Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation

Abstract

Higher-order genome organization shows tissue-specific patterns. However, functional relevance and the mechanisms shaping the genome architecture are poorly understood. Here we report a profound shift from promiscuous to highly selective genome organization that accompanies the effector lineage choice of differentiating T cells. As multipotent naive cells receive antigenic signals and commit to a T helper (Th) pathway, the genome-wide contacts of a lineage-specific cytokine locus are preferentially enriched for functionally relevant genes. Despite the establishment of divergent interactomes and global reprogramming of transcription in Th1 versus Th2, the overall expression status of the contact genes is surprisingly similar between the two lineages. Importantly, during differentiation, the genomic contacts are retained and strengthened precisely at DNA binding sites of the specific lineage-determining STAT transcription factor. In cells from the specific STAT knock-out mouse, the signature cytokine locus is unable to shed the promiscuous contacts established in the naive T cells, indicating the importance of genomic STAT binding. Altogether, the global aggregation of STAT binding loci from genic and nongenic regions highlights a new role for differentiation-promoting transcription factors in direct specification of higher-order nuclear architecture through interacting with regulatory regions. Such subnuclear environments have significant implications for efficient functioning of the mature effector lymphocytes.

Chromatin landscape and circadian dynamics: Spatial and temporal organization of clock transcription

“…Spatial congregation of transcription factor binding sites into preestablished architectural domains is a recurrent characteristic of various transcriptional networks (75)(76)(77). Circadian E-box elements appear 2.5-fold enriched at the Dbp contact sites, illustrating that the circadian program of gene expression in MEFs happens in established nuclear domains (71).…”

A new role for STAT3 as a regulator of chromatin topology

“…Furthermore, a recent report on striking global reorganization of the nuclear architecture that occurs in naive T cells as they take on one of the two distinct fates, Th1 or Th2, suggested that the lineage-inducing transcription factors, STAT proteins, play a critical role in specifying such a functional nuclear architecture through their direct association with genic and non-genic loci. 27 These data provide a basis for understanding how STAT transcription factors not only regulate gene expression but also may play a role in shaping a nuclear architecture that supports specialized effector function in cellular differentiation. 27 We propose that ND interactions may have a role in 3D chromatin organization not only via P-STAT tetramerization, but also through ND-dependent dimerization of some U-STAT proteins, in particular for STAT3.…”

“…27 These data provide a basis for understanding how STAT transcription factors not only regulate gene expression but also may play a role in shaping a nuclear architecture that supports specialized effector function in cellular differentiation. 27 We propose that ND interactions may have a role in 3D chromatin organization not only via P-STAT tetramerization, but also through ND-dependent dimerization of some U-STAT proteins, in particular for STAT3. Recently, roles for unphosphorylated STAT proteins in regulation of gene expression have been reported, based on their ability to shuttle between cytoplasm and nucleus, to bind DNA and activate or suppress gene transcription, and even to maintain stability of heterochromatin.…”

Comparative Analysis of T4 DNA Ligases and DNA Polymerases used in Chromosome Conformation Capture Assays

“…To comprehensively and quantitatively appraise the performance of these polymerases for 4C, we tested two baits, sequenced the 4C libraries, and performed computational analyses (Figure 1, Supplementary Figure S2). We also included Expand Long Template (Expand LT) Enzyme mix (# 11681834001; Roche), which is commonly used in 4C (5, 9, 10), in our analysis. We found that the four different polymerases that passed our screen exhibited similar amplification levels and patterns (Figure 1B, Supplementary Figure S2A).…”