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  1. Article ; Online: Promoter and Terminator Optimization for DNA Methylation Targeting in Arabidopsis

    Jason Gardiner / Jenny M. Zhao / Kendall Chaffin / Steven E. Jacobsen

    Epigenomes, Vol 4, Iss 9, p

    2020  Volume 9

    Abstract: DNA methylation is an important epigenetic mark involved in gene regulation and silencing of transposable elements. The presence or absence of DNA methylation at specific sites can influence nearby gene expression and cause phenotypic changes that remain ...

    Abstract DNA methylation is an important epigenetic mark involved in gene regulation and silencing of transposable elements. The presence or absence of DNA methylation at specific sites can influence nearby gene expression and cause phenotypic changes that remain stable over generations. Recently, development of new technologies has enabled the targeted addition or removal of DNA methylation at specific sites of the genome. Of these new technologies, the targeting of the catalytic domain of Nicotiana tabacum DOMAINS REARRANGED METHYLTRANSFERASE 2 (ntDRM2cd) offers a promising tool for the addition of DNA methylation as it can directly methylate DNA. However, the methylation targeting efficiency of constructs using ntDRM2cd thus far has been relatively low. Previous studies have shown that the use of different promoters or terminators can greatly improve genome-editing efficiencies. In this study, we systematically survey a variety of promoter and terminator combinations to identify optimal combinations to use when targeting the addition of DNA methylation in Arabidopsis thaliana .
    Keywords epigenetics ; DNA methylation ; targeting ; zinc finger ; Arabidopsis ; plant ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

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

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis. ...

    Abstract Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis.
    Keywords Science ; Q
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

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

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis. ...

    Abstract Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis.
    Keywords Science ; Q
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14

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

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

    2023  Volume 13

    Abstract: TRB proteins have been shown to recruit PRC2 for H3K27me3 deposition. This work shows that TRBs also recruit JMJ14 to remove H3K4me3, demonstrating that TRBs silence the target genes via a combinatorial histone modification mechanism. ...

    Abstract TRB proteins have been shown to recruit PRC2 for H3K27me3 deposition. This work shows that TRBs also recruit JMJ14 to remove H3K4me3, demonstrating that TRBs silence the target genes via a combinatorial histone modification mechanism.
    Keywords Science ; Q
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

    Zhenhui Zhong / Yan Xue / C. Jake Harris / Ming Wang / Zheng Li / Yunqing Ke / Mukun Liu / Jessica Zhou / Yasaman Jami-Alahmadi / Suhua Feng / James A. Wohlschlegel / Steven E. Jacobsen

    Genome Biology, Vol 24, Iss 1, Pp 1-

    2023  Volume 16

    Abstract: Abstract Background The microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway, where ... ...

    Abstract Abstract Background The microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway, where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing. However, MORC proteins also have RdDM-independent functions although their underlying mechanisms are unknown. Results In this study, we examine MORC binding regions where RdDM does not occur in order to shed light on the RdDM-independent functions of MORC proteins. We find that MORC proteins compact chromatin and reduce DNA accessibility to transcription factors, thereby repressing gene expression. We also find that MORC-mediated repression of gene expression is particularly important under conditions of stress. MORC-regulated transcription factors can in some cases regulate their own transcription, resulting in feedback loops. Conclusions Our findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.
    Keywords Microrchidia ; MORC ; Chromatin compaction ; TF binding ; Transcription regulation ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 570
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation

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

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

    2023  Volume 16

    Abstract: 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 ...

    Abstract 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.
    Keywords Science ; Q
    Subject code 570
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: MORC3, a novel MIWI2 association partner, as an epigenetic regulator of piRNA dependent transposon silencing in male germ cells

    Kanako Kojima-Kita / Satomi Kuramochi-Miyagawa / Manabu Nakayama / Haruhiko Miyata / Steven E. Jacobsen / Masahito Ikawa / Haruhiko Koseki / Toru Nakano

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 19

    Abstract: Abstract The PIWI (P-element-induced wimpy testis)-interacting-RNA (piRNA) pathway plays a crucial role in the repression of TE (transposable element) expression via de novo DNA methylation in mouse embryonic male germ cells. Various proteins, including ... ...

    Abstract Abstract The PIWI (P-element-induced wimpy testis)-interacting-RNA (piRNA) pathway plays a crucial role in the repression of TE (transposable element) expression via de novo DNA methylation in mouse embryonic male germ cells. Various proteins, including MIWI2 are involved in the process. TE silencing is ensured by piRNA-guided MIWI2 that recruits some effector proteins of the DNA methylation machinery to TE regions. However, the molecular mechanism underlying the methylation is complex and has not been fully elucidated. Here, we identified MORC3 as a novel associating partner of MIWI2 and also a nuclear effector of retrotransposon silencing via piRNA-dependent de novo DNA methylation in embryonic testis. Moreover, we show that MORC3 is important for transcription of piRNA precursors and subsequently affects piRNA production. Thus, we provide the first mechanistic insights into the role of this effector protein in the first stage of piRNA biogenesis in embryonic TE silencing mechanism.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Comprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant components

    Jorge Hernández-García / Borja Diego-Martin / Peggy Hsuanyu Kuo / Yasaman Jami-Alahmadi / Ajay A. Vashisht / James Wohlschlegel / Steven E. Jacobsen / Miguel A. Blázquez / Javier Gallego-Bartolomé

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 11

    Abstract: The ancestral history of SWI/SNF subunits, responsible for nucleosome positioning, are explored in this work, revealing a plant SWI/SNF complex similar to the animal BAF subclass. ...

    Abstract The ancestral history of SWI/SNF subunits, responsible for nucleosome positioning, are explored in this work, revealing a plant SWI/SNF complex similar to the animal BAF subclass.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase

    Wanlu Liu / Javier Gallego-Bartolomé / Yuxing Zhou / Zhenhui Zhong / Ming Wang / Somsakul Pop Wongpalee / Jason Gardiner / Suhua Feng / Peggy Hsuanyu Kuo / Steven E. Jacobsen

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: The ability to target DNA methylation to specific loci is important for both basic and applied research. Here, the authors fuse CG-specific methyltransferase SssI with an artificial zinc finger protein for DNA methylation targeting and show the chromatin ...

    Abstract The ability to target DNA methylation to specific loci is important for both basic and applied research. Here, the authors fuse CG-specific methyltransferase SssI with an artificial zinc finger protein for DNA methylation targeting and show the chromatin features favorable for efficient gain of methylation.
    Keywords Science ; Q
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation

    Pierre Bourguet / Colette L. Picard / Ramesh Yelagandula / Thierry Pélissier / Zdravko J. Lorković / Suhua Feng / Marie-Noëlle Pouch-Pélissier / Anna Schmücker / Steven E. Jacobsen / Frédéric Berger / Olivier Mathieu

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: T-DNA mutants have been widely used for Arabidopsis gene function characterization. Here, by characterizing a null mutant created by CRISPR, the authors show that previous reported function of H2A.W is confounded by a T-DNA insertion induced chromosomal ... ...

    Abstract T-DNA mutants have been widely used for Arabidopsis gene function characterization. Here, by characterizing a null mutant created by CRISPR, the authors show that previous reported function of H2A.W is confounded by a T-DNA insertion induced chromosomal rearrangement and reveal its role in regulating heterochromatin accessibility.
    Keywords Science ; Q
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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