Contributors: David A. Orlando, Mei Wei Chen, Victoria E. Brown, Snehakumari Solanki, Yoon J. Choi, Eric R. Olson, Christian C. Fritz, James E. Bradner, Matthew G. Guenther

Date: 2014-01-01

orange). ChIP-seq signals were calculated based on traditional or Drosophila-reference-normalized... of ChIP-Seq Data (A) Schematic representation of a typical ChIP-seq data...ChIP-Seq Normalization Reveals Global Modulation of the Epigenome...ChIP-seq peaks (blue). A comparison of the peaks as a percentage of the...ChIP-seq in the presence of the reference Drosophila epigenome (orange...ChIP-Seq Data (A) Schematic representation of a typical ChIP-seq data ...ChIP-seq) is a prevailing methodology used to investigate chromatin-based...subjected to ChIP-seq in the presence of the reference Drosophila epigenome...reveals ChIP-seq peaks (blue). A comparison of the peaks as a percentage...ChIP-seq experiments enables the discovery of disease-relevant changes...ChIP-seq signals were calculated based on traditional or Drosophila-reference-normalized...ChIP-seq reads aligning to either test (human, blue) or Drosophila (reference ... Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx) that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.

Contributors: Alexander (Garrett) Garruss, Alexander S Garruss, Hans-Martin Herz, Ali Shilatifard

Date: 2012-12-01

ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq...ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells. ChIP-seq of H3K4me1,...Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax...Drosophila Trithorax-related, the Drosophila homolog of Mll3/Mll4...Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila...Drosophila melanogaster) Organism: Mus musculus Published on 2012-12 ... Accession Number: GSE41440 Platform: GPL13112: Illumina HiSeq 2000 (Mus musculus) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Mus musculus Published on 2012-12-01 Summary: Mono-methylation of histone H3 on lysine 4 (H3K4me1) and acetylation of histone H3 on lysine 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and enhancers. Although in yeast all H3K4 methylation patterns including H3K4me1 are implemented by Set1/COMPASS, there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of mammalian Mll3/4, can function as a major H3K4 mono-methyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac in various tissues. Assays with the cut wing margin enhancer imply a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrates that Trr is required for H3K4me1 and H3K27ac on chromatin signatures that resemble the histone modification patterns described for enhancers. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 mono-methyltransferase Trr, and the H3K27 demethylase, UTX, cooperate to regulate the transition from inactive/poised to active enhancers. Overall Design: ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells. ChIP-seq of H3K4me1, H3K4me3, H3K27ac, H3K27me3 in WT and Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila S2 cells. ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1 and H3K27me3 in MLL1(+/+), MLL1(-/-), MLL3(+/+), and MLL3(-/-) Mouse Embryonic Fibroblasts (MEFs). Contact: Name: Alexander (Garrett) Garruss Organization: Stowers Institute for Medical Research Laboratory: Shilatifard Address: 1000 East 50th Street Kansas CIty Missouri 64110 USA Email: asg@stowers.org Organization: GEO Address: USA

Contributors: David Rossell, Marta Lloret-Llinares, Fernando Azorin

Date: 2012-08-30

Drosophila melanogaster) Organism: Drosophila melanogaster Published...ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster ... Accession Number: GSE27078 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-08-30 Summary: LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where LID is localized and the effects of LID downregulation in the distribution of H3K4me3. Overall Design: Analysis of LID-binding sites in wild type, and of H3K4me3-binding sites in wild type and LID RNAi wing imaginal discs. Contact: Name: David Rossell Organization: IRB Barcelona Address: Baldiri Reixac 10 Barcelona 08028 Spain Email: david.rossell@irbbarcelona.org Organization: GEO Address: USA

Contributors: DCC modENCODE, David MacAlpine, Heather MacAlpine, Matthew Eaton, Joseph Prinz

Date: 2012-02-27

Drosophila ORC2p); Developmental Stage Embryo 4-7h Contact: Name: DCC...ChIP-Seq experiment...CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... Accession Number: GSE36106 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-02-27 Summary: modENCODE_submission_4192 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 4-7h; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); read length (read_length) ; Antibody dORC2 (target is Drosophila ORC2p); Developmental Stage Embryo 4-7h Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA

Contributors: Jian Zhou, Wangjie Yu, Paul E. Hardin

Date: 2015-01-01

Drosophila that can be used to assess protein–DNA-binding rhythms at specific...Drosophila Clock...ChIP-seq. ChIP analysis has revealed the relationship between clock factor...Drosophila...ChIP-seq). ChIP has been widely used in circadian biology to assess rhythmic ... In eukaryotes, the circadian clock controls 24h rhythms in physiology, metabolism, and behavior via cell autonomous transcriptional feedback loops. These feedback loops keep circadian time and control rhythmic outputs by driving rhythms in transcription; thus, it is important to determine when clock transcription factors bind their target sequences in vivo to promote or repress transcription. Interactions between proteins and DNA can be measured in cells, tissue, or whole organisms using a technique called chromatin immunoprecipitation (ChIP). The principle underlying ChIP is that protein is cross-linked to associated chromatin to form a protein–DNA complex, the DNA is then sheared, and the protein of interest is immunoprecipitated. The cross-links are then removed from the antibody–protein–DNA complex, and the associated DNA fragments are purified. The DNA is then used to quantify specific targets by real-time quantitative PCR or to generate libraries for global analysis of protein target sites by high-throughput sequencing (ChIP-seq). ChIP has been widely used in circadian biology to assess rhythmic binding of clock components, RNA polymerase II, and rhythms in chromatin modifications such as histone acetylation and methylation. Here, we present a detailed method for ChIP analysis in Drosophila that can be used to assess protein–DNA-binding rhythms at specific genomic target sites. With minor modifications, this technique can be used to assess protein–DNA-binding rhythms at all target sites via ChIP-seq. ChIP analysis has revealed the relationship between clock factor binding, transcription, and chromatin modifications and promises to reveal circadian transcription networks that control phase and tissue specificity.

Contributors: Georgi K. Marinov, Jie Wang, Dominik Handler, Barbara J. Wold, Zhiping Weng, Gregory J. Hannon, Alexei A. Aravin, Phillip D. Zamore, Julius Brennecke, Katalin Fejes Toth

Date: 2015-03-23

ChIP-seq dataset and high enrichment of H3K9me3 (from Muerdter et al.,...ChIP-seq and background (input) data from Huang et al. showing (1) unique...Piwi ChIP-seq dataset. (B) Strong apparent enrichment over individual ...ChIP-seq enrichment observed over some individual transposable elements...ChIP-seq and input RPM levels over the transposon consensus sequences ...Drosophila. Their study also reported that loss of Piwi causes widespread...ChIP-seq data from Huang et al. (red) and H3K9me3 data from Muerdter et...ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided ... Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors’ genome-wide conclusions.

Contributors: DCC modENCODE, David MacAlpine, Heather MacAlpine, Matthew Eaton, Joseph Prinz

Date: 2012-05-29

Drosophila ORC2p); read length (read_length) Contact: Name: DCC modENCODE...ChIP-Seq experiment...Drosophila melanogaster) Organism: Drosophila melanogaster Published...CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Embryo 0-2h; EXPERIMENTAL ... Accession Number: GSE38293 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-05-29 Summary: modENCODE_submission_3628 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Developmental Stage: Embryo 0-2h; EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-2h; Antibody dORC2 (target is Drosophila ORC2p); read length (read_length) Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA

Contributors: Petr Laktionov, Petr P Laktionov, Olga V Posukh, Daniil A Maksimov, Dmitry E Koryakov, Stepan N Belyakin

Date: 2017-03-30

Drosophila melanogaster. We processed two biological replicates of every...Drosophila spermatogenesis, we studied the effects of comr and can mutations...Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila spermatogenesis [ChIP-Seq]...Drosophila testes by H3K27me3 ChIP-Seq. Overall Design: ChIP-Seq of H3K27me3 ... Accession Number: GSE97127 Platform: GPL16479: Illumina MiSeq (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-03-30 Summary: To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we studied the effects of comr and can mutations on the chromatin of the cells in Drosophila testes by H3K27me3 ChIP-Seq. Overall Design: ChIP-Seq of H3K27me3 histone modification in comr- and can-mutant testes of Drosophila melanogaster. We processed two biological replicates of every sample and corresponding input specimen. Contact: Name: Petr Laktionov Organization: Institute of molecular and cellular biology SD RAS Laboratory: Genomics lab Address: Lavrenitev ave 8/2 Novosibirsk Russia Email: laktionov@mcb.nsc.ru Organization: GEO Address: USA

Contributors: Barbara M Bryant, Brian Egan, Paul Labhart, Chih-Chi Yuan, Feng Zhao, Charlie Hatton, Patrick Trojer

Date: 2016-12-01

Drosophila chromatin into human ChIP samples and added a Drosophila-specific...ChIP-seq spike-in method enables detection of global histone modification...Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila...ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO ...ChIP-seq data and will improve the quantitative comparison of histone ... Accession Number: GSE63494 Platform: GPL16791: Illumina HiSeq 2500 (Homo sapiens) Organism: Homo sapiens Published on 2016-12-01 Summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context. Overall Design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment. Contact: Name: Barbara M Bryant Organization: Constellation Pharmaceuticals Address: 215 First Street Cambridge MA 02142 USA Email: barbara.bryant@constellationpharma.com Phone: 617-714-0561 Organization: GEO Address: USA

Contributors: unknown

Date: 2015-06-12

ChIP-seq workflow and simple bioinformatic processing. Using High-resolution...ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies....X-ChIP-seq achieves single base pair resolution of transcription factor...X-ChIP-seq we determined the genome-wide binding profile of various DNA...ChIP-seq) has problems with poor resolution and newer techniques require ... Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing. Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.