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Cited by 10Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

Two possible modes of pioneering associated with combinations of H2A.Z and p300/CBP at nucleosome-occupied enhancers

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Cauchy, Pierre, Koch, Frederic, Andrau, Jean-Christophe·2017·Transcription
DOI 10.1080/21541264.2017.1291395PMC PMC5501375
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Abstract

Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.

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  • H2A.Z occupancy seems to correlate with pioneer TF binding to nucleosome-occupied regions and has been suggested to act as a scaffold for binding of pioneer TFs and chromatin remodelers.

    “The role of H2A.Z in closed chromatin is less clear, but H2A.Z occupancy seems to correlate with pioneer TF binding to nucleosome-occupied regions and has been suggested to act as a scaffold for binding of pioneer TFs and chromatin remodelers (72,73).”

    From SOX9 reprograms endothelial cells by altering the chromatin landscape (2022) · cites this paper as [72]

    The Results and discussion (page unavailable) report H2A.Z enrichment at nucleosome-occupied sites bound by the pioneer factors Ets1 and Oct4, supporting the proposed correlation. The Introduction and Results and discussion mention pioneer factors recruiting chromatin remodelers, but do not suggest that H2A.Z acts as a scaffold for binding either the factors or remodelers. (LLM, conf=0.85)

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Research works printed but not linked: 24

  1. Goldberg AD, Allis CD, Bernstein E. Epigenetics: a land- scape takes shape. Cell 2007; 128:635-638; PMID:17320500; https://doi.org/10.1016/j.cell.2007.02.006 · DOI · Paper page
  2. Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011; 25:2227-2241; PMID:22056668; https://doi. org/10.1101/gad.176826.111 · DOI · Paper page
  3. Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magni- tude and shape. Nat Biotechnol 2014; 32:171-178; PMID:24441470; https://doi.org/10.1038/nbt.2798 · DOI
  4. Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. The pioneer transcription factor foxA maintains an accessible nucleosome configuration at enhancers for tis- sue-specific gene activation. Mol Cell 2016; 62:79-91; PMID:27058788; https://doi.org/10.1016/j.molcel.2016 .03.001 · DOI · Paper page
  5. Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 2013; 12:180-192; PMID:23260488; https://doi. org/10.1016/j.stem.2012.11.003 · DOI
  6. Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ. The essential histone variant H2A.Z regulates the equilib- rium between different chromatin conformational states. Nat Struct Biol 2002; 9:172-176; PMID:11850638; https://doi.org/10.1038/nsb0402-316b · DOI
  7. Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, Schreiber SL, Rando OJ, Madhani HD. Histone vari- ant H2A.Z marks the 5 0 ends of both active and inactive genes in euchromatin. Cell 2005; 123:233- 248; PMID:16239142; https://doi.org/10.1016/j.cell.2005. 10.002 · DOI
  8. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleo- some positioning in the human genome. Cell 2008; 132:887-898; PMID:18329373; https://doi.org/10.1016/j. cell.2008.02.022 · DOI
  9. Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet 2009; 41:941-945; PMID:19633671; https://doi.org/10.1038/ng.409 · DOI
  10. Tolstorukov MY, Kharchenko PV, Goldman JA, King- ston RE, Park PJ. Comparative analysis of H2A.Z nucleo- some organization in the human and yeast genomes. Genome Res 2009; 19:967-977; PMID:19246569; https:// doi.org/10.1101/gr.084830.108 · DOI
  11. Bao Y, Konesky K, Park YJ, Rosu S, Dyer PN, Ran- gasamy D, Tremethick DJ, Laybourn PJ, Luger K. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBO J 2004; 23:3314-3324; PMID:15257289; https://doi.org/ 10.1038/sj.emboj.7600316 · DOI
  12. Rudnizky S, Bavly A, Malik O, Pnueli L, Melamed P, Kaplan A. H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes. Nat Commun 2016; 7:12958; PMID:27653784; https://doi. org/10.1038/ncomms12958 · DOI
  13. Barozzi I, Simonatto M, Bonifacio S, Yang L, Rohs R, Ghisletti S, Natoli G. Coregulation of transcription factor binding and nucleosome occupancy through DNA fea- tures of mammalian enhancers. Mol Cell 2014; 54:844- 857; PMID:24813947; https://doi.org/10.1016/j.molcel. 2014.04.006 · DOI · Paper page
  14. Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A et al. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2016; 44:3567-3585; PMID:26673693; https://doi.org/ 10.1093/nar/gkv1475 · DOI
  15. Mieczkowski J, Cook A, Bowman SK, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ et al. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun 2016; 7:11485; PMID:27151365; https://doi. org/10.1038/ncomms11485 · DOI
  16. Holmqvist PH, Mannervik M. Genomic occupancy of the transcriptional co-activators p300 and CBP. Transcrip- tion 2013; 4:18-23; PMID:23131664; https://doi.org/ 10.4161/trns.22601 · DOI
  17. Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA. Master transcrip- tion factors and mediator establish super-enhancers at key cell identity genes. Cell 2013; 153:307-319; PMID:23582322; https://doi.org/10.1016/j.cell.2013.03.035 · DOI · Paper page
  18. Sun X, Chuang JC, Kanchwala M, Wu L, Celen C, Li L, Liang H, Zhang S, Maples T, Nguyen LH et al. Suppression of the SWI/SNF component arid1a promotes mammalian regener- ation. Cell Stem Cell 2016; 18:456-466; PMID:27044474; https://doi.org/10.1016/j.stem.2016.03.001 · DOI · Paper page
  19. Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopou- los JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Dro- sophila transcription factor binding. Genome Biol 2011; 12:R34; PMID:21473766; https://doi.org/10.1186/gb- 2011-12-4-r34 · DOI · Paper page
  20. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y et al. Sequence fea- tures and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2012; 22:1798-1812; PMID:22955990; https://doi.org/ 10.1101/gr.139105.112 · DOI
  21. Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zaca- rias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 2011; 18:956-963; PMID:21765417; https://doi.org/10.1038/nsmb.2085 · DOI
  22. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357-359; PMID:22388286; https://doi.org/10.1038/nmeth.1923 · DOI · Paper page
  23. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008; 9:R137; PMID:18798982; https://doi. org/10.1186/gb-2008-9-9-r137 · DOI · Paper page
  24. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combina- tions of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010; 38:576-589; PMID:20513432; https://doi.org/10.1016/j.molcel.2010.05.004 · DOI · Paper page

Cited by

Sorted by citations

Authors
Cauchy, P., Koch, F., & Andrau, J.-C.
Affiliations
  • Max Planck Institute of Immunobiology and Epigenetics (DE)
  • Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
  • Centre National de la Recherche Scientifique (FR)
Corresponding author
Andrau, Jean-Christophe
ORCID
Venue
Transcription
Publisher
Informa UK Limited
Published
2017-02-13
Volume
8
Issue
3
Pages
179-184
ISSN
  • 2154-1264 (ISSN-L)
  • 2154-1272
DOI
10.1080/21541264.2017.1291395
PMC
PMC5501375
OpenAlex
W2588242437
Cited by
10
References
1
Citations by year
2026: 2 · 2024: 1 · 2022: 2 · 2021: 1 · 2020: 1 · 2019: 2 · 2018: 1
FWCI
0.45
Type
journal article
Language
en
Open access
Locations
  • Transcription (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
pioneer transcription factors, H2A.Z, P300, CBP, nucleosome occupancy, enhancers, nucleosome-depleted regions, chromatin accessibility, histone modifications, transcriptional regulation
MeSH terms
Animals, Enhancer Elements, Genetic, Histones, Humans, Nucleosomes, p300-CBP Transcription Factors

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