The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

Abstract Heterochromatin, a transcriptionally silenced chromatin domain, is important for genome stability and gene expression. Histone 3 lysine 9 methylation (H3K9me) and histone hypoacetylation are conserved epigenetic hallmarks of heterochromatin. In fission yeast, RNA interference (RNAi) plays a key role in H3K9 methylation and heterochromatin silencing. However, how RNAi machinery and histone deacetylases (HDACs) are coordinated to ensure proper heterochromatin assembly is still unclear. Previously, we showed that Dpb4, a conserved DNA polymerase epsilon subunit, plays a key role in the recruitment of HDACs to heterochromatin during S phase. Here, we identified a novel RNA-binding protein Dri1 that interacts with Dpb4. GFP-tagged Dri1 forms distinct foci mostly in the nucleus, showing a high degree of colocalization with Swi6/Heterochromatin Protein 1. Deletion of dri1+ leads to defects in silencing, H3K9me, and heterochromatic siRNA generation. We also showed that Dri1 physically associates with heterochromatic transcripts, and is required for the recruitment of the RNA-induced transcriptional silencing (RITS) complex via interacting with the complex. Furthermore, loss of Dri1 decreases the association of the Sir2 HDAC with heterochromatin. We further demonstrated that the C-terminus of Dri1 that includes an intrinsically disordered (IDR) region and three zinc fingers is crucial for its role in silencing. Together, our evidences suggest that Dri1 facilitates heterochromatin assembly via the RNAi pathway and HDAC.

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Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

Genome Biology ◽

10.1186/s13059-021-02424-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yongzheng Li ◽

Boxin Xue ◽

Mengling Zhang ◽

Liwei Zhang ◽

Yingping Hou ◽

...

Keyword(s):

Dna Replication ◽

Structural Dynamics ◽

Replication Origin ◽

High Efficiency ◽

S Phase ◽

Chromatin Domain ◽

Replication Origins ◽

Replication Efficiency ◽

Topologically Associating Domains ◽

Epigenetic Signatures

Abstract Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. Results We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. Conclusion Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.

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Assembly of Two Transgenes in an Artificial Chromatin Domain Gives Highly Coordinated Expression in Tobacco

Genetics ◽

10.1093/genetics/160.2.727 ◽

2002 ◽

Vol 160 (2) ◽

pp. 727-740

Author(s):

Ludmila Mlynárová ◽

Annelies Loonen ◽

Elzbieta Mietkiewska ◽

Ritsert C Jansen ◽

Jan-Peter Nap

Keyword(s):

Enzyme Activities ◽

Firefly Luciferase ◽

Chromatin Domain ◽

Mrna Levels ◽

Loop Model ◽

Data Generation ◽

Genome Data ◽

The Matrix ◽

Coordinated Expression ◽

Firefly Luciferase Gene

Abstract The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli β-glucuronidase gene and the firefly luciferase gene, driven by different promoters, were placed between copies of the chicken lysozyme A element, a member of the matrix-associated region (MAR) group of chromatin boundary elements, and introduced in tobacco (Nicotiana tabacum). In plants carrying A elements, quantitative enzyme activities and mRNA levels of both genes show high correlations compared to control plants. The A element thus creates an artificial chromatin domain that yields coordinated expression. Surprisingly, enzyme activities correlated poorly with their respective mRNA levels. We hypothesize that this indicates the occurrence of “error pipelines” in data generation: systematic errors of a given analytical method will point in the same direction and cancel out in correlation analysis, resulting in better correlations. In combining different methods of analysis, however, such errors do not cancel out and as a result relevant correlations can be masked. Such error pipelines will have to be taken into account when different types of (e.g., whole-genome) data sets are combined in quantitative analyses.

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Gene insulation. Part II: natural strategies in vertebrates

Biochemistry and Cell Biology ◽

10.1139/o10-111 ◽

2010 ◽

Vol 88 (6) ◽

pp. 885-898 ◽

Cited By ~ 8

Author(s):

Michèle Amouyal

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Protein Interactions ◽

Dna Looping ◽

Chromatin Domain ◽

Trna Genes ◽

Binding Factor ◽

Genomic Environment ◽

Nuclear Structures ◽

Definition Of

The way a gene is insulated from its genomic environment in vertebrates is not basically different from what is observed in yeast and Drosophila (preceding article in this issue). If the formation of a looped chromatin domain, whether generated by attachment to the nuclear matrix or not, has become a classic way to confine an enhancer to a specific genomic domain and to coordinate, sequentially or simultaneously, gene expression in a given program, its role has been extended to new networks of genes or regulators within the same gene. A wider definition of the bases of the chromatin loops (nonchromosomal nuclear structures or genomic interacting elements) is also available. However, whereas insulation in Drosophila is due to a variety of proteins, in vertebrates insulators are still practically limited to CTCF (the CCCTC-binding factor), which appears in all cases to be the linchpin of an architecture that structures the assembly of DNA–protein interactions for gene regulation. As in yeast and Drosophila, the economy of means is the rule and the same unexpected diversion of known transcription elements (active or poised RNA polymerases, TFIIIC elements out of tRNA genes, permanent histone replacement) is observed, with variants peculiar to CTCF. Thus, besides structuring DNA looping, CTCF is a barrier to DNA methylation or interferes with all sorts of transcription processes, such as that generating heterochromatin.

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Epigenetic dysregulation by nickel through repressive chromatin domain disruption

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1406923111 ◽

2014 ◽

Vol 111 (40) ◽

pp. 14631-14636 ◽

Cited By ~ 22

Author(s):

Cynthia C. Jose ◽

Beisi Xu ◽

Lakshmanan Jagannathan ◽

Candi Trac ◽

Ramya K. Mallela ◽

...

Keyword(s):

Chromatin Domain ◽

Repressive Chromatin

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Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

Science ◽

10.1126/science.aau1783 ◽

2018 ◽

Vol 362 (6413) ◽

pp. eaau1783 ◽

Cited By ~ 269

Author(s):

Bogdan Bintu ◽

Leslie J. Mateo ◽

Jun-Han Su ◽

Nicholas A. Sinnott-Armstrong ◽

Mirae Parker ◽

...

Keyword(s):

Spatial Organization ◽

Single Cells ◽

Domain Boundary ◽

Super Resolution ◽

Chromatin Domain ◽

Imaging Method ◽

Imaging Data ◽

Chromatin Interactions ◽

Population Average ◽

Binding Factor

The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish TAD-like structures in single cells but eliminated preferential domain boundary positions. Moreover, we observed widespread, cooperative, multiway chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.

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