FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis

Jennifer M. Frost, M. Yvonne Kim, Guen Tae Park, Ping Hung Hsieh, Miyuki Nakamura, Samuel J.H. Lin, Hyunjin Yoo, Jaemyung Choi, Yoko Ikeda, Tetsu Kinoshita, Yeonhee Choi, Daniel Zilberman, Robert L. Fischer

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

Original languageEnglish
Pages (from-to)E4720-E4729
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number20
DOIs
Publication statusPublished - May 15 2018

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Heterochromatin
Arabidopsis
Chromatin
Reproduction
DNA
Genomic Imprinting
Endosperm
Genome
DNA Glycosylases
Nucleosomes
Protein Subunits
Histones
Embryonic Structures

Keywords

  • Chromatin
  • DEMETER demethylase
  • FACT complex
  • Genomic imprinting
  • Reproduction

ASJC Scopus subject areas

  • General

Cite this

FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. / Frost, Jennifer M.; Kim, M. Yvonne; Park, Guen Tae; Hsieh, Ping Hung; Nakamura, Miyuki; Lin, Samuel J.H.; Yoo, Hyunjin; Choi, Jaemyung; Ikeda, Yoko; Kinoshita, Tetsu; Choi, Yeonhee; Zilberman, Daniel; Fischer, Robert L.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 115, No. 20, 15.05.2018, p. E4720-E4729.

Research output: Contribution to journalArticle

Frost, JM, Kim, MY, Park, GT, Hsieh, PH, Nakamura, M, Lin, SJH, Yoo, H, Choi, J, Ikeda, Y, Kinoshita, T, Choi, Y, Zilberman, D & Fischer, RL 2018, 'FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis', Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 20, pp. E4720-E4729. https://doi.org/10.1073/pnas.1713333115
Frost, Jennifer M. ; Kim, M. Yvonne ; Park, Guen Tae ; Hsieh, Ping Hung ; Nakamura, Miyuki ; Lin, Samuel J.H. ; Yoo, Hyunjin ; Choi, Jaemyung ; Ikeda, Yoko ; Kinoshita, Tetsu ; Choi, Yeonhee ; Zilberman, Daniel ; Fischer, Robert L. / FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. In: Proceedings of the National Academy of Sciences of the United States of America. 2018 ; Vol. 115, No. 20. pp. E4720-E4729.
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abstract = "The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.",
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T1 - FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis

AU - Frost, Jennifer M.

AU - Kim, M. Yvonne

AU - Park, Guen Tae

AU - Hsieh, Ping Hung

AU - Nakamura, Miyuki

AU - Lin, Samuel J.H.

AU - Yoo, Hyunjin

AU - Choi, Jaemyung

AU - Ikeda, Yoko

AU - Kinoshita, Tetsu

AU - Choi, Yeonhee

AU - Zilberman, Daniel

AU - Fischer, Robert L.

PY - 2018/5/15

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N2 - The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

AB - The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

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