Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Fišerová, Jindřiška; Efenberková, Michaela; Sieger, Tomáš; Maninová, Miloslava; Uhlířová, Jana; Hozák, Pavel

doi:10.1242/jcs.198424

Cited by 23 publications

(13 citation statements)

References 61 publications

(49 reference statements)

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“…A complex meshwork made of intermediate filaments, the nuclear lamina, mediates between the chromatin and the nuclear membrane, and consists of a well-defined set of interacting factors that are enriched at the nuclear periphery. In vertebrates, the nuclear periphery seems to be primarily repressive for transcription with the exception of the active chromatin surrounding the NPs (Fiserova et al 2017 ). The nucleolar periphery in contrast is occupied by heterochromatin interspersed with larger euchromatin volumes, suggesting that the nucleolar periphery is less repressive than the nuclear periphery.…”

Section: Nucleolus Perinucleolar Chromatin and Organization Of Nuclmentioning

confidence: 99%

Nucleolus and chromatin

Schöfer

Weipoltshammer

2018

Histochem Cell Biol

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The nucleolus as site of ribosome biogenesis holds a pivotal role in cell metabolism. It is composed of ribosomal DNA (rDNA), which is present as tandem arrays located in nucleolus organizer regions (NORs). In interphase cells, rDNA can be found inside and adjacent to nucleoli and the location is indicative for transcriptional activity of ribosomal genes—inactive rDNA (outside) versus active one (inside). Moreover, the nucleolus itself acts as a spatial organizer of non-nucleolar chromatin. Microscopy-based approaches offer the possibility to explore the spatially distinct localization of the different DNA populations in relation to the nucleolar structure. Recent technical developments in microscopy and preparatory methods may further our understanding of the functional architecture of nucleoli. This review will attempt to summarize the current understanding of mammalian nucleolar chromatin organization as seen from a microscopist’s perspective.

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Section: Nucleolus Perinucleolar Chromatin and Organization Of Nuclmentioning

confidence: 99%

Nucleolus and chromatin

Schöfer

Weipoltshammer

2018

Histochem Cell Biol

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“…H3K23 methylation was discovered in alfalfa in 1990 ( Waterborg, 1990 ) and has subsequently been found in yeast, Tetrahymena, C. elegans , mouse, rat, pig and human ( Waterborg, 1990 ; Garcia et al, 2007 ; Liu et al, 2010 ; Liu et al, 2013 ; Zhang et al, 2013 ; Papazyan et al, 2014 ; Vandamme et al, 2015 ; Sidoli et al, 2016b ; Su et al, 2016 ; Fišerová et al, 2017 ; Myers et al, 2018 ; Woodhouse et al, 2018 ; Lin et al, 2020 ). Despite its high degree of evolutionary conservation, H3K23me remains an understudied histone modification.…”

Section: Discussionmentioning

confidence: 99%

Caenorhabditis elegans nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3

Schwartz-Orbach

Zhang

Amin

et al. 2020

eLife

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Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies have indicated that the regulation and function of nuclear RNAi-mediated heterochromatin are highly complex. Our knowledge of histone modifications and the corresponding histonemodifying enzymes involved in the system remains limited. In this study, we show that the heterochromatin mark, H3K23me3, is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, dsRNA-induced H3K23me3 can persist for multiple generations after the dsRNA exposure has stopped. We demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as an additional chromatin modification in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.

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“…Both H3K9me3 and H3K23me3 have been shown to bind HP1 or its orthologs in vitro 41 . In addition, both HP1α and H3K23me2 are enriched in the nuclear pore complex in HeLa cells (H3K23me3 was not tested) 36 .…”

Section: Discussionmentioning

confidence: 99%

C. elegansnuclear RNAi factor SET-32 deposits the transgenerational heritable histone modification, H3K23me3

Schwartz-Orbach

Zhang

Amin

et al. 2020

Preprint

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Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies have indicated that the regulation and function of nuclear RNAi-mediated heterochromatin are highly complex. Our knowledge of histone modifications and the corresponding histone modifying enzymes involved in the system remains limited. In this study, we show that the heterochromatin mark, H3K23me3, is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, dsRNA-induced H3K23me3 can be inherited for four generations. We demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as an additional chromatin modification in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.

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Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

Cited by 23 publications

References 61 publications

Nucleolus and chromatin

Nucleolus and chromatin

Caenorhabditis elegans nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3

C. elegansnuclear RNAi factor SET-32 deposits the transgenerational heritable histone modification, H3K23me3

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