Issue 1, Page(s) 4135

Abstract: MORPHEUS' MOLECULE1 (MOM1) is an Arabidopsis factor previously shown to mediate transcriptional silencing independent of major DNA methylation changes. Here we find that MOM1 localizes with sites of RNA-directed DNA methylation (RdDM). Tethering MOM1 ... ...

Abstract	MORPHEUS' MOLECULE1 (MOM1) is an Arabidopsis factor previously shown to mediate transcriptional silencing independent of major DNA methylation changes. Here we find that MOM1 localizes with sites of RNA-directed DNA methylation (RdDM). Tethering MOM1 with an artificial zinc finger to an unmethylated FWA promoter leads to establishment of DNA methylation and FWA silencing. This process is blocked by mutations in components of the Pol V arm of the RdDM machinery, as well as by mutation of MICRORCHIDIA 6 (MORC6). We find that at some endogenous RdDM sites, MOM1 is required to maintain DNA methylation and a closed chromatin state. In addition, efficient silencing of newly introduced FWA transgenes is impaired in the mom1 mutant. In addition to RdDM sites, we identify a group of MOM1 peaks at active chromatin near genes that colocalized with MORC6. These findings demonstrate a multifaceted role of MOM1 in genome regulation.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Chromatin/genetics ; DNA ; DNA Methylation ; Homeodomain Proteins ; RNA ; Transcription Factors/genetics ; Adenosine Triphosphatases/genetics
Chemical Substances	Arabidopsis Proteins ; Chromatin ; DNA (9007-49-2) ; FWA protein, Arabidopsis ; Homeodomain Proteins ; RNA (63231-63-0) ; Transcription Factors ; MOM protein, Arabidopsis (EC 3.6.4.-) ; MORC6 protein, Arabidopsis (EC 3.6.1.-) ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2023-07-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39751-4
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Article: The MOM1 complex recruits the RdDM machinery via MORC6 to establish

Li, Zheng / Wang, Ming / Zhong, Zhenhui / Gallego-Bartolomé, Javier / Feng, Suhua / Jami-Alahmadi, Yasaman / Wang, Xinyi / Wohlschlegel, James / Bischof, Sylvain / Long, Jeffrey A / Jacobsen, Steven E

bioRxiv : the preprint server for biology

2023

Abstract: ... MOM1 is ... ...

Abstract	MOM1 is an
Language	English
Publishing date	2023-01-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.10.523455
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Article ; Online: Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14.

Wang, Ming / Zhong, Zhenhui / Gallego-Bartolomé, Javier / Feng, Suhua / Shih, Yuan-Hsin / Liu, Mukun / Zhou, Jessica / Richey, John Curtis / Ng, Charmaine / Jami-Alahmadi, Yasaman / Wohlschlegel, James / Wu, Keqiang / Jacobsen, Steven E

Nature communications

2023 Volume 14, Issue 1, Page(s) 1736

Abstract: Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain ... ...

Abstract	Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.
MeSH term(s)	Histones/genetics ; Histones/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Polycomb Repressive Complex 2/genetics ; Polycomb Repressive Complex 2/metabolism ; Telomere-Binding Proteins/metabolism ; Demethylation ; Gene Expression Regulation, Plant ; Polycomb-Group Proteins/genetics ; Polycomb-Group Proteins/metabolism ; Jumonji Domain-Containing Histone Demethylases/genetics ; Jumonji Domain-Containing Histone Demethylases/metabolism
Chemical Substances	histone H3 trimethyl Lys4 ; Histones ; Arabidopsis Proteins ; Polycomb Repressive Complex 2 (EC 2.1.1.43) ; Telomere-Binding Proteins ; Polycomb-Group Proteins ; JMJ14 protein, Arabidopsis (EC 1.14.11.-) ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-)
Language	English
Publishing date	2023-03-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-37263-9
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Article ; Online: DNA methylation-linked chromatin accessibility affects genomic architecture in

Zhong, Zhenhui / Feng, Suhua / Duttke, Sascha H / Potok, Magdalena E / Zhang, Yiwei / Gallego-Bartolomé, Javier / Liu, Wanlu / Jacobsen, Steven E

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 5

Abstract: DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains unclear, particularly in plants. ...

Abstract	DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains unclear, particularly in plants. Here, we present genome-wide chromatin accessibility profiles of 18
MeSH term(s)	Arabidopsis/genetics ; Chromatin/genetics ; DNA Methylation/genetics ; Genome, Plant ; Mutation/genetics ; Transcription, Genetic
Chemical Substances	Chromatin
Language	English
Publishing date	2021-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2023347118
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