Chromosomal Contact Permits Transcription between Coregulated Genes

Abstract

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.

Interallelic interaction and gene regulation in budding yeast

“…This observation is consistent with previous statistical analysis, indicating that coregulated genes tend to cluster, and genes that are physically proximal tend to coexpress (21,31,32). Coactivated genes can also form "transcription factories" or "multigene complexes" in higher eukaryotic species (33,34), so our findings here are likely to be one example of a more general phenomenon. This result can also explain why there have been conflicting observations on homologous pairing in yeast (12)(13)(14)(15): The experimental outcome likely depends on the inspected regions and their transcription status.…”

Transcription organizes euchromatin similar to an active microemulsion

“…These microenvironments are characterized by high concentrations of transcription factors that can potentiate the induction of target genes (Mir et al, 2017;Tsai et al, 2017). The localization of genes to accumulations of transcription factors (Papantonis et al, 2012;Liu et al, 2014) might also explain observations of proximity-based gene regulation (Fanucchi et al, 2013). Our work explains how transcription establishes microenvironments that can retain several transcribed genes and potentially facilitate the accumulation of transcription factors.…”

Are genes switched on when they kiss?

“…45 Recently, we developed a novel single cell microscopy-based assay, to address the role of loop-mediated contact on transcription of interacting genes in the SAMD4A/TNFAIP2/SLC6A5 multigene complex. 46 In the assay, TALE nucleases (TALENs) were used to induce a DSB at the approximate site within each of these three gene loops that was established by 3C-technologies to engage in contact. 4,46 We have also tested the ability of other site-specific nucleases to disrupt the SAMD4A gene loop (Fig.…”

“…34 Consistent with previous studies, 4 co-localization between the FISH foci of these three genes was only observed at a low percentage of all alleles across the population (~5%). 46 This would suggest that this small fraction of the population represents a "special pool" of primed cells that permit loop-mediated contact.…”

“…4 prior to activation, DNa FISH reveals that, in a fraction of the population, these three genes are in close proximity, but not physical contact. 46 after activation by tNFα, the promoters of the three genes associate via rNa pol II to form a multigene complex. consistent with other studies, 48,49 we observed silencing of SAMD4A transcription 3′ of the DSB (Fig.…”