Chromatin states and nuclear organization in development — a view from the nuclear lamina

Mattout, Anna; Cabianca, Daphne S.; Gasser, Susan M.

doi:10.1186/s13059-015-0747-5

Cited by 72 publications

(62 citation statements)

References 150 publications

(212 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The LINC complex senses stimuli from the outside of the cell and transmits information through the cytoskeleton to the nucleus, contributes to nuclear migration required to correctly position the nucleus within the cell, and can interact with nucleoskeleton components such as lamins inside the nucleus. Lamins can form direct or indirect contacts with chromatin in many organisms (Mattout et al, 2015), and the nucleoskeleton and the NE are therefore expected to participate in the position of chromatin within the nucleus (Bickmore and van Steensel, 2013). The NE is an elastic structure and can expand or retract upon constraints from within or from outside the nucleus.…”

Section: Introductionmentioning

confidence: 99%

The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

Poulet

Duc

Voisin

et al. 2017

Journal of Cell Science

View full text Add to dashboard Cite

The linker of nucleoskeleton and cytoskeleton (LINC) complex is an evolutionarily well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane. While recent data support its function in nuclear morphology and meiosis, its involvement in chromatin organisation has not been studied in plants. Here, 3D imaging methods have been used to investigate nuclear morphology and chromatin organisation in interphase nuclei of the model plant Arabidopsis thaliana in which heterochromatin clusters in conspicuous chromatin domains called chromocentres. Chromocentres form a repressive chromatin environment contributing to transcriptional silencing of repeated sequences, a general mechanism needed for genome stability. Quantitative measurements of the 3D position of chromocentres indicate their close proximity to the nuclear periphery but that their position varies with nuclear volume and can be altered in specific mutants affecting the LINC complex. Finally, we propose that the plant LINC complex contributes to proper heterochromatin organisation and positioning at the nuclear periphery, since its alteration is associated with the release of transcriptional silencing as well as decompaction of heterochromatic sequences.

show abstract

Section: Introductionmentioning

confidence: 99%

The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

Poulet

Duc

Voisin

et al. 2017

Journal of Cell Science

View full text Add to dashboard Cite

show abstract

“…The nuclear lamina is a layer of meshwork beneath the nuclear envelope, consisting of lamin and lamin-associated membrane proteins (Dechat et al 2008). The nuclear lamin was found to participate in organizing chromatin structures by serving as an anchoring site for heterochromatin (for review, see Mattout et al 2015). Genome-wide identification of chromatin regions associated with the nuclear lamina in animals led to the discovery of lamin-associated domains (LADs), which are large-sized, depleted of active histone marks, and low in gene density (Pickersgill et al 2006;Guelen et al 2008).…”

mentioning

confidence: 99%

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Cheng

et al. 2017

Genome Res.

106

View full text Add to dashboard Cite

The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme-mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%-20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.

show abstract

“…Nuclear pore proteins also copurify with SWI/SNF factors in mouse embryonic stem cells (Ho et al 2009). However, although it is accepted that chromatin and the nuclear envelope are mechanistically coupled (Mattout et al 2015), it is quite speculative how components of both structures coordinate their functions. The small interfering RNA knockdown of the SWI/SNF core component BRG1 produces nuclear shape changes (Imbalzano et al 2013).…”

Section: Swsn-22 and The Nuclear Envelope In The Early Embryomentioning

confidence: 99%

“…We find the interaction of SWSN-2.2 with a set of myosin-related proteins particularly interesting, since some unconventional myosins have been related to the mitotic spindle dynamics and the regulation of gene expression (Woolner and Bement 2009;Sarshad et al 2013). HAM-3 and SWSN-2.2 During Development 969 SWSN-2.2 colocalizes with MEL-28 and is required for nuclear reassembly after mitosis and correct chromosome inheritance in the early embryo: Since mel-28(t1684) and swsn-2.2(ok3161) mutants present similar phenotypes (adults that produce dead embryos at an early stage displaying chromosomal segregation defects) (Galy et al 2006), chromatin and the nuclear envelope are mechanistically coupled (Mattout et al 2015), and SWI/SNF proteins copurify with nuclear pore proteins in mouse embryonic stem cells (Ho et al 2009), we decided to further investigate the functional relationship between these two genes. Taking advantage of a strain expressing GFP::MEL-28, we performed immunofluorescence to test if SWSN-2.2 and MEL-28 colocalize.…”

mentioning

confidence: 99%

Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling Accessory Subunits DuringCaenorhabditis elegansDevelopment

et al. 2016

View full text Add to dashboard Cite

SWI/SNF ATP-dependent chromatin-remodeling complexes have been related to several cellular processes such as transcription, regulation of chromosomal stability, and DNA repair. The Caenorhabditis elegans gene ham-3 (also known as swsn-2.1) and its paralog swsn-2.2 encode accessory subunits of SWI/SNF complexes. Using RNA interference (RNAi) assays and diverse alleles we investigated whether ham-3 and swsn-2.2 have different functions during C. elegans development since they encode proteins that are probably mutually exclusive in a given SWI/SNF complex. We found that ham-3 and swsn-2.2 display similar functions in vulva specification, germline development, and intestinal cell proliferation, but have distinct roles in embryonic development. Accordingly, we detected functional redundancy in some developmental processes and demonstrated by RNA sequencing of RNAi-treated L4 animals that ham-3 and swsn-2.2 regulate the expression of a common subset of genes but also have specific targets. Cell lineage analyses in the embryo revealed hyper-proliferation of intestinal cells in ham-3 null mutants whereas swsn-2.2 is required for proper cell divisions. Using a proteomic approach, we identified SWSN-2.2-interacting proteins needed for early cell divisions, such as SAO-1 and ATX-2, and also nuclear envelope proteins such as MEL-28. swsn-2.2 mutants phenocopy mel-28 loss-of-function, and we observed that SWSN-2.2 and MEL-28 colocalize in mitotic and meiotic chromosomes. Moreover, we demonstrated that SWSN-2.2 is required for correct chromosome segregation and nuclear reassembly after mitosis including recruitment of MEL-28 to the nuclear periphery.KEYWORDS SWI/SNF; Caenorhabditis elegans; chromatin; development; nuclear envelope C HROMATIN is a dynamic structure required not only for the packaging of large amounts of DNA in the limited space of eukaryotic nuclei, but also for the regulation of gene expression (Ho and Crabtree 2010;Narlikar et al. 2013). SWI/SNF complexes, which are conserved from yeast to mammals, modify the state of the chromatin in an ATPdependent manner and, therefore, the accessibility of distinct proteins to a given DNA region (Hargreaves and Crabtree 2011;Euskirchen et al. 2012). Such activity in the DNA regulates various cellular aspects like proliferation, differentiation, chromosomal stability, and DNA repair (Reisman et al. 2009;Lans et al. 2010;Euskirchen et al. 2011). SWI/SNF complexes are involved in gene-specific regulation since only a low percentage of gene expression (6% in budding yeast, 7.5% in Caenorhabditis elegans) is regulated by these complexes (Holstege et al. 1998;Riedel et al. 2013).A canonical SWI/SNF complex consists of a central ATPase subunit, two or three core components, and several (five to eight) accessory subunits (Hargreaves and Crabtree 2011). While all SWI/SNF complexes include core subunits that are in charge of remodeling nucleosomes (Phelan et al. 1999), the accessory proteins confer specificity to a given complex and their presence varies depending on the ...

show abstract

Chromatin states and nuclear organization in development — a view from the nuclear lamina

Cited by 72 publications

References 150 publications

The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling Accessory Subunits DuringCaenorhabditis elegansDevelopment

Contact Info

Product

Resources

About