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Genome wide chromatin profiling in C. elegans

experiment: Genome wide chromatin profiling in C. elegans project: Histone Variants PI: Steven Henikoff Labs: Steven Henikoff
We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated C. elegans chromatin. Chromatin fractions extracted with 80 mM or 350 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 8 tracks I II III IV V X
All entries in public repositories generated by this experiment
There are 8 ChIP-chip submissions for this experiment:
DCC id Name developmental stage biochemical fraction extraction time sodium chloride concentration strain Embargoed until Features, GBrowse and Data Files
modENCODE_2533

600 mM Embryonic Salt Extracted Chromatin Pellet Mixed Stage Embryos [ALL]
precipitate [ALL]
18 hours [ALL]
600 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: 600mM_Pellet
GEO: GSM468571
GEO: GSM468573


6 files Download data files
modENCODE_2532

600 mM Embryonic Salt Extracted Chromatin Mixed Stage Embryos [ALL]
soluble fraction [ALL]
2 hours [ALL]
600 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: 600mM_fraction
GEO: GSM468562
GEO: GSM468570


6 files Download data files
modENCODE_2534

H3.3 80 mM Salt Extracted Chromatin Mixed Stage Embryos [ALL]
soluble fraction [ALL]
2 hours [ALL]
80 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: 80mM_fraction
GEO: GSM468564
GEO: GSM468569


6 files Download data files
modENCODE_2535

H3.3 350 mM Salt Extracted Chromatin Mixed Stage Embryos [ALL]
soluble fraction [ALL]
1 - 4 hours [ALL]
350 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: 350mM_fraction
GEO: GSM468560
GEO: GSM468576


6 files Download data files
modENCODE_2536

H3.3 600 mM Salt Extracted Chromatin Mixed Stage Embryos [ALL]
soluble fraction [ALL]
18 hours [ALL]
600 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: 600mM_fraction
GEO: GSM468563
GEO: GSM468572


6 files Download data files
modENCODE_2538

Adult Mononucleosomes Young Adult [ALL]
soluble fraction [ALL]
1 - 4 hours [ALL]
80 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: Adt_Mononucleosomes
GEO: GSM468565
GEO: GSM468566
GEO: GSM468567


9 files Download data files
modENCODE_2531

80 mM Embryonic Salt Extracted Chromatin Mixed Stage Embryos [ALL]
soluble fraction [ALL]
18 hours [ALL]
80 mMs [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: 80mM_fraction
GEO: GSM468561
GEO: GSM468568


6 files Download data files
modENCODE_5326

ChIP-chip C. elegans JJ2061 Embryonic mononucleosomes chromatin profile Mixed Stage Embryos [ALL]
JJ2061 [ALL] / his-72
embargo expired
GBrowse tracks: Embryo_Mononucleosomes
GEO: GSM468574
GEO: GSM468575
GEO: GSM468577


9 files Download data files