Lee 2017, Histone H3, Pol2 and various chromatin remodelers in wild type and mutant S. pombe strains

ChIP-seq experiments on S. pombe growing in rich media for

• Histone 3 (H3)
• RNA Pol2 un-phosphorylated (RNAPII-CTDun)
• RNA Pol2 phosphorylated at Ser2 (RNAPII-CTDS2P), a form prevalent during transcription elongation
• Fft2 and Fft3 two paralogues of Fun30, a chromatin remodeller
• Ino80, the name-giving component of a chromatin-remodelling complex
• Snf21 a part of the chromatin remodelling complex RSC
• Spt-16 a part of the histone-chaperone FACT (FAcilitates Chromatin Transcription) complex.

These factors were asseyed in wild type (WT) cells, in sevral mutants (see "Notes on samples") and examinated under three growing conditions 22C, 33C, 37C.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 18-8-2017

From S. pombe (Aug 2015 ASM294v2/spo2).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM2210714.sga	fft2-5xFLAG|Fft2-FLAG|30C|rep1	Fft2	GSM2210714
2	GSM2210715.sga	fft2-5xFLAG|Fft2-FLAG|30C|rep2	Fft2	GSM2210715
3	GSM2210716.sga	fft3-5xFLAG|Fft2-FLAG|30C|rep1	Fft2	GSM2210716
4	GSM2210717.sga	fft3-5xFLAG|Fft2-FLAG|30C|rep2	Fft2	GSM2210717
5	GSM2210767.sga	H3H4DD|H3|22C|rep1	H3	GSM2210767
6	GSM2210768.sga	H3H4DD|H3|22C|rep2	H3	GSM2210768
7	GSM2210751.sga	H3H4DD|RNAPII-CTDS2P|22C|rep1	RNAPII-CTDS2P	GSM2210751
8	GSM2210752.sga	H3H4DD|RNAPII-CTDS2P|22C|rep2	RNAPII-CTDS2P	GSM2210752
9	GSM2210759.sga	H3H4DD|RNAPII-CTDun|22C|rep1	RNAPII-CTDun	GSM2210759
10	GSM2210760.sga	H3H4DD|RNAPII-CTDun|22C|rep2	RNAPII-CTDun	GSM2210760
11	GSM2210718.sga	ino80-5xFLAG|Ino80-FLAG|30C|rep1	Ino80	GSM2210718
12	GSM2210719.sga	ino80-5xFLAG|Ino80-FLAG|30C|rep2	Ino80	GSM2210719
13	GSM2210720.sga	snf21-5xFLAG|Snf21-FLAG|30C|rep1	Snf21	GSM2210720
14	GSM2210721.sga	snf21-5xFLAG|Snf21-FLAG|30C|rep2	Snf21	GSM2210721
15	GSM2210694.sga	spt16-18|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210694
16	GSM2210695.sga	spt16-18|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210695
17	GSM2210710.sga	spt16-18|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210710
18	GSM2210711.sga	spt16-18|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210711
19	GSM2210723.sga	spt16-GFP|Spt16-GFP|30C|rep1	Spt16	GSM2210723
20	GSM2210724.sga	spt16-GFP|Spt16-GFP|30C|rep2	Spt16	GSM2210724
21	GSM2210763.sga	WT|H3|22C|rep1	H3	GSM2210763
22	GSM2210764.sga	WT|H3|22C|rep2	H3	GSM2210764
23	GSM2210741.sga	WT|H3|37C|rep1	H3	GSM2210741
24	GSM2210742.sga	WT|H3|37C|rep2	H3	GSM2210742
25	GSM2210747.sga	WT|RNAPII-CTDS2P|22C|rep1	RNAPII-CTDS2P	GSM2210747
26	GSM2210748.sga	WT|RNAPII-CTDS2P|22C|rep2	RNAPII-CTDS2P	GSM2210748
27	GSM2210660.sga	WT|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210660
28	GSM2210661.sga	WT|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210661
29	GSM2210725.sga	fft3Dxspt16-1|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210725
30	GSM2210726.sga	fft3Dxspt16-1|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210726
31	GSM2432124.sga	fft2Dfft3D|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2432124
32	GSM2432125.sga	fft2Dfft3D|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2432125
33	GSM2210686.sga	WT|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210686
34	GSM2210687.sga	WT|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210687
35	GSM2210755.sga	WT|RNAPII-CTDun|22C|rep1	RNAPII-CTDun	GSM2210755
36	GSM2210756.sga	WT|RNAPII-CTDun|22C|rep2	RNAPII-CTDun	GSM2210756
37	GSM2210670.sga	WT|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210670
38	GSM2210671.sga	WT|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210671
39	GSM2210733.sga	fft3Dxspt16-1|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210733
40	GSM2210734.sga	fft3Dxspt16-1|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210734
41	GSM2432126.sga	fft2Dfft3D|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2432126
42	GSM2432127.sga	fft2Dfft3D|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2432127
43	GSM2210702.sga	WT|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210702
44	GSM2210703.sga	WT|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210703
45	GSM2210773.sga	WT|input|22C	input	GSM2210773
46	GSM2210771.sga	WT|input|30C|rep1	input	GSM2210771
47	GSM2210772.sga	WT|input|30C|rep2	input	GSM2210772
48	GSM2210774.sga	WT|input|37C|rep1	input	GSM2210774
49	GSM2210775.sga	WT|input|37C|rep2	input	GSM2210775
50	GSM2210662.sga	fft1D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210662
51	GSM2210663.sga	fft1D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210663
52	GSM2210672.sga	fft1D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210672
53	GSM2210673.sga	fft1D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210673
54	GSM2210668.sga	fft2Dfft3D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210668
55	GSM2210669.sga	fft2Dfft3D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210669
56	GSM2432121.sga	fft2Dfft3D|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2432121
57	GSM2432122.sga	fft2Dfft3D|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2432122
58	GSM2210678.sga	fft2Dfft3D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210678
59	GSM2210679.sga	fft2Dfft3D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210679
60	GSM2432123.sga	fft2Dfft3D|RNAPII-CTDun|37C	RNAPII-CTDun	GSM2432123
61	GSM2210664.sga	fft2D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210664
62	GSM2210665.sga	fft2D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210665
63	GSM2210674.sga	fft2D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210674
64	GSM2210675.sga	fft2D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210675
65	GSM2210769.sga	fft3DH3H4DD|H3|22C|rep1	H3	GSM2210769
66	GSM2210770.sga	fft3DH3H4DD|H3|22C|rep2	H3	GSM2210770
67	GSM2210753.sga	fft3DH3H4DD|RNAPII-CTDS2P|22C|rep1	RNAPII-CTDS2P	GSM2210753
68	GSM2210754.sga	fft3DH3H4DD|RNAPII-CTDS2P|22C|rep2	RNAPII-CTDS2P	GSM2210754
69	GSM2210761.sga	fft3DH3H4DD|RNAPII-CTDun|22C|rep1	RNAPII-CTDun	GSM2210761
70	GSM2210762.sga	fft3DH3H4DD|RNAPII-CTDun|22C|rep2	RNAPII-CTDun	GSM2210762
71	GSM2210731.sga	fft3Dspt16-1|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210731
72	GSM2210732.sga	fft3Dspt16-1|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210732
73	GSM2210739.sga	fft3Dspt16-1|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210739
74	GSM2210740.sga	fft3Dspt16-1|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210740
75	GSM2210765.sga	fft3D|H3|22C|rep1	H3	GSM2210765
76	GSM2210766.sga	fft3D|H3|22C|rep2	H3	GSM2210766
77	GSM2210743.sga	fft3D|H3|37C|rep1	H3	GSM2210743
78	GSM2210744.sga	fft3D|H3|37C|rep2	H3	GSM2210744
79	GSM2210749.sga	fft3D|RNAPII-CTDS2P|22C|rep1	RNAPII-CTDS2P	GSM2210749
80	GSM2210750.sga	fft3D|RNAPII-CTDS2P|22C|rep2	RNAPII-CTDS2P	GSM2210750
81	GSM2210666.sga	fft3D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210666
82	GSM2210667.sga	fft3D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210667
83	GSM2210727.sga	fft3D|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210727
84	GSM2210728.sga	fft3D|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210728
85	GSM2210757.sga	fft3D|RNAPII-CTDun|22C|rep1	RNAPII-CTDun	GSM2210757
86	GSM2210758.sga	fft3D|RNAPII-CTDun|22C|rep2	RNAPII-CTDun	GSM2210758
87	GSM2210676.sga	fft3D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210676
88	GSM2210677.sga	fft3D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210677
89	GSM2210735.sga	fft3D|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210735
90	GSM2210736.sga	fft3D|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210736
91	GSM2210680.sga	hrp1D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210680
92	GSM2210681.sga	hrp1D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210681
93	GSM2210696.sga	hrp1D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210696
94	GSM2210697.sga	hrp1D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210697
95	GSM2210682.sga	hrp3D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210682
96	GSM2210683.sga	hrp3D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210683
97	GSM2210698.sga	hrp3D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210698
98	GSM2210699.sga	hrp3D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210699
99	GSM2210684.sga	ies6D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210684
100	GSM2210685.sga	ies6D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210685
101	GSM2210700.sga	ies6D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210700
102	GSM2210701.sga	ies6D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210701
103	GSM2210712.sga	WT|FLAG|30C mock|rep1	mock	GSM2210712
104	GSM2210713.sga	WT|FLAG|30C mock|rep2	mock	GSM2210713
105	GSM2210722.sga	WT|IgG|30C mock	IgG	GSM2210722
106	GSM2210688.sga	snf21-36|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210688
107	GSM2210689.sga	snf21-36|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210689
108	GSM2210704.sga	snf21-36|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210704
109	GSM2210705.sga	snf21-36|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210705
110	GSM2210690.sga	snf22D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210690
111	GSM2210691.sga	snf22D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210691
112	GSM2210706.sga	snf22D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210706
113	GSM2210707.sga	snf22D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210707
114	GSM2210745.sga	spt16-18|H3|37C|rep1	H3	GSM2210745
115	GSM2210746.sga	spt16-18|H3|37C|rep2	H3	GSM2210746
116	GSM2210729.sga	spt16-1|RNAPII-CTDS2P|37C|rep1	RNAPII-CTDS2P	GSM2210729
117	GSM2210730.sga	spt16-1|RNAPII-CTDS2P|37C|rep2	RNAPII-CTDS2P	GSM2210730
118	GSM2210737.sga	spt16-1|RNAPII-CTDun|37C|rep1	RNAPII-CTDun	GSM2210737
119	GSM2210738.sga	spt16-1|RNAPII-CTDun|37C|rep2	RNAPII-CTDun	GSM2210738
120	GSM2210692.sga	swr1D|RNAPII-CTDS2P|30C|rep1	RNAPII-CTDS2P	GSM2210692
121	GSM2210693.sga	swr1D|RNAPII-CTDS2P|30C|rep2	RNAPII-CTDS2P	GSM2210693
122	GSM2210708.sga	swr1D|RNAPII-CTDun|30C|rep1	RNAPII-CTDun	GSM2210708
123	GSM2210709.sga	swr1D|RNAPII-CTDun|30C|rep2	RNAPII-CTDun	GSM2210709

Notes on samples:

Sevral mutants were used for this study:

• fft1D, fft2D and fft3D deletion mutants of fft1, fft2 and fft3
• fft2Dfft3D double mutant of fft2 and fft3
• spt16-1 temperature-sensitive mutant of spt16
• spt16-18 mutant of spt16
• H3H4DD double mutant of H3 and H4
• fft3DH3H4DD triple mutant of fft3, H3 and H4
• fft3Dxspt16-1 combined mutant of fft3 and spt16
• hrp1D and hrp3D deletion mutants of hrp1 and hrp3, parts of the CHD major chromatin-remodelling complex
• ies6D deletion mutant of ies6, part of the Ino80 complex
• snf21-36 deletion mutant, part of the RSC complex
• snf22D deletion mutant of snf22, part of the SWI/SNF chromatin-remodelling complex
• swr1D deletion mutant of swr1, part of the SWR1 chromatin-remodelling complex

GFP- (green fluorescent protein) and FLAG-tags were added to proteins when specific antibodies against the target proteins were not available.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 v2.2.9. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Lee J, Choi ES, Seo HD, Kang K, Gilmore JM, Florens L, Washburn MP, Choe J, Workman JL, Lee D
  Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation. Nat Commun. 2017 Feb 20;8:14527. doi: 10.1038/ncomms14527. 28218250
• GEO series GSE83600: Chromatin remodeler Fun30-Fft3 disassembles nucleosomes to facilitate RNAPII elongation in fission yeast