From Structural Variation of Gene Molecules to Chromatin Dynamics and Transcriptional Bursting

Boeger, Hinrich; Shelansky, Robert; Patel, Heta; Brown, Christopher R.

doi:10.3390/genes6030469

Cited by 12 publications

(10 citation statements)

References 57 publications

(105 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our study indicates a radially arranged structural organization of CDCs based on layers of different chromatin compaction with most decondensed, transcriptionally competent chromatin at the CDC periphery to the most compact chromatin within the CDC interior. This layered organization suggests transition zones of chromatin compaction between CDs with a fully ‘closed’ and a fully ‘open’ configuration [ 6 , 54 , 55 ]. Hi-C experiments revealed two higher-order compartments A and B, respectively, of ~1-Mb CDs corresponding to open (transcriptionally competent) and closed (transcriptionally silent) chromatin [ 33 ], but their relationship to CDCs has remained elusive.…”

Section: Discussionmentioning

confidence: 99%

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Cremer

Schmid

Kraus

et al. 2017

Epigenetics & Chromatin

View full text Add to dashboard Cite

Background The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an ‘open’ local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC–INC) form two spatially co-aligned and functionally interacting networks.ResultsUsing 3D structured illumination microscopy, we performed 3D FISH with differently labeled DNA probe sets targeting either sites with DHS[+], apparently active TREs, or DHS[−] sites harboring inactive TREs. Using an in-house image analysis tool, DNA targets were quantitatively mapped on chromatin compaction shaped 3D nuclear landscapes. Our analyses present evidence for a radial 3D organization of chromatin domain clusters (CDCs) with layers of increasing chromatin compaction from the periphery to the CDC core. Segments harboring active TREs are significantly enriched at the decondensed periphery of CDCs with loops penetrating into interchromatin compartment channels, constituting the ANC. In contrast, segments lacking active TREs (DHS[−]) are enriched toward the compacted interior of CDCs (INC).ConclusionsOur results add further evidence in support of the ANC–INC network model. The different 3D topographies of DHS[+] and DHS[−] sites suggest positional changes of TREs between the ANC and INC depending on their functional state, which might provide additional protection against an inappropriate activation. Our finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an ‘open,’ active and ‘closed,’ inactive state.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-017-0146-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Cremer

Schmid

Kraus

et al. 2017

Epigenetics & Chromatin

View full text Add to dashboard Cite

show abstract

“…With time, the “slow” recruitment of transcriptional complexes has found an explanation in a contemporary model of the transcriptional process [ 22 ]. The patterns and periodicities of transcriptional complexes correlate well with the formation of transcriptional “bursts” in eukaryotic cells [ 23 ]. There are models that attempt to simulate the “bursting” process of transcription.…”

Section: Nuclear Dynamic Of the Transcriptional Complexesmentioning

confidence: 99%

On the way of revealing coactivator complexes cross-talk during transcriptional activation

et al. 2016

View full text Add to dashboard Cite

Transcriptional activation is a complex, multistage process implemented by hundreds of proteins. Many transcriptional proteins are organized into coactivator complexes, which participate in transcription regulation at numerous genes and are a driver of this process. The molecular action mechanisms of coactivator complexes remain largely understudied. Relevant publications usually deal with the involvement of these complexes in the entire process of transcription, and only a few studies are aimed to elucidate their functions at its particular stages. This review summarizes available information on the participation of key coactivator complexes in transcriptional activation. The timing of coactivator complex binding/removal has been used for restructuring previously described information about the transcriptional process. Several major stages of transcriptional activation have been distinguished based on the presence of covalent histone modifications and general transcriptional factors, and the recruitment and/or removal phases have been determined for each coactivator included in analysis. Recruitment of Mediator, SWItch/Sucrose Non-Fermentable and NUcleosome Remodeling Factor complexes during transcription activation has been investigated thoroughly; CHD and INOsitol auxotrophy 80 families are less well studied. In most cases, the molecular mechanisms responsible for the removal of certain coactivator complexes after the termination of their functions at the promoters are still not understood. On the basis of the summarized information, we propose a scheme that illustrates the involvement of coactivator complexes in different stages of the transcription activation process. This scheme may help to gain a deeper insight into the molecular mechanism of functioning of coactivator complexes, find novel participants of the process, and reveal novel structural or functional connections between different coactivators.

show abstract

“…In this article, we refer to these two types of programmed monoallelic expression as simply imprinted or random monoallelic expression. In both types, the choice of the expressed allele is maintained through numerous rounds of cell division and is therefore distinct from stochastic “bursting” of transcription that can be detected on individual alleles in single cells ( Boeger et al, 2015 ; Corrigan et al, 2016 ). We previously found that ASAR6 and ASAR15 are subject to random monoallelic expression ( Stoffregen et al, 2011 ; Donley et al, 2013 , 2015 ).…”

Section: Introductionmentioning

confidence: 99%

L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing

Platt

Thayer

2017

Journal of Cell Biology

View full text Add to dashboard Cite

show abstract

From Structural Variation of Gene Molecules to Chromatin Dynamics and Transcriptional Bursting

Cited by 12 publications

References 57 publications

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

On the way of revealing coactivator complexes cross-talk during transcriptional activation

L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing

Contact Info

Product

Resources

About