Noncoding Transcription Is a Driving Force for Nucleosome Instability in spt16 Mutant Cells

Abstract

FACT (facilitates chromatin transcription) consists of two essential subunits, Spt16 and Pob3, and functions as a histone chaperone. Mutation of spt16 results in a global loss of nucleosomes as well as aberrant transcription. Here, we show that the majority of nucleosome changes upon Spt16 depletion are alterations in nucleosome fuzziness and position shift. Most nucleosomal changes are suppressed by the inhibition of RNA polymerase II (Pol II) activity. Surprisingly, a small subgroup of nucleosome changes is resistant to transcriptional inhibition. Notably, Spt16 and distinct histone modifications are enriched at this subgroup of nucleosomes. We also report 1,037 Spt16-suppressed noncoding transcripts (SNTs) and found that the SNT start sites are enriched with the subgroup of nucleosomes resistant to Pol II inhibition. Finally, the nucleosomes at genes overlapping SNTs are more susceptible to changes upon Spt16 depletion than those without SNTs. Taken together, our results support a model in which Spt16 has a role in maintaining local nucleosome stability to inhibit initiation of SNT transcription, which once initiated drives additional nucleosome loss upon Spt16 depletion.

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Article of Significant Interest Selected from This Issue by the Editors

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00152-16.

ACKNOWLEDGMENTS

We thank Tim Formosa for helpful discussions. We thank Alain Verreault, Tim Formosa, and Michael Hampsey for plasmids and yeast strains. We thank Yun Zhang and Wenping Ma of the NGS group at Peking University for assistance with library preparation and Illumina sequencing.

This work was supported by grants from the NIH (GM81838) to Z.Z., NIH (GM104097) to D.M.M., National Science Foundation for Excellent Young Scholars of China Grant (31322017) and National Natural Science Foundation of China Grant (31370767) to Q.L. Q.L. is also a scholar from the Chinese 1000 Plan-The Young Talents Group.