Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock
Proc Natl Acad Sci U S A. 2019-09-24;116(39):19431-19439.
- Abstract
- Heat shock (HS) initiates rapid, extensive, and evolutionarily conserved changes in transcription that are accompanied by chromatin decondensation and nucleosome loss at HS loci. Here we have employed in situ Hi-C to determine how heat stress affects long-range chromatin conformation in human and Drosophila cells. We found that compartments and topologically associating domains (TADs) remain unchanged by an acute HS. Knockdown of Heat Shock Factor 1 (HSF1), the master transcriptional regulator of the HS response, identified HSF1-dependent genes and revealed that up-regulation is often mediated by distal HSF1 bound enhancers. HSF1-dependent genes were usually found in the same TAD as the nearest HSF1 binding site. Although most interactions between HSF1 binding sites and target promoters were established in the nonheat shock (NHS) condition, a subset increased contact frequency following HS. Integrating information about HSF1 binding strength, RNA polymerase abundance at the HSF1 bound sites (putative enhancers), and contact frequency with a target promoter accurately predicted which up-regulated genes were direct targets of HSF1 during HS. Our results suggest that the chromatin conformation necessary for a robust HS response is preestablished in NHS cells of diverse metazoan species.
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- Data summary
- Hi-C. Human K562 and Drosophila S2 cells were subjected to HS or not (NHS) and cross-linked with 1% formaldehyde for 10 min at room temperature followed by quenching with glycine for 5 min. In situ Hi-C was performed based on the protocol described previously (16). Further details are provided in SI Appendix, Materials and Methods. Hi-C Data Analysis. Files containing sequenced read pairs were processed using the Juicer pipeline as described previously (16). Reads for human K562 cells and Drosophila S2 cells were aligned to hg19 and dm3, respectively. We required that all alignments were high quality by filtering for a MAPQ score greater than 30. Reads for Drosophila Kc167 cells (SI Appendix, Fig. S8) from refs. 21 and 29 (available at GEO database accessions GSE63518 and GSM942889, respectively) were processed in a similar fashion (i.e., aligned to dm3 and processed using the Juicer pipeline). Map resolution was calculated according to the definition proposed in ref. 16, as the smallest bin size such that 80% of loci have at least 1,000 contacts. For human K562 data, we used scripts that were part of the Juicer pipeline to compute resolution (50). For Drosophila, we used an alternative script specifically designed for the Drosophila genome (51), because we noted inconsistent results using Juicer. We used this definition to determine the finest scale at which one can reliably discern local features. Details of computational methods and analyses are provided in SI Appendix, Materials and Methods. Additional Datasets Used in This Study. The following datasets were also used in this study: K562 HSF1 ChIP-seq data, GSE43579 (7); K562 PRO-seq data, GSE89230 (8); K562 H4ac ChIP-seq data, GSE89382 (8); S2 HSF ChIP-seq data, GSE19025 (4); and S2 PRO-seq data, GSE77607 (5). Code Repository. All other code was custom written in Python 2.7. The significant parts of this code, and example data, are available on the Danko Lab’s GitHub website (https://github.com/Danko-Lab/HS_transcription_regulation). Danko-Lab/Hi-C_contact_caller is the program for determining the significance of interactions for pairs of points within a chromosome using a Hi-C contact map (https://github.com/Danko-Lab/Hi-C_contact_caller, version: 88efbbf).