Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites

Larkin, Joshua D.; Papantonis, Argyris; Cook, Peter R.

doi:10.1242/jcs.123653

Cited by 12 publications

(11 citation statements)

References 51 publications

(71 reference statements)

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“…Therefore, these data argue neither in favor of nor against putative ''transcription factories'' as they are currently defined (Cook, 1999) but suggest that such factories may be dynamically assembled rather than immobile structures. A recent study revealed that sequences within the promoter might drive the colocalization between these NFkB-regulated genes (Larkin et al, 2013). Therefore, an alternative model might involve sequencespecific elements within the promoters that facilitate the accumulation of different thresholds of general transcription factors for the three genes.…”

Section: Discussionmentioning

confidence: 99%

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi

Shibayama

Burd

et al. 2013

Cell

191

167

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Transcription of coregulated genes occurs in the context of long-range chromosomal contacts that form multigene complexes. Such contacts and transcription are lost in knockout studies of transcription factors and structural chromatin proteins. To ask whether chromosomal contacts are required for cotranscription in multigene complexes, we devised a strategy using TALENs to cleave and disrupt gene loops in a well-characterized multigene complex. Monitoring this disruption using RNA FISH and immunofluorescence microscopy revealed that perturbing the site of contact had a direct effect on transcription of other interacting genes. Unexpectedly, this effect on cotranscription was hierarchical, with dominant and subordinate members of the multigene complex engaged in both intra-and interchromosomal contact. This observation reveals the profound influence of these chromosomal contacts on the transcription of coregulated genes in a multigene complex.

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Section: Discussionmentioning

confidence: 99%

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi

Shibayama

Burd

et al. 2013

Cell

191

167

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“…It has been suggested that these preferences are a reflection of gene regulation by shared sets of transcription factors; a high frequency of clustering has been detected for genes regulated by both Klf1 and TNF-a (19,21). It also seems that promoter identity directs the coassociation preference (22). It is not clear how specialization of factories is achieved, but preferences may be established through self-organization principles, driven by the sharing of specific transcription factors (23).…”

Section: Introductionmentioning

confidence: 99%

Molecular Pathways: Transcription Factories and Chromosomal Translocations

Osborne

2014

Clinical Cancer Research

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The mammalian nucleus is a highly complex structure that carries out a diverse range of functions such as DNA replication, cell division, RNA processing, and nuclear export/import. Many of these activities occur at discrete subcompartments that intersect with specific regions of the genome. Over the past few decades, evidence has accumulated to suggest that RNA transcription also occurs in specialized sites, called transcription factories, that may influence how the genome is organized. There may be certain efficiency benefits to cluster transcriptional activity in this way. However, the clustering of genes at transcription factories may have consequences for genome stability, and increase the susceptibility to recurrent chromosomal translocations that lead to cancer. The relationships between genome organization, transcription, and chromosomal translocation formation will have important implications in understanding the causes of therapy-related cancers. Clin Cancer Res; 20(2); 296-300. Ó2013 AACR.

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“…When introduced into cells, mini‐chromosomes were recruited to specific foci within the nucleus in a promoter‐specific manner (Xu and Cook, ). Mini‐chromosomes carrying identical (intron‐less) transcription units were transcribed in the same factories, but those with intronic sequence were targeted to and transcribed in a different factory (Xu and Cook, ; Larkin et al, ). In support of this finding, ChIA‐PET experiments show that intron‐less genes often contact each other (Li et al, ).…”

Section: Transcriptional Microenvironments: Coming Together Keeping mentioning

confidence: 99%

The Dynamic Architectural and Epigenetic Nuclear Landscape: Developing the Genomic Almanac of Biology and Disease

Tai

Zaidi

et al. 2014

J. Cell. Physiol.

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Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively-parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology.

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Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites

Cited by 12 publications

References 51 publications

Chromosomal Contact Permits Transcription between Coregulated Genes

Chromosomal Contact Permits Transcription between Coregulated Genes

Molecular Pathways: Transcription Factories and Chromosomal Translocations

The Dynamic Architectural and Epigenetic Nuclear Landscape: Developing the Genomic Almanac of Biology and Disease

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