Noncoding transcription is a driving force for nucleosome instability in spt16 mutant cells

Jianxun Feng, Haiyun Gan, Matthew L. Eaton, Hui Zhou, Shuqi Li, Jason A. Belsky, David M. MacAlpine, Zhiguo Zhang, Qing Li

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1856-1867
Number of pages12
JournalMolecular and cellular biology
Issue number13
StatePublished - 2016

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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