Choi 2017, The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3.

Genomic maps of histone H3 and centromere histon CENP-A (H3 variant) along with maps of some subunits of the Ino80 chromatin remodelling factor in wild type and mutant S. pombe strains.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 16-10-2017

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM2648234.sga	wt|Iec1-Flag|30C|rep2	Iec1-Flag	GSM2648234
2	GSM2648233.sga	wt|Iec1-Flag|30C|rep1	Iec1-Flag	GSM2648233
3	GSM2648232.sga	wt|notag|30C|rep2	notag	GSM2648232
4	GSM2648231.sga	wt|notag|30C|rep1	notag	GSM2648231
5	GSM2648230.sga	wt|Ies6-Flag|30C|rep2	Ies6-Flag	GSM2648230
6	GSM2648229.sga	wt|Ies6-Flag|30C|rep1	Ies6-Flag	GSM2648229
7	GSM2648228.sga	cnp1-1|Iec1-Flag|36C|rep2	Iec1-Flag	GSM2648228
8	GSM2648227.sga	cnp1-1|Iec1-Flag|36C|rep1	Iec1-Flag	GSM2648227
9	GSM2648226.sga	cnp1-1|notag|36C|rep2	notag	GSM2648226
10	GSM2648225.sga	cnp1-1|notag|36C|rep1	notag	GSM2648225
11	GSM2648224.sga	cnp1-1|Ies6-Flag|36C|rep2	Ies6-Flag	GSM2648224
12	GSM2648223.sga	cnp1-1|Ies6-Flag|36C|rep1	Ies6-Flag	GSM2648223
13	GSM2648222.sga	wt|Iec1-Flag|36C|rep2	Iec1-Flag	GSM2648222
14	GSM2648221.sga	wt|Iec1-Flag|36C|rep1	Iec1-Flag	GSM2648221
15	GSM2648220.sga	wt|notag|36C|rep2	notag	GSM2648220
16	GSM2648219.sga	wt|notag|36C|rep1	notag	GSM2648219
17	GSM2648218.sga	wt|Ies6-Flag|36C|rep2	Ies6-Flag	GSM2648218
18	GSM2648217.sga	wt|Ies6-Flag|36C|rep1	Ies6-Flag	GSM2648217
19	GSM2648216.sga	hrp1D|input|30C|rep2	input	GSM2648216
20	GSM2648215.sga	hrp1D|input|30C|rep1	input	GSM2648215
21	GSM2648214.sga	hrp1D|H3|30C|rep2	H3	GSM2648214
22	GSM2648213.sga	hrp1D|H3|30C|rep1	H3	GSM2648213
23	GSM2648212.sga	wt|input|30C|rep2	input	GSM2648212
24	GSM2648211.sga	wt|input|30C|rep1	input	GSM2648211
25	GSM2648210.sga	ies6D|input|30C|rep2	input	GSM2648210
26	GSM2648209.sga	ies6D|input|30C|rep1	input	GSM2648209
27	GSM2648208.sga	wt|H3|30C|rep2	H3	GSM2648208
28	GSM2648207.sga	wt|H3|30C|rep1	H3	GSM2648207
29	GSM2648206.sga	ies6D|H3|30C|rep2	H3	GSM2648206
30	GSM2648205.sga	ies6D|H3|30C|rep1	H3	GSM2648205
31	GSM2648204.sga	tel1R-neocen|notag|30C|rep2	notag	GSM2648204
32	GSM2648203.sga	tel1R-neocen|notag|30C|rep1	notag	GSM2648203
33	GSM2648202.sga	tel1R-neocen|Ies6-Flag|30C|rep2	Ies6-Flag	GSM2648202
34	GSM2648201.sga	tel1R-neocen|Ies6-Flag|30C|rep1	Ies6-Flag	GSM2648201
35	GSM2648200.sga	wt|notag|30C|rep2	notag	GSM2648200
36	GSM2648199.sga	wt|notag|30C|rep1	notag	GSM2648199
37	GSM2648198.sga	wt|Ies6-Flag|30C|rep2	Ies6-Flag	GSM2648198
38	GSM2648197.sga	wt|Ies6-Flag|30C|rep1	Ies6-Flag	GSM2648197
39	GSM2648196.sga	tel1R-neocen|H3|30C|rep2	H3	GSM2648196
40	GSM2648195.sga	tel1R-neocen|H3|30C|rep1	H3	GSM2648195
41	GSM2648194.sga	tel1R-neocen|input|30C|rep2	input	GSM2648194
42	GSM2648193.sga	tel1R-neocen|input|30C|rep1	input	GSM2648193
43	GSM2648192.sga	tel1R-neocen|Cnp1|30C|rep2	Cnp1	GSM2648192
44	GSM2648191.sga	tel1R-neocen|Cnp1|30C|rep1	Cnp1	GSM2648191
45	GSM2648190.sga	mis18-262|input|36C|rep2	input	GSM2648190
46	GSM2648189.sga	mis18-262|input|36C|rep1	input	GSM2648189
47	GSM2648188.sga	mis18-262|Cnp1|36C|rep2	Cnp1	GSM2648188
48	GSM2648187.sga	mis18-262|Cnp1|36C|rep1	Cnp1	GSM2648187
49	GSM2648186.sga	wt|input|36C|rep2	input	GSM2648186
50	GSM2648185.sga	wt|input|36C|rep1	input	GSM2648185
51	GSM2648184.sga	wt|Cnp1|36C|rep2	Cnp1	GSM2648184
52	GSM2648183.sga	wt|Cnp1|36C|rep1	Cnp1	GSM2648183
53	GSM2648182.sga	TetR-Flag-Iec1|H3|AHT-30C|rep2	H3	GSM2648182
54	GSM2648181.sga	TetR-Flag-Iec1|H3|AHT-30C|rep1	H3	GSM2648181
55	GSM2648180.sga	TetR-Flag-Iec1|H3|30C|rep2	H3	GSM2648180
56	GSM2648179.sga	TetR-Flag-Iec1|H3|30C|rep1	H3	GSM2648179
57	GSM2648178.sga	TetR-Flag|H3|30C|rep2	H3	GSM2648178
58	GSM2648177.sga	TetR-Flag|H3|30C|rep1	H3	GSM2648177
59	GSM2648176.sga	TetR-Flag-Iec1|input|AHT-30C|rep2	input	GSM2648176
60	GSM2648175.sga	TetR-Flag-Iec1|input|AHT-30C|rep1	input	GSM2648175
61	GSM2648174.sga	TetR-Flag-Iec1|Cnp1|AHT-30C|rep2	Cnp1	GSM2648174
62	GSM2648173.sga	TetR-Flag-Iec1|Cnp1|AHT-30C|rep1	Cnp1	GSM2648173
63	GSM2648172.sga	TetR-Flag-Iec1|input|30C|rep2	input	GSM2648172
64	GSM2648171.sga	TetR-Flag-Iec1|input|30C|rep1	input	GSM2648171
65	GSM2648170.sga	TetR-Flag-Iec1|Cnp1|30C|rep2	Cnp1	GSM2648170
66	GSM2648169.sga	TetR-Flag-Iec1|Cnp1|30C|rep1	Cnp1	GSM2648169
67	GSM2648168.sga	TetR-Flag|input|30C|rep2	input	GSM2648168
68	GSM2648167.sga	TetR-Flag|input|30C|rep1	input	GSM2648167
69	GSM2648166.sga	TetR-Flag|Cnp1|30C|rep2	Cnp1	GSM2648166
70	GSM2648165.sga	TetR-Flag|Cnp1|30C|rep1	Cnp1	GSM2648165
71	GSM2648164.sga	ino80-11|input|20C|rep2	input	GSM2648164
72	GSM2648163.sga	ino80-11|input|20C|rep1	input	GSM2648163
73	GSM2648162.sga	ino80-11|Cnp1|20C|rep2	Cnp1	GSM2648162
74	GSM2648161.sga	ino80-11|Cnp1|20C|rep1	Cnp1	GSM2648161
75	GSM2648160.sga	hrp1D|input|20C|rep2	input	GSM2648160
76	GSM2648159.sga	hrp1D|input|20C|rep1	input	GSM2648159
77	GSM2648158.sga	hrp1D|Cnp1|20C|rep2	Cnp1	GSM2648158
78	GSM2648157.sga	hrp1D|Cnp1|20C|rep1	Cnp1	GSM2648157
79	GSM2648156.sga	ino80-11|input|20C|rep2	input	GSM2648156
80	GSM2648155.sga	ino80-11|input|20C|rep1	input	GSM2648155
81	GSM2648154.sga	ino80-11|Cnp1|20C|rep2	Cnp1	GSM2648154
82	GSM2648153.sga	ino80-11|Cnp1|20C|rep1	Cnp1	GSM2648153
83	GSM2648152.sga	wt|input|20C|rep2	input	GSM2648152
84	GSM2648151.sga	wt|input|20C|rep1	input	GSM2648151
85	GSM2648150.sga	wt|Cnp1|20C|rep2	Cnp1	GSM2648150
86	GSM2648149.sga	wt|Cnp1|20C|rep1	Cnp1	GSM2648149
87	GSM2648148.sga	hrp1D|input|30C|rep2	input	GSM2648148
88	GSM2648147.sga	hrp1D|input|30C|rep1	input	GSM2648147
89	GSM2648146.sga	hrp1D|Cnp1|30C|rep2	Cnp1	GSM2648146
90	GSM2648145.sga	hrp1D|Cnp1|30C|rep1	Cnp1	GSM2648145
91	GSM2648144.sga	ies6D|input|30C|rep2	input	GSM2648144
92	GSM2648143.sga	ies6D|input|30C|rep1	input	GSM2648143
93	GSM2648142.sga	ies6D|Cnp1|30C|rep2	Cnp1	GSM2648142
94	GSM2648141.sga	ies6D|Cnp1|30C|rep1	Cnp1	GSM2648141
95	GSM2648140.sga	wt|input|30C|rep2	input	GSM2648140
96	GSM2648139.sga	wt|input|30C|rep1	input	GSM2648139
97	GSM2648138.sga	wt|Cnp1|30C|rep2	Cnp1	GSM2648138
98	GSM2648137.sga	wt|Cnp1|30C|rep1	Cnp1	GSM2648137

Notes on samples nomenclature:

The ChIP-seq targets are the following:

• H3: hisone H3
• Cnp1: centromere H3 variant CENP-A
• Iec1: subunit Iec1 of the Ino80 complex
• Ies6: subunit Ies6 of the Ino80 complex

For the following mutants:

• wt: Wild Type strain
• cnp1-1: mutant of CENP-A
• ino80-11: cold-sensitive silencing-defective mutant of Ino80
• hrp1D: mutant of the chromatin-remodeling factor Chd1
• ies6D: mutant of the Ies6 subunit of the Ino80 complex
• tel1R-neocen: mutant that carries an ectopic centromere assembled at a non-centromeric region near the right telomere of chromosome 1
• mis18-262: Ino80 mutation that disrupts kinetochore assembly
• TetR-Flag: tethered control
• TetR-Flag-Iec1: tethered Iec1 to tetO sites in a 4.5 kb non-centromeric DNA

And conditions / treatments:

• 30C
• 36C
• AHT: anhydrotetracycline

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. 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).

• Choi ES, Cheon Y, Kang K, Lee D
  The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3. Nat Commun. 2017 Sep 13;8(1):529. doi: 10.1038/s41467-017-00704-3. 28904333
• GEO series GSE99589: The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3