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Genome-wide Chromatin Profiling

experiment: Genome-wide Chromatin Profiling project: Histone Variants PI: Steven Henikoff Labs: Kamran Ahmad, Steven Henikoff
We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical ??active?? chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics.

NO FEATURES GENERATED BY THIS EXPERIMENT All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All entries in public repositories generated by this experiment
There are 32 ChIP-chip submissions for this experiment:
DCC id Name developmental stage biochemical fraction cell line extraction time sodium chloride concentration Embargoed until Features, GBrowse and Data Files
modENCODE_2518

80 mM Salt Extracted Chromatin H2A soluble fraction [ALL]
S2-Mt-Bio-H2A [ALL]
1 - 2 hours [ALL]
80 mMs [ALL]
embargo expired
GBrowse tracks: 80mM_fraction_H2A
GEO: GSM333846
GEO: GSM333847


6 files Download data files
modENCODE_2519

80 mM Salt Extracted Chromatin H2Av soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1 - 2 hours [ALL]
80 mMs [ALL]
embargo expired
GBrowse tracks: 80mM_fraction_H2Av
GEO: GSM333851
GEO: GSM333858
GEO: GSM333863


9 files Download data files
modENCODE_2520

80 mM Salt Extracted Chromatin H3.3 soluble fraction [ALL]
S2-Mt-Bio-H3.3 [ALL]
1 - 2 hours [ALL]
80 mMs [ALL]
embargo expired
GBrowse tracks: 80mM_fraction_H3.3
GEO: GSM333850
GEO: GSM333853
GEO: GSM333855


9 files Download data files
modENCODE_2515

Fly wing disc 600 mM Salt Extracted Chromatin soluble fraction [ALL]
ML-DmD16-c3 [ALL]
1-2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_fraction_wing_disc
GEO: GSM624877
GEO: GSM624878


6 files Download data files
modENCODE_2516

Fly wing disc 600 mM Salt Extracted Chromatin Pellet precipitate [ALL]
ML-DmD16-c3 [ALL]
1-2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_pellet_wing_disc
GEO: GSM624879
GEO: GSM624880


6 files Download data files
modENCODE_2517

80 mM Salt Extracted Chromatin S2 soluble fraction [ALL]
S2-DRSC [ALL]
1 - 2 hours [ALL]
80 mMs [ALL]
embargo expired
GBrowse tracks: 80mM_fraction_S2
GEO: GSM387595
GEO: GSM387600


6 files Download data files
modENCODE_2502

600 mM Salt Extracted Chromatin Pellet precipitate [ALL]
S2-Mt-Bio-H2Av [ALL]
1 - 2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_pellet
GEO: GSM333864
GEO: GSM333866
GEO: GSM333867
GEO: GSM387598


12 files Download data files
modENCODE_2522

80-150 mM Salt Extracted Chromatin S2 soluble fraction [ALL]
S2-DRSC [ALL]
3 hours [ALL]
80-150 mMs [ALL]
embargo expired
GBrowse tracks: 80-150mM_fraction_S2
GEO: GSM387593


3 files Download data files
modENCODE_2505

H2A EDTA soluble fraction [ALL]
S2-Mt-Bio-H2A [ALL]
1-2 hours [ALL]
15 mMs [ALL]
embargo expired
GBrowse tracks: Henikoff_VARS
GEO: GSM333848
GEO: GSM387596
GEO: GSM391380


9 files Download data files
modENCODE_2523

80-600 mM Salt Extracted Chromatin H3.3 soluble fraction [ALL]
S2-Mt-Bio-H3.3 [ALL]
1 - 2 hours [ALL]
80-600 mMs [ALL]
embargo expired
GBrowse tracks: 80-600mM_fraction_H3.3
GEO: GSM333852
GEO: GSM333854


6 files Download data files
modENCODE_2504

H2Av EDTA soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1-2 hours [ALL]
15 mMs [ALL]
embargo expired
GBrowse tracks: Henikoff_VARS
GEO: GSM333849
GEO: GSM387597
GEO: GSM391381


9 files Download data files
modENCODE_2521

80-150 mM Salt Extracted Chromatin H2Av soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
4.5 hours [ALL]
1.5 hours [ALL]
80-150 mMs [ALL]
embargo expired
GBrowse tracks: 80-150mM_fraction_H2Av
GEO: GSM333859
GEO: GSM333861


6 files Download data files
modENCODE_2503

150 mM Salt Extracted Chromatin soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1-2 hours [ALL]
150 mMs [ALL]
embargo expired
GBrowse tracks: 150mM_fraction
GEO: GSM333836
GEO: GSM333839
GEO: GSM333843


9 files Download data files
modENCODE_2757

Kc 600 mM Salt Extracted Chromatin Pellet precipitate [ALL]
Kc167 [ALL]
1 to 2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: Kc_600_mM_Salt_Extracted_Chromatin_Pellet
GEO: GSM624883
GEO: GSM624884


6 files Download data files
modENCODE_2527

150-600 mM Salt Extracted Chromatin S2 soluble fraction [ALL]
S2-DRSC [ALL]
1 - 2 hours [ALL]
150-600 mMs [ALL]
embargo expired
GBrowse tracks: 150-600mM_fraction_S2
GEO: GSM387594


3 files Download data files
modENCODE_2510

Fly embryos 4-6 hr 150 mM Salt Extracted Chromatin Embryo 1-3 h [ALL]
Embryo 4-6 h [ALL]
soluble fraction [ALL]
1-2 hours [ALL]
150 mMs [ALL]
embargo expired
GBrowse tracks: 150mM_fraction_Emb_4-6hr
GEO: GSM624866
GEO: GSM624867


6 files Download data files
modENCODE_2509

Fly embryos 1-3 hr 600 mM Salt Extracted Chromatin Pellet Embryo 1-3 h [ALL]
precipitate [ALL]
1-2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_pellet_Emb_1-3hr
GEO: GSM624864
GEO: GSM624865


6 files Download data files
modENCODE_2529

Mononucleosomes H2Av soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1 - 2 hours [ALL]
15 mMs [ALL]
embargo expired
GBrowse tracks: Mononucleosomes_H2Av
GEO: GSM333841


3 files Download data files
modENCODE_2508

Fly embryos 1-3 hr 600 mM Salt Extracted Chromatin Embryo 1-3 h [ALL]
soluble fraction [ALL]
1-2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_fraction_Emb_1-3hr
GEO: GSM624862
GEO: GSM624863


6 files Download data files
modENCODE_2528

Mononucleosomes H3.3 soluble fraction [ALL]
S2-Mt-Bio-H3.3 [ALL]
1 - 2 hours [ALL]
15 mMs [ALL]
embargo expired
GBrowse tracks: Mononucleosomes_H3.3
GEO: GSM333837


3 files Download data files
modENCODE_2525

150-600 mM Salt Extracted Chromatin H2Av soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1 - 2 hours [ALL]
150-600 mMs [ALL]
embargo expired
GBrowse tracks: 150-600mM_fraction_H2Av
GEO: GSM333832
GEO: GSM333838
GEO: GSM333842


9 files Download data files
modENCODE_2759

Kc H2Av Knockdown 600 mM Salt Extracted Chromatin soluble fraction [ALL]
Kc167 [ALL]
1 to 2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin
GEO: GSM624887
GEO: GSM624888


6 files Download data files
modENCODE_2507

Fly embryos 1-3 hr 150 mM Salt Extracted Chromatin Embryo 1-3 h [ALL]
soluble fraction [ALL]
1-2 hours [ALL]
150 mMs [ALL]
embargo expired
GBrowse tracks: 150mM_fraction_Emb_1-3hr
GEO: GSM624859
GEO: GSM624860
GEO: GSM624861


9 files Download data files
modENCODE_2524

80-600 mM Salt Extracted Chromatin H2Av soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1 - 2 hours [ALL]
80-600 mMs [ALL]
embargo expired
GBrowse tracks: 80-600mM_fraction_H2Av
GEO: GSM333856


3 files Download data files
modENCODE_2506

Nucleosome Density S2 soluble fraction [ALL]
S2-Mt-Bio-H2Av [ALL]
1-2 hours [ALL]
15 mMs [ALL]
embargo expired
GBrowse tracks: Nucleosome_Density_S2
GEO: GSM333835
GEO: GSM333840
GEO: GSM333844


9 files Download data files
modENCODE_2526

150-600 mM Salt Extracted Chromatin H3.3 soluble fraction [ALL]
S2-Mt-Bio-H3 [ALL]
1 - 2 hours [ALL]
150-600 mMs [ALL]
embargo expired
GBrowse tracks: 150-600mM_fraction_H3.3
GEO: GSM333834


3 files Download data files
modENCODE_2760

Kc H2Av Knockdown 600 mM Salt Extracted Chromatin Pellet precipitate [ALL]
Kc167 [ALL]
1 to 2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin_Pellet
GEO: GSM624889
GEO: GSM624890


6 files Download data files
modENCODE_2514

Fly wing disc 150 mM Salt Extracted Chromatin soluble fraction [ALL]
ML-DmD16-c3 [ALL]
1-2 hours [ALL]
150 mMs [ALL]
embargo expired
GBrowse tracks: 150mM_fraction_wing_disc
GEO: GSM624875
GEO: GSM624876


6 files Download data files
modENCODE_2513

Fly wing disc 80 mM Salt Extracted Chromatin soluble fraction [ALL]
ML-DmD16-c3 [ALL]
1-2 hours [ALL]
80 mMs [ALL]
embargo expired
GBrowse tracks: 80mM_fraction_wing_disc
GEO: GSM624873
GEO: GSM624874


6 files Download data files
modENCODE_2512

Fly embryos 4-6 hr 600 mM Salt Extracted Chromatin Pellet Embryo 1-3 h [ALL]
Embryo 4-6 h [ALL]
precipitate [ALL]
1-2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_Pellet_Emb_4-6hr
GEO: GSM624870
GEO: GSM624871
GEO: GSM624872


9 files Download data files
modENCODE_2756

Kc 600 mM Salt Extracted Chromatin soluble fraction [ALL]
Kc167 [ALL]
1 to 2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: Kc_600_mM_Salt_Extracted_Chromatin
GEO: GSM624881
GEO: GSM624882


6 files Download data files
modENCODE_2511

Fly embryos 4-6 hr 600 mM Salt Extracted Chromatin Embryo 1-3 h [ALL]
Embryo 4-6 h [ALL]
soluble fraction [ALL]
1-2 hours [ALL]
600 mMs [ALL]
embargo expired
GBrowse tracks: 600mM_fraction_Emb_4-6hr
GEO: GSM624868
GEO: GSM624869


6 files Download data files