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Differential contribution of steady-state RNA and active transcription in chromatin organization.

ABSTRACT: Nuclear RNA and the act of transcription have been implicated in nuclear organization. However, their global contribution to shaping fundamental features of higher-order chromatin organization such as topologically associated domains (TADs) and genomic compartments remains unclear. To investigate these questions, we perform genome-wide chromatin conformation capture (Hi-C) analysis in the presence and absence of RNase before and after crosslinking, or a transcriptional inhibitor. TAD boundaries are largely unaffected by RNase treatment, although a subtle disruption of compartmental interactions is observed. In contrast, transcriptional inhibition leads to weaker TAD boundary scores. Collectively, our findings demonstrate differences in the relative contribution of RNA and transcription to the formation of TAD boundaries detected by the widely used Hi-C methodology.

SUBMITTER: Barutcu AR

PROVIDER: S-EPMC6776903 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Differential contribution of steady-state RNA and active transcription in chromatin organization.

Barutcu A Rasim AR Blencowe Benjamin J BJ Rinn John L JL

EMBO reports 20190826 10

Nuclear RNA and the act of transcription have been implicated in nuclear organization. However, their global contribution to shaping fundamental features of higher-order chromatin organization such as topologically associated domains (TADs) and genomic compartments remains unclear. To investigate these questions, we perform genome-wide chromatin conformation capture (Hi-C) analysis in the presence and absence of RNase before and after crosslinking, or a transcriptional inhibitor. TAD boundaries ...[more]

PMID: 31448565

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Project description:RationaleMacrophages populate the steady-state myocardium. Previously, all macrophages were thought to arise from monocytes; however, it emerged that, in several organs, tissue-resident macrophages may self-maintain through local proliferation.ObjectiveOur aim was to study the contribution of monocytes to cardiac-resident macrophages in steady state, after macrophage depletion in CD11b(DTR/+) mice and in myocardial infarction.Methods and resultsUsing in vivo fate mapping and flow cytometry, we estimated that during steady state the heart macrophage population turns over in ≈1 month. To explore the source of cardiac-resident macrophages, we joined the circulation of mice using parabiosis. After 6 weeks, we observed blood monocyte chimerism of 35.3±3.4%, whereas heart macrophages showed a much lower chimerism of 2.7±0.5% (P<0.01). Macrophages self-renewed locally through proliferation: 2.1±0.3% incorporated bromodeoxyuridine 2 hours after a single injection, and 13.7±1.4% heart macrophages stained positive for the cell cycle marker Ki-67. The cells likely participate in defense against infection, because we found them to ingest fluorescently labeled bacteria. In ischemic myocardium, we observed that tissue-resident macrophages died locally, whereas some also migrated to hematopoietic organs. If the steady state was perturbed by coronary ligation or diphtheria toxin-induced macrophage depletion in CD11b(DTR/+) mice, blood monocytes replenished heart macrophages. However, in the chronic phase after myocardial infarction, macrophages residing in the infarct were again independent from the blood monocyte pool, returning to the steady-state situation.ConclusionsIn this study, we show differential contribution of monocytes to heart macrophages during steady state, after macrophage depletion or in the acute and chronic phase after myocardial infarction. We found that macrophages participate in the immunosurveillance of myocardial tissue. These data correspond with previous studies on tissue-resident macrophages and raise important questions on the fate and function of macrophages during the development of heart failure.

Dataset Information

Differential contribution of steady-state RNA and active transcription in chromatin organization.

Publications

Differential contribution of steady-state RNA and active transcription in chromatin organization.

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