Goldberg 2010, Factors controlling histone variant H3.3 localization.


Genome-wide survey of H3.3 localization and of its deposition mechanisms. H3.3 histone variant is encoded by two genes : H3.3A and H3.3B. H3.3B was edited using zing finger nucleases in several ways : i) to add an HA tag to the protein, ii) to turn H3.3 into H3.2 (one of the two H3 canonical variant) and to add an HA tag and iii) to turn H3.3 into H3.1 (one of the two H3 canonical variants) with an H3.3 specific serin residue at position 31 (H3.1S31). H3.1S31, H3.2 and H3.3 occupancy was measured by ChIP-seq targetting the HA tag. under native condition and using crosslinking in three cell lines : in mouse embryonic stem cells (ES), in mouse neuronal progenitors (NCP) and in hybrid ES cells. Additionally, H3K4me1, H3K4me3, H3K27me3, H3K36me3 and RNAPII phosphorylated on serine 5 of its Cterm domain (RNAPII-S5P) occupancies were also measured.



From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM423355.sga ES|c H3.3-HA|H3.3HA H3.3_HA GSM423355
2 GSM423356.sga ES|c H3K36me3|H3.3HA H3K36me3 GSM423356
3 GSM423357.sga ES|c H3K4me1|H3.3HA H3K4me1 GSM423357
4 GSM423358.sga ES|c RNAPII-Ser5P|H3.3HA RNAPII_Ser5p GSM423358
5 GSM423359.sga ES|c H3.2-HA|H3.2HA H3.2_HA GSM423359
6 GSM423360.sga ES|c H3K36me3|H3.2HA H3K36me3 GSM423360
7 GSM423361.sga NCP|c H3.3-HA|H3.3HA H3.3_HA GSM423361
8 GSM423362.sga NCP|c H3K36me3|H3.3HA H3K36me3 GSM423362
9 GSM423363.sga NCP|c H3K4me1|H3.3HA H3K4me1 GSM423363
10 GSM423364.sga NCP|c RNAPII-Ser5P|H3.3HA RNAPII_Ser5p GSM423364
11 GSM423365.sga NCP|c H3.2-H|H3.2HAA H3.2_HA GSM423365
12 GSM423366.sga NCP|c H3K36me3|H3.2HA H3K36me3 GSM423366
13 GSM487538.sga ES-hyb|c input|H3.3HA input GSM487538
14 GSM487539.sga ES-hyb|c H3.3-HA|H3.3HA H3.3_HA GSM487539
15 GSM487540.sga ES-hyb|c H3K36me3|H3.3HA H3K36me3 GSM487540
16 GSM487541.sga ES-hyb|c input|H3.1S31HA input GSM487541
17 GSM487542.sga ES-hyb|c H3.1S31-HA|H3.1S31HA H3.1S31_HA GSM487542
18 GSM487543.sga ES-hyb|c H3K36me3|H3.1S31HA H3K36me3 GSM487543
19 GSM487544.sga ES|n H3.3-HA|H3.3HA H3.3_HA GSM487544
20 GSM487545.sga ES|n H3K4me3|H3.3HA H3K4me3 GSM487545
21 GSM487546.sga ES|n input|H3.3HA input GSM487546
22 GSM487547.sga ES|n H3.2-HA|H3.2HA H3.2_HA GSM487547
23 GSM487548.sga ES|n H3K4me3|H3.2HA H3K4me3 GSM487548
24 GSM487549.sga ES|n H3K27me3|H3.2HA H3K27me3 GSM487549
25 GSM487550.sga ES|n input|H3.2HA input GSM487550
26 GSM487551.sga ES|n H3.3-EYFP|H3.3EYFP H3.3_EYFP GSM487551
27 GSM487552.sga ES|n input|H3.3EYFP input GSM487552
28 GSM487553.sga ES|n H3K4me1|H3.3EYFP H3K4me1 GSM487553
29 GSM487554.sga ES|n H3K36me3|H3.3EYFP H3K36me3 GSM487554
30 GSM487555.sga ES|n H3.3-EYF|H3.3EYFP Hira.nullP H3.3_EYFP GSM487555
31 GSM487556.sga ES|n H3K4me1|H3.3EYFP Hira.null H3K4me1 GSM487556
32 GSM487557.sga ES|n H3K36me3|H3.3EYFP Hira.null H3K36me3 GSM487557
33 GSM487558.sga ES|n input|H3.3EYFP Hira.null input GSM487558
34 GSM487559.sga ES|n H3.3-EYFP|H3.3EYFP Atrx.flox H3.3_EYFP GSM487559
35 GSM487560.sga ES|n input|H3.3EYFP Atrx.flox input GSM487560
36 GSM487561.sga ES|n H3.3-EYFP|H3.3EYFP Atrx.null H3.3_EYFP GSM487561
37 GSM487562.sga ES|n input|H3.3EYFP Atrx.null input GSM487562
38 GSM487563.sga ES|c HA|wildtype HA GSM487563

Notes on samples nomenclature:

H3.1 and H3.2 are the two H3 canonical variants and are often referred to as H3.
The sample description field contains 3 information separated by a '|' character : i) the cell line from which the data were generated, ii) the ChIP-seq condition ('c' for crosslink, 'n' for native) and the ChIP-seq target and iii) the cellular context.
In the cellular context information, 'H3.3HA' means that gene H3.3B was edited to contain an extra HA tag, 'H3.2HA' that the gene was edited to turn H3.3 sequence into an H3.2 sequence followed by an HA tag, 'H3.1S31HA' that the gene was edited to be turned into an H3.1 sequence with a serine at position 31 (H3.3 specific residue) followed by an HA tag, 'Hira.null' that HirA was totally missing in the cells and 'Atrx.flox' and 'Atrx.null' that Atrx was subjected to a target truncation using the Cre-recombinase system.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the mm9 mouse 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 (ChIP-Seq v. 1.5.2).


Last update: 1 Oct 2018