CR Name:
Species:    Tissue or Cell: 

Chromatin Regulator

Alias

CHD1DKFZp686E2337

External Links:

Wiki    GeneCards    NCBI    UniProt

Related histone modifications:

H3K4me3

Introduction

Full name: Chromodomain helicase DNA-binding protein 1 . CHD1 is a chromatin remodeler belonging to the SNF2 family. It contains two chromodomains in its N-terminus, a central helicase-like ATPase motor, and a C-terminal DNA-binding domain that preferentially binds to A/T-rich sequences. CHD1 can assemble, slide, and space nucleosomes in vitro and is required to maintain the pluripotency of embryonic stem cells (1-4).

Function and Interaction

CHD1 is essential for assembling H3.3, a conserved histone variant, into chromatin in vivo, suggesting its involvement in replication-independent nucleosome assembly (5). CHD1 has been shown to interact with the transcription elongation modulator Rtf1 and elongation factors Spt4-Spt5 and Spt16-Pob3, indicating that CHD1 participates in the transcription elongation process (6). CHD1 is thought to bind to trimethylated H3K4 in active genes, rather than bivalent regions (which contain both H3K4me3 and H3K27me3), which is accomplished via a mediator through association with the assembly of an active transcription complex (7-10).

Disease Association

NA

ChIP-Seq data


SpeciesCell lineCell typeTissueDataDownloadSend to CistromeAnalysis FiguresComparisonReference
Homo sapiensK562ErythroblastBone MarrowGSE29611 ,GSM1003575
Click  DownloadClick22955616

ChIP-Seq data of related histone modifications


Products/SubstratesSpeciesCell lineCell typeTissueDataDownload Send to CistromeAnalysis FiguresReference
H3K4me3 Mus musculus MEL Erythroid Progenitor Cell Blood GSE49847 ,GSM1000087 Bed     Big wiggle
Click   Download25409824
H3K4me3 Mus musculus CH12 Lymphoblastoid Blood GSE49847 ,GSM1000114 Bed     Big wiggle
Click   Download25409824
H3K4me3 Homo sapiens H1 Embryonic Stem Cell Embryo GSE41009 ,GSM1006722 Bed     Big wiggle
Click   Download23382218
H3K4me3 Homo sapiens A549 Epithelium Lung GSE42375 ,GSM1038455 Bed     Big wiggle
Click   Download24004852
H3K4me3 Homo sapiens A549 Epithelium Lung GSE42375 ,GSM1038456 Bed     Big wiggle
Click   Download24004852
H3K4me3 Homo sapiens IMR90 Fibroblast Lung GSE43070 ,GSM1055816 Bed     Big wiggle
Click   Download24141950
H3K4me3 Homo sapiens IMR90 Fibroblast Lung GSE43070 ,GSM1055817 Bed     Big wiggle
Click   Download24141950
H3K4me3 Homo sapiens GM12878 Lymphoblastoid Blood GSE50893 ,GSM1233906 Bed     Big wiggle
Click   Download24136358
H3K4me3 Homo sapiens GM12878 Lymphoblastoid Blood GSE50893 ,GSM1233907 Bed     Big wiggle
Click   Download24136358
H3K4me3 Homo sapiens IMR90 Fibroblast Lung GSE58740 ,GSM1418959 Bed     Big wiggle
Click   Download25391375
H3K4me3 Homo sapiens A549 Epithelium Lung GSE67471 ,GSM1647626 Bed     Big wiggle
Click   DownloadNA
H3K4me3 Homo sapiens A549 Epithelium Lung GSE67471 ,GSM1647627 Bed     Big wiggle
Click   DownloadNA
H3K4me3 Homo sapiens H1 Embryonic Stem Cell Embryo GSE16256 ,GSM605315 Bed     Big wiggle
Click   Download19829295
H3K4me3 Homo sapiens K562 Erythroblast Bone Marrow GSE28162 ,GSM608165 Bed     Big wiggle
Click   Download21596310
H3K4me3 Mus musculus MEL Erythroid Progenitor Cell Blood GSE49847 ,GSM798324 Bed     Big wiggle
Click   Download25409824
H3K4me3 Mus musculus CH12 Lymphoblastoid Blood GSE49847 ,GSM798327 Bed     Big wiggle
Click   Download25409824
H3K4me3 Mus musculus MEL Erythroid Progenitor Cell Blood GSE49847 ,GSM798328 Bed     Big wiggle
Click   Download25409824
H3K4me3 Homo sapiens K562 Erythroblast Bone Marrow GSE35294 ,GSM865280 Bed     Big wiggle
Click   Download23754963
H3K4me3 Homo sapiens K562 Erythroblast Bone Marrow GSE35294 ,GSM865281 Bed     Big wiggle
Click   Download23754963
H3K4me3 Homo sapiens IMR90 Fibroblast Lung GSE36641 ,GSM897556 Bed     Big wiggle
Click   Download23934658
H3K4me3 Homo sapiens H1 Embryonic Stem Cell Embryo GSE16256 ,GSM906405 Bed     Big wiggle
Click   Download19829295
H3K4me3 Homo sapiens A549 Epithelium Lung GSE35583 ,GSM945244 Bed     Big wiggle
Click   Download22955617
H3K4me3 Mus musculus CH12 Lymphoblastoid Blood GSE49847 ,GSM946528 Bed     Big wiggle
Click   Download25409824

Notice: For bigwiggle or bed file download, if the browser cannot automatically download the file, users can right click the hyperlink and then click the "Save link as..." button, which will automatically redirect to download dialogue box, or click the "Copy link address" button and access the website in a new tab page. For data analysis in Cistrome, users should first login into the Cistrome website, then press the "Send Bed" or "Send Big wiggle" button. For data download by Cistrome, users can follow this tutorial.

References

1. Eisen, J.A., Sweder, K.S. and Hanawalt, P.C. (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res, 23, 2715-2723.
2. Gaspar-Maia, A., Alajem, A., Polesso, F., Sridharan, R., Mason, M.J., Heidersbach, A., Ramalho-Santos, J., McManus, M.T., Plath, K., Meshorer, E. et al. (2009) Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature, 460, 863-868.
3. Lusser, A., Urwin, D.L. and Kadonaga, J.T. (2005) Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat Struct Mol Biol, 12, 160-166.
4. Stockdale, C., Flaus, A., Ferreira, H. and Owen-Hughes, T. (2006) Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J Biol Chem, 281, 16279-16288.
5. Konev, A.Y., Tribus, M., Park, S.Y., Podhraski, V., Lim, C.Y., Emelyanov, A.V., Vershilova, E., Pirrotta, V., Kadonaga, J.T., Lusser, A. et al. (2007) CHD1 motor protein is required for deposition of histone variant h3.3 into chromatin in vivo. Science, 317, 1087-1090.
6. Simic, R., Lindstrom, D.L., Tran, H.G., Roinick, K.L., Costa, P.J., Johnson, A.D., Hartzog, G.A. and Arndt, K.M. (2003) Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. Embo Journal, 22, 1846-1856.
7. Sims, R.J., Chen, C.F., Santos-Rosa, H., Kouzarides, T., Patel, S.S. and Reinberg, D. (2005) Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. J Biol Chem, 280, 41789-41792.
8. Vermeulen, M., Eberl, H.C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K.K., Olsen, J.V., Hyman, A.A., Stunnenberg, H.G. et al. (2010) Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers. Cell, 142, 967-980.
9. Bartke, T., Vermeulen, M., Xhemalce, B., Robson, S.C., Mann, M. and Kouzarides, T. (2010) Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation. Cell, 143, 470-484.
10. Lin, J.J., Lehmann, L.W., Bonora, G., Sridharan, R., Vashisht, A.A., Tran, N., Plath, K., Wohlschlegel, J.A. and Carey, M. (2011) Mediator coordinates PIC assembly with recruitment of CHD1. Gene Dev, 25, 2198-2209.

Figure Gallery

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About Chromatin Regulator

Chromatin Regulator Cistrome
is a unique database integrating curated information of CRs, CR ChIP-seq datasets, CR related HM ChIP-seq datasets, and analysis of the relationship between CRs and HMs ChIP-seq pairs in human and mouse.

Contact

houshuang [at] tongji dot edu dot cn