Cryptic transcription is the primary driving force for nucleosome instability in Spt16 mutant cells

FACT consists of two essential subunits Spt16 and Pob3 and is a histone chaperone. Depletion of Spt16 using a an spt16 mutant results in a global alteration of nucleosome positions as well as aberrant transcription. Here we show that the majority of nucleosomal changes at gene body upon Spt16 depletion are independent of gene activity, but correlates with cryptic gene transcription and are suppressed by inhibition of RNA Polymerase II activities. In addition, A small fraction of nucleosomal changes is resistant to Pol II inhibition, and Spt16 is enriched at this subgroup of nucleosomes. Moreover, nucleosomes surrounding the initiation sites of cryptic transcription in the spt16 mutant cells are more dynamic than other regions. These results support a model that Spt16 maintains nucleosome stability locally to inhibit the initiation from cryptic transcription, which that once initiated drives additional nucleosome loss upon Spt16 depletion. Overall design: To gain further insight into how Spt16 inactivation/depletion alters chromatin structure, we mapped the location of nucleosomes of wild type, spt16(G132D), spt16(G132D) rpb1-1, rpb1-1 cells by high-throughput next generation sequencing of MNase digested fragments. To resolve the apparent discrepancy, we first analyzed transcription including mRNA and non-coding RNA transcription in wild type, spt16(G132D), spt16(G132D) rpb1-1, rpb1-1 cells using strand-specific RNA-seq.