Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Austenaa, Liv; Barozzi, Iros; Simonatto, Marta; Masella, Silvia; Chiara, Giulia Della; Ghisletti, Serena; Curina, Alessia; Wit, Elzo de; Bouwman, Britta A. M.; Pretis, Stefano de; Piccolo, Viviana; Termanini, Alberto; Prosperini, Elena; Pelizzola, Mattia; Laat, Wouter de

doi:10.1016/j.molcel.2015.09.018

Cited by 80 publications

(104 citation statements)

References 73 publications

(96 reference statements)

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“…The murine macrophage cell line RAW264.7 (ECACC) was grown in DMEM (Lonza) supplemented with 10% FBS NA (HyClone), 1% glutamine (Euroclone) and 1% penicillin/streptomycin (Life Technologies) under 5% CO 2 at 37°C. Normal bone marrow macrophages were derived from of C57/BL6 mice (Harlan) …”

Section: Methodsmentioning

confidence: 60%

Mutual epithelium‐macrophage dependency in liver carcinogenesis mediated by ST18

et al. 2016

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The ST18 gene has been proposed to act either as a tumor suppressor or as an oncogene in different human cancers, but direct evidence for its role in tumorigenesis has been lacking thus far. Here, we demonstrate that ST18 is critical for tumor progression and maintenance in a mouse model of liver cancer, based on oncogenic transformation and adoptive transfer of primary precursor cells (hepatoblasts). ST18 messenger RNA (mRNA) and protein were detectable neither in normal liver nor in cultured hepatoblasts, but were readily expressed after subcutaneous engraftment and tumor growth. ST18 expression in liver cells was induced by inflammatory cues, including acute or chronic inflammation in vivo, as well as coculture with macrophages in vitro. Knocking down the ST18 mRNA in transplanted hepatoblasts delayed tumor progression. Induction of ST18 knockdown in pre‐established tumors caused rapid tumor involution associated with pervasive morphological changes, proliferative arrest, and apoptosis in tumor cells, as well as depletion of tumor‐associated macrophages, vascular ectasia, and hemorrhage. Reciprocally, systemic depletion of macrophages in recipient animals had very similar phenotypic consequences, impairing either tumor development or maintenance, and suppressing ST18 expression in hepatoblasts. Finally, RNA sequencing of ST18‐depleted tumors before involution revealed down‐regulation of inflammatory response genes, pointing to the suppression of nuclear factor kappa B–dependent transcription. Conclusion: ST18 expression in epithelial cells is induced by tumor‐associated macrophages, contributing to the reciprocal feed‐forward loop between both cell types in liver tumorigenesis. Our findings warrant the exploration of means to interfere with ST18‐dependent epithelium–macrophage interactions in a therapeutic setting. (Hepatology 2017;65:1708‐1719).

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Section: Methodsmentioning

confidence: 60%

Mutual epithelium‐macrophage dependency in liver carcinogenesis mediated by ST18

et al. 2016

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“…How human CDK7 activity might promote termination is unclear, but it could potentially stimulate cleavage/polyadenylation or slow pol II elongation to facilitate termination by the torpedo mechanism (Fong et al, 2015). CDK7 effects on termination may also be mediated via recruitment of SETD1A/B or PAF1 complexes (Figure 2C) that have both been linked to regulation of pol II termination (Austenaa et al, 2015; Yang et al, 2016). In contrast to CDK7 inhibition in human cells, Kin28 inhibition in yeast showed depleted pol II occupancy at gene 3′-ends, likely due to premature termination (Kim et al, 2010; Rodriguez-Molina et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

et al. 2017

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CDK7 phosphorylates the RNA polymerase II (pol II) CTD and activates the P-TEFb-associated kinase, CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3′-ends upon CDK7 inhibition. We also noted CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5′-ends and H3K36me3 was displaced toward gene 3′-ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated vs. P-TEFb-phosphorylated CTD (vs. unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent “CTD code” that regulates chromatin marks in addition to RNA processing and pol II pausing.

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“…Many promoter and enhancers display bi-directional transcription, which is actively suppressed but has also been suggested to contribute to function of regulatory elements. Natoli and colleagues showed that upon knock-down of the Set complex protein WDR82, there is a dramatic increase in the amount of non-coding divergent transcription from promoters and enhancers (Austenaa et al, 2015). Remarkably, these authors also showed that such non-coding transcription appears to end abruptly at the boundaries of TADs.…”

Section: Function Of Tadsmentioning

confidence: 99%

Chromatin Domains: The Unit of Chromosome Organization

2016

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Summary How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the existence of chromatin domains and loops as a pervasive feature of interphase chromosomes, but the biological implications of such organizational features were obscure. Genome-wide analysis of pair-wise chromatin interactions using chromatin conformation capture (3C)-based techniques has shed new light on the organization of chromosomes in interphase nuclei. Particularly, the finding of cell type invariant, evolutionarily conserved topologically associating domains (TADs) in a broad spectrum of cell types has provided a new molecular framework for study of animal development and human diseases. Here we review recent progress in characterization of such chromatin domains and delineation of mechanisms of their formation in animal cells.

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Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Cited by 80 publications

References 73 publications

Mutual epithelium‐macrophage dependency in liver carcinogenesis mediated by ST18

Mutual epithelium‐macrophage dependency in liver carcinogenesis mediated by ST18

Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

Chromatin Domains: The Unit of Chromosome Organization

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