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Local rewiring of genome - nuclear lamina interactions by transcription

Laura Brueckner, Peiyao A Zhao, Tom van Schaik, Christ Leemans, Jiao Sima, Daniel Peric-Hupkes, David M Gilbert, Bas van Steensel

Posted on: 15 July 2019 , updated on: 19 March 2020

Preprint posted on 27 June 2019

Article now published in EMBO Journal at https://www.embopress.org/doi/10.15252/embj.2019103159

Modulating transcriptional activity alters local interactions between the genome and the nuclear lamina

Selected by Sergio Menchero

Categories: genomics

Background & Summary:

The genome is spatially organised within each cell nucleus and this 3D conformation is important for gene regulation. Lamina-associated domains (LADs) are large chromatin regions that interact with the nuclear lamina in the interphase nucleus. These domains are associated with repressive functions, and genes located within LADs usually have low transcriptional activity. The contacts between LADs and the nuclear lamina are very stable in some cases and consistent between different cell types, while in other cases, there are cell-type specific interactions.

It was not clear if the link between repression of genes and interactions of these genes with the nuclear lamina was direct or something secondary. Very recently, the same lab showed that positioning LAD-associated promoters in a neutral context made them become active, suggesting that LADs form a repressive environment (Leemans et al. 2019). In this preprint, the authors forcedly activate or inactivate gene transcription in different contexts to test how this affects the contacts with the nuclear lamina.

 

Major experiments in the preprint:

  • Activation of genes inside LADs by expressing the transcriptional activator VP64 targeted to selected promoters using a guideRNA.Activation of gene transcription caused detachment of chromatin from the nuclear lamina along the gene body. In some cases, this detachment expanded a bit to the flanking regions but it was mainly specific to the gene. A gain of nuclear lamina interactions in a nearby region was rarely observed but it was not consistent in order to determine whether there are compensatory rearrangements. When activating several genes within the same domain, detachments were still local, and they did not cause a more global detachment due to synergistic or cooperative effects.
Figure 1 (Fig 1a and 6a in the preprint). Effect of activation of one gene (left) or multiple neighbouring genes (right). DamID domainograms show detachment regions in blue.

 

  • Inactivation of transcription by heterozygous deletion of promoters or insertion of a polyadenylation sequence. The authors targeted genes whose association to the nuclear lamina is dependent on the cell-type and therefore, changes in attachment are more likely to occur. An increase in nuclear lamina interactions could be observed specifically in the mutant allele while the wildtype remained unaffected. These re-attachments were also local and specific to the targeted genes.
Figure 2 (Fig 7a-b in the preprint). Specific deletion of promoters (left, highlighted in yellow) increased interactions to the nuclear lamina as shown by the red colour in the DamID domainograms. The wildtype allele (right) did not show important changes.

 

  • Insertion of an active transgene into a LAD. Similarly to the activation of endogenous genes, the integration sites showed a reduction of contacts with the nuclear lamina as compared to the corresponding wildtype sites.General comments and why I chose this preprint:The spatial organization of the genome within the nucleus is important for the regulation of gene expression. Recent works try to decipher if this is also important in the other direction and ask if transcription can modulate genome organization. As usually in biology, there is not a clear yes/no answer but there are nuances and different behaviours in different contexts and at different genomic scales. Recent studies showed that, in general, transcription is not required for global genome architecture, but could have a role at a local scale for the formation of subcompartments (reviewed in van Steensel and Furlong. 2019). The results of this preprint point to the same direction. Activation or inactivation of transcription leads to detachments and re-attachments of chromatin to the nuclear lamina, but mainly in a site-specific manner. The fact that there is an inherent layer of variability and context-dependent effects, assessing several strategies is key to get a better understanding. I like that Brueckner and colleagues use different approaches and complementary assays by activating and repressing transcription to get to their conclusions. The selection of DamID mapping of Lamin B1 interactions as a method to measure detachment and re-attachment to the nuclear lamina is key to interpret the results. It gives a detailed view not only of the specific gene but also of the flanking regions. Again, it is difficult to generalize but I think this work is important for the field to try to build a more general picture of how the genome is spatially organized based on different strategies and different contexts.

    Questions to the authors

    The authors mention that some interactions between LADs and the nuclear lamina are very stable between cell types while others are cell or tissue specific. The experiments that address transcriptional inactivation are performed in genes whose contacts are more susceptible to change given that they are different in mouse embryonic stem cells or in neural precursor cells. Have the authors tried to see what happens in LADs that are more stable between cell types? Are genes contained in those LADs always transcriptionally silenced? Or are there genes that are expressed in low but constant levels across different cell types that could be susceptible to transcriptional changes?

     

    References

    Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B. (2019). Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. Cell 177(4):852-864.

    van Steensel B, Furlong EEM. (2019). The role of transcription in shaping the spatial organization of the genome. Nat Rev Mol Cell Biol 20(6):327-37.

Tags: genomic organization, lads, nuclear lamina, transcription

doi: https://doi.org/10.1242/prelights.12015

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Author's response

Bas van Steensel shared

Questions to the authors

The authors mention that some interactions between LADs and the nuclear lamina are very stable between cell types while others are cell or tissue specific. The experiments that address transcriptional inactivation are performed in genes whose contacts are more susceptible to change given that they are different in mouse embryonic stem cells or in neural precursor cells. Have the authors tried to see what happens in LADs that are more stable between cell types? Are genes contained in those LADs always transcriptionally silenced? Or are there genes that are expressed in low but constant levels across different cell types that could be susceptible to transcriptional changes?

Very good point. We have not analyzed or tested this. The definition of constitutive/stable vs facultative/unstable LADs is a bit tricky, because we have not mapped NL interactions in all possible cell types. In earlier work we found that constitutive LADs (definition based on a small number of cell types) are rather gene poor. Extrapolating this — perhaps the only true constitutive/stable LADs are those that have no genes at all? Taking into account the results in the preprint, I am inclined to view it that way, but we would have to map NL interactions in a lot of cell types in order to get a good view of this issue.

 

Update: Comment on the peer review process

This preprint was published in The EMBO Journal on the 21st February 2020

The authors shared:

In the case of this paper, the reviewer comments helped us to:

– Improve and clarify the text in terms of presentation and discussion of our findings.

– Add and modify some figures for improved clarity.

– Add a comparison to external data.

None of the conclusions in the paper were altered.

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