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Series GSE66215 Query DataSets for GSE66215
Status Public on May 05, 2016
Title Cryptic transcription is the primary driving force for nucleosome instability in Spt16 mutant cells
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary 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.
Contributor(s) Li Q, Feng J, Gan H, Zhang Z
Citation(s) 27141053
Submission date Feb 23, 2015
Last update date May 15, 2019
Contact name zhiguo zhang
Phone 212-851-4936
Organization name Columbia University
Department Pediatric and Genetics and Development
Lab Irving Cancer Research Center
Street address 1130 St. Nicholas Avenue
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (2)
GPL9134 Illumina Genome Analyzer (Saccharomyces cerevisiae)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (28)
GSM1617325 WT T0 MNase-seq_1
GSM1617326 WT T0 MNase-seq_2
GSM1617327 WT T0 MNase-seq_3
BioProject PRJNA276131
SRA SRP055441

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Supplementary file Size Download File type/resource
GSE66215_RAW.tar 923.4 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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