 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 05, 2020 |
| Title |
Essential histone chaperones collaborate to regulate transcription and chromatin integrity |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. We have discovered that the physical interaction between two essential histone chaperones, Spt6 and Spn1/Iws1, is required for transcriptional accuracy and nucleosome organization. To understand this requirement, we have isolated suppressors of an spt6 mutation that disrupts the Spt6-Spn1 interaction. Several suppressors are in a third essential histone chaperone, FACT, while another suppressor is in the transcription elongation factor Spt5/DSIF. The FACT suppressors weaken FACT-nucleosome interactions and bypass the requirement for Spn1, possibly by restoring a necessary balance between Spt6 and FACT on chromatin. In contrast, the Spt5 suppressor modulates Spt6 function in a Spn1-dependent manner. Despite these distinct mechanisms, both suppressors alleviate the nucleosome organization defects caused by disruption of the Spt6-Spn1 interaction. Taken together, we have uncovered a network in which histone chaperones and other elongation factors coordinate transcriptional integrity and chromatin structure.
|
| |
|
| Overall design |
Multiple assays of transcription and chromatin state in spt6 mutants and suppressors of spt6-YW, including transcription start site sequencing (TSS-seq), native elongating transcript sequencing (NET-seq), MNase-seq, and ChIP-seq of Rpb1, Spn1, Spt6, and Spt16.
|
| |
|
| Contributor(s) |
Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 04, 2020 |
| Last update date |
Nov 10, 2020 |
| Contact name |
Fred Winston |
| E-mail(s) |
winston@genetics.med.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Winston
|
| Street address |
77 Avenue Louis Pasteur, Room 239
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
| Samples (179)
|
| GSM4879761 |
TSS-seq: wild type, 37C 2 |
| GSM4879762 |
TSS-seq: spt6-1004, 30C 1 |
| GSM4879763 |
TSS-seq: spt6-1004, 30C 2 |
| GSM4879764 |
TSS-seq: spt6-1004, 37C 1 |
| GSM4879765 |
TSS-seq: spt6-1004, 37C 2 |
| GSM4879766 |
TSS-seq: spt6-YW, 30C 1 |
| GSM4879767 |
TSS-seq: spt6-YW, 30C 2 |
| GSM4879768 |
TSS-seq: spt6-YW, 37C 1 |
| GSM4879769 |
TSS-seq: spt6-YW, 37C 2 |
| GSM4879770 |
NET-seq: wild type, 30C 1 |
| GSM4879771 |
NET-seq: wild type, 30C 2 |
| GSM4879772 |
NET-seq: wild type, 37C 1 |
| GSM4879773 |
NET-seq: wild type, 37C 2 |
| GSM4879774 |
NET-seq: spt6-YW, 30C 1 |
| GSM4879775 |
NET-seq: spt6-YW, 30C 2 |
| GSM4879776 |
NET-seq: spt6-YW, 37C 1 |
| GSM4879777 |
NET-seq: spt6-YW, 37C 2 |
| GSM4879778 |
MNase-seq: wild type, 30C 2 |
| GSM4879779 |
MNase-seq: wild type, 30C 6 |
| GSM4879780 |
MNase-seq: wild type, 37C 1 |
| GSM4879781 |
MNase-seq: wild type, 37C 3 |
| GSM4879782 |
MNase-seq: wild type, 37C 4 |
| GSM4879783 |
MNase-seq: wild type, 37C 5 |
| GSM4879784 |
MNase-seq: spn1-K192N, 30C 1 |
| GSM4879785 |
MNase-seq: spn1-K192N, 30C 2 |
| GSM4879786 |
MNase-seq: spn1-K192N, 37C 1 |
| GSM4879787 |
MNase-seq: spn1-K192N, 37C 2 |
| GSM4879788 |
MNase-seq: spt6-YW, 30C, 1 |
| GSM4879789 |
MNase-seq: spt6-YW, 30C, 2 |
| GSM4879790 |
MNase-seq: spt6-YW, 30C, 3 |
| GSM4879791 |
MNase-seq: spt6-YW, 37C, 1 |
| GSM4879792 |
MNase-seq: spt6-YW, 37C, 2 |
| GSM4879793 |
MNase-seq: pob3-E154K, 30C, 1 |
| GSM4879794 |
MNase-seq: pob3-E154K, 30C, 2 |
| GSM4879795 |
MNase-seq: pob3-E154K, 37C, 1 |
| GSM4879796 |
MNase-seq: pob3-E154K, 37C, 2 |
| GSM4879797 |
MNase-seq: pob3-E154K, 37C, 4 |
| GSM4879798 |
MNase-seq: spt5-QS, 30C, 1 |
| GSM4879799 |
MNase-seq: spt5-QS, 30C, 2 |
| GSM4879800 |
MNase-seq: spt5-QS, 37C, 1 |
| GSM4879801 |
MNase-seq: spt5-QS, 37C, 2 |
| GSM4879802 |
MNase-seq: spt5-QS, 37C, 3 |
| GSM4879803 |
MNase-seq: spt5-QS, 37C, 4 |
| GSM4879804 |
MNase-seq: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879805 |
MNase-seq: spt6-YW pob3-E154K, 30C, 3 |
| GSM4879806 |
MNase-seq: spt6-YW pob3-E154K, 30C, 4 |
| GSM4879807 |
MNase-seq: spt6-YW pob3-E154K, 37C, 1 |
| GSM4879808 |
MNase-seq: spt6-YW pob3-E154K, 37C, 2 |
| GSM4879809 |
MNase-seq: spt6-YW pob3-E154K, 37C, 3 |
| GSM4879810 |
MNase-seq: spt6-YW pob3-E154K, 37C, 4 |
| GSM4879811 |
MNase-seq: spt6-YW spt5-QS, 30C, 1 |
| GSM4879812 |
MNase-seq: spt6-YW spt5-QS, 30C, 2 |
| GSM4879813 |
MNase-seq: spt6-YW spt5-QS, 37C, 1 |
| GSM4879814 |
MNase-seq: spt6-YW spt5-QS, 37C, 2 |
| GSM4879815 |
MNase-seq: spt6-YW spt5-QS, 37C, 3 |
| GSM4879816 |
MNase-seq: spt6-YW spt5-QS, 37C, 4 |
| GSM4879817 |
ChIP-seq input DNA: Spt6-FLAG background: wild type, 30C, 1 |
| GSM4879818 |
ChIP-seq input DNA: Spt6-FLAG background: wild type, 30C, 2 |
| GSM4879819 |
ChIP-seq input DNA: Spt6-FLAG background: wild type, 37C, 1 |
| GSM4879820 |
ChIP-seq input DNA: Spt6-FLAG background: wild type, 37C, 2 |
| GSM4879821 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 30C, 1 |
| GSM4879822 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 30C, 2 |
| GSM4879823 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 37C, 1 |
| GSM4879824 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 37C, 2 |
| GSM4879825 |
ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 30C, 1 |
| GSM4879826 |
ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 30C, 2 |
| GSM4879827 |
ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 37C, 1 |
| GSM4879828 |
ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 37C, 2 |
| GSM4879829 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 1 |
| GSM4879830 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879831 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 1 |
| GSM4879832 |
ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 2 |
| GSM4879833 |
ChIP-seq input DNA: Spt16-myc background: wild type, 30C, 1 |
| GSM4879834 |
ChIP-seq input DNA: Spt16-myc background: wild type, 30C, 2 |
| GSM4879835 |
ChIP-seq input DNA: Spt16-myc background: wild type, 37C, 1 |
| GSM4879836 |
ChIP-seq input DNA: Spt16-myc background: wild type, 37C, 2 |
| GSM4879837 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW, 30C, 1 |
| GSM4879838 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW, 30C, 2 |
| GSM4879839 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW, 37C, 1 |
| GSM4879840 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW, 37C, 2 |
| GSM4879841 |
ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 30C, 1 |
| GSM4879842 |
ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 30C, 2 |
| GSM4879843 |
ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 37C, 1 |
| GSM4879844 |
ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 37C, 2 |
| GSM4879845 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 1 |
| GSM4879846 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879847 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 1 |
| GSM4879848 |
ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 2 |
| GSM4879849 |
ChIP-seq input DNA: V5-Spn1 background: wild type, 30C, 1 |
| GSM4879850 |
ChIP-seq input DNA: V5-Spn1 background: wild type, 30C, 2 |
| GSM4879851 |
ChIP-seq input DNA: V5-Spn1 background: spt6-YW, 30C, 1 |
| GSM4879852 |
ChIP-seq input DNA: V5-Spn1 background: spt6-YW, 30C, 2 |
| GSM4879853 |
ChIP-seq input DNA: V5-Spn1 background: pob3-E154K, 30C, 1 |
| GSM4879854 |
ChIP-seq input DNA: V5-Spn1 background: pob3-E154K, 30C, 2 |
| GSM4879855 |
ChIP-seq input DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 1 |
| GSM4879856 |
ChIP-seq input DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879857 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 1 |
| GSM4879858 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 2 |
| GSM4879859 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 1 |
| GSM4879860 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 2 |
| GSM4879861 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 1 |
| GSM4879862 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 2 |
| GSM4879863 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 1 |
| GSM4879864 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 2 |
| GSM4879865 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 1 |
| GSM4879866 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 2 |
| GSM4879867 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 1 |
| GSM4879868 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 2 |
| GSM4879869 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 1 |
| GSM4879870 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879872 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 1 |
| GSM4879874 |
Rpb1 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 2 |
| GSM4879875 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 1 |
| GSM4879877 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 2 |
| GSM4879878 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 1 |
| GSM4879880 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 2 |
| GSM4879881 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 30C, 1 |
| GSM4879882 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 30C, 2 |
| GSM4879883 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 37C, 1 |
| GSM4879884 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW, 37C, 2 |
| GSM4879885 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 1 |
| GSM4879886 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 2 |
| GSM4879887 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 1 |
| GSM4879888 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 2 |
| GSM4879889 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 1 |
| GSM4879890 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879891 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 1 |
| GSM4879892 |
Rpb1 ChIP-seq, ChIP DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 2 |
| GSM4879893 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 1 |
| GSM4879894 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 2 |
| GSM4879895 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 1 |
| GSM4879896 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 2 |
| GSM4879897 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 1 |
| GSM4879898 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 2 |
| GSM4879899 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 1 |
| GSM4879900 |
Rpb1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW pob3-E154K, 30C, 2 |
| GSM4879901 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 1 |
| GSM4879902 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 30C, 2 |
| GSM4879903 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 1 |
| GSM4879904 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: wild type, 37C, 2 |
| GSM4879905 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 1 |
| GSM4879906 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 30C, 2 |
| GSM4879907 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 1 |
| GSM4879908 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW, 37C, 2 |
| GSM4879909 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 1 |
| GSM4879910 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 30C, 2 |
| GSM4879911 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 1 |
| GSM4879912 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: pob3-E154K, 37C, 2 |
| GSM4879913 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 30C, 1 |
| GSM4879914 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 30C, 2 |
| GSM4879915 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 37C, 1 |
| GSM4879916 |
Spt6 ChIP-seq, ChIP DNA: Spt6-FLAG background: spt6-YW-pob3-E154K, 37C, 2 |
| GSM4879917 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 1 |
| GSM4879919 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 30C, 2 |
| GSM4879920 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 1 |
| GSM4879922 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: wild type, 37C, 2 |
| GSM4879923 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 30C, 1 |
| GSM4879925 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 30C, 2 |
| GSM4879926 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 37C, 1 |
| GSM4879927 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW, 37C, 2 |
| GSM4879928 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 1 |
| GSM4879929 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 30C, 2 |
| GSM4879930 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 1 |
| GSM4879931 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: pob3-E154K, 37C, 2 |
| GSM4879932 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 30C, 1 |
| GSM4879933 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 30C, 2 |
| GSM4879934 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 37C, 1 |
| GSM4879935 |
Spt16 ChIP-seq, ChIP DNA: Spt16-myc background: Spt16-YW-pob3-E154K, 37C, 2 |
| GSM4879936 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 1 |
| GSM4879937 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: wild type, 30C, 2 |
| GSM4879938 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 1 |
| GSM4879939 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW, 30C, 2 |
| GSM4879940 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 1 |
| GSM4879941 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: pob3-E154K, 30C, 2 |
| GSM4879942 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW-pob3-E154K, 30C, 1 |
| GSM4879943 |
Spn1 ChIP-seq, ChIP DNA: V5-Spn1 background: spt6-YW-pob3-E154K, 30C, 2 |
|
| Relations |
| BioProject |
PRJNA674587 |
| SRA |
SRP291126 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE160821_RAW.tar |
14.8 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...