Cooperation between bHLH transcription factors and histones for DNA access.

ARNTL Transcription Factors / genetics Basic Helix-Loop-Helix Transcription Factors / metabolism DNA / genetics Helix-Loop-Helix Motifs / genetics Histones / chemistry Nucleosomes / chemistry Protein Binding CLOCK Proteins / chemistry Proto-Oncogene Proteins c-myc / chemistry Allosteric Regulation Leucine Zippers Octamer Transcription Factor-3 / metabolism Protein Multimerization

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
Jul 2023
Historique:
received: 22 07 2022
accepted: 02 06 2023
medline: 14 7 2023
pubmed: 6 7 2023
entrez: 5 7 2023
Statut: ppublish

Résumé

The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members

Identifiants

DOI: 10.1038/s41586-023-06282-3 PMID: 37407816 PMC: PMC10338342
pubmed: 37407816
doi: 10.1038/s41586-023-06282-3
pii: 10.1038/s41586-023-06282-3
pmc: PMC10338342
doi:

Substances chimiques

ARNTL Transcription Factors 0
Basic Helix-Loop-Helix Transcription Factors 0
DNA 9007-49-2
Histones 0
Nucleosomes 0
CLOCK Proteins EC 2.3.1.48
Proto-Oncogene Proteins c-myc 0
Myc associated factor X 0
Octamer Transcription Factor-3 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

385-393

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM107069
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM145737
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS054794
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM141849
Pays : United States

Informations de copyright

© 2023. The Author(s).

Références

de Martin, X., Sodaei, R. & Santpere, G. Mechanisms of binding specificity among bHLH transcription factors. Int. J. Mol. Sci. 22, 9150 (2021).
pubmed: 34502060 pmcid: 8431614 doi: 10.3390/ijms22179150
Nair, S. K. & Burley, S. K. X-ray structures of Myc-Max and Mad-Max recognizing DNA: molecular bases of regulation by proto-oncogenic transcription factors. Cell 112, 193–205 (2003).
pubmed: 12553908 doi: 10.1016/S0092-8674(02)01284-9
Huang, N. et al. Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex. Science 337, 189–194 (2012).
pubmed: 22653727 pmcid: 3694778 doi: 10.1126/science.1222804
McGinty, R. K. & Tan, S. Principles of nucleosome recognition by chromatin factors and enzymes. Curr. Opin. Struct. Biol. 71, 16–26 (2021).
pubmed: 34198054 pmcid: 8648869 doi: 10.1016/j.sbi.2021.05.006
Rey, G. et al. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol. 9, e1000595 (2011).
pubmed: 21364973 pmcid: 3043000 doi: 10.1371/journal.pbio.1000595
Sobel, J. A. et al. Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol. 15, e2001069 (2017).
pubmed: 28414715 pmcid: 5393560 doi: 10.1371/journal.pbio.2001069
Nakahata, Y. et al. A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes. BMC Mol. Biol. 9, 1 (2008).
pubmed: 18177499 pmcid: 2254435 doi: 10.1186/1471-2199-9-1
Lambert, S. A. et al. The human transcription factors. Cell 175, 598–599 (2018).
pubmed: 30290144 doi: 10.1016/j.cell.2018.09.045
Carroll, P. A., Freie, B. W., Mathsyaraja, H. & Eisenman, R. N. The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis. Front. Med. 12, 412–425 (2018).
pubmed: 30054853 pmcid: 7358075 doi: 10.1007/s11684-018-0650-z
Lee, J. E. et al. Conversion of Xenopus ectoderm into neurons by NeuroD, a basic helix–loop–helix protein. Science 268, 836–844 (1995).
pubmed: 7754368 doi: 10.1126/science.7754368
Weintraub, H. et al. Muscle-specific transcriptional activation by MyoD. Genes Dev. 5, 1377–1386 (1991).
pubmed: 1651276 doi: 10.1101/gad.5.8.1377
Semenza, G. L., Nejfelt, M. K., Chi, S. M. & Antonarakis, S. E. Hypoxia-inducible nuclear factors bind to an enhancer element located 3′ to the human erythropoietin gene. Proc. Natl Acad. Sci. USA 88, 5680–5684 (1991).
pubmed: 2062846 pmcid: 51941 doi: 10.1073/pnas.88.13.5680
Gekakis, N. et al. Role of the CLOCK protein in the mammalian circadian mechanism. Science 280, 1564–1569 (1998).
pubmed: 9616112 doi: 10.1126/science.280.5369.1564
Murre, C. Helix–loop–helix proteins and the advent of cellular diversity: 30 years of discovery. Genes Dev. 33, 6–25 (2019).
pubmed: 30602438 pmcid: 6317319 doi: 10.1101/gad.320663.118
Ma, P. C., Rould, M. A., Weintraub, H. & Pabo, C. O. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell 77, 451–459 (1994).
pubmed: 8181063 doi: 10.1016/0092-8674(94)90159-7
Liu, Z., Venkatesh, S. S. & Maley, C. C. Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples. BMC Genomics 9, 509 (2008).
pubmed: 18973670 pmcid: 2628393 doi: 10.1186/1471-2164-9-509
Dang, C. V. MYC on the path to cancer. Cell 149, 22–35 (2012).
pubmed: 22464321 pmcid: 3345192 doi: 10.1016/j.cell.2012.03.003
Dhanasekaran, R. et al. The MYC oncogene—the grand orchestrator of cancer growth and immune evasion. Nat. Rev. Clin. Oncol. 19, 23–36 (2022).
pubmed: 34508258 doi: 10.1038/s41571-021-00549-2
Gustafson, C. L. & Partch, C. L. Emerging models for the molecular basis of mammalian circadian timing. Biochemistry 54, 134–149 (2015).
pubmed: 25303119 doi: 10.1021/bi500731f
Zhang, R., Lahens, N. F., Ballance, H. I., Hughes, M. E. & Hogenesch, J. B. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc. Natl Acad. Sci. USA 111, 16219–16224 (2014).
pubmed: 25349387 pmcid: 4234565 doi: 10.1073/pnas.1408886111
Koike, N. et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338, 349–354 (2012).
pubmed: 22936566 pmcid: 3694775 doi: 10.1126/science.1226339
Li, G. & Widom, J. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11, 763–769 (2004).
pubmed: 15258568 doi: 10.1038/nsmb801
Adams, C. C. & Workman, J. L. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol. Cell. Biol. 15, 1405–1421 (1995).
pubmed: 7862134 pmcid: 230365 doi: 10.1128/MCB.15.3.1405
Consortium, E. P. et al. Perspectives on ENCODE. Nature 583, 693–698 (2020).
doi: 10.1038/s41586-020-2449-8
Michael, A. K. et al. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science 368, 1460–1465 (2020).
pubmed: 32327602 doi: 10.1126/science.abb0074
Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998).
pubmed: 9514715 doi: 10.1006/jmbi.1997.1494
Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).
pubmed: 29140473 doi: 10.1093/nar/gkx1126
Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).
pubmed: 9305837 doi: 10.1038/38444
Michael, A. K. et al. Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proc. Natl Acad. Sci. USA 114, 1560–1565 (2017).
pubmed: 28143926 pmcid: 5321004 doi: 10.1073/pnas.1615310114
Fribourgh, J. L. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife 9, e55275 (2020).
pubmed: 32101164 pmcid: 7064333 doi: 10.7554/eLife.55275
Skrajna, A. et al. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Nucleic Acids Res. 48, 9415–9432 (2020).
pubmed: 32658293 pmcid: 7515726 doi: 10.1093/nar/gkaa544
He, S. et al. Structure of nucleosome-bound human BAF complex. Science 367, 875–881 (2020).
pubmed: 32001526 doi: 10.1126/science.aaz9761
Mashtalir, N. et al. A structural model of the endogenous human BAF complex informs disease mechanisms. Cell 183, 802–817 (2020).
pubmed: 33053319 pmcid: 7717177 doi: 10.1016/j.cell.2020.09.051
Pathare, G. R. et al. Structural mechanism of cGAS inhibition by the nucleosome. Nature 587, 668–672 (2020).
pubmed: 32911482 doi: 10.1038/s41586-020-2750-6
Schalch, T., Duda, S., Sargent, D. F. & Richmond, T. J. X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436, 138–141 (2005).
pubmed: 16001076 doi: 10.1038/nature03686
Dodonova, S. O., Zhu, F., Dienemann, C., Taipale, J. & Cramer, P. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature 580, 669–672 (2020).
pubmed: 32350470 doi: 10.1038/s41586-020-2195-y
Becker, P. B. & Wu, C. Cell-free system for assembly of transcriptionally repressed chromatin from Drosophila embryos. Mol. Cell. Biol. 12, 2241–2249 (1992).
pubmed: 1569951 pmcid: 364396
Eggers, N. & Becker, P. B. Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions. Nucleic Acids Res. 49, 7602–7617 (2021).
pubmed: 34181732 pmcid: 8287947 doi: 10.1093/nar/gkab558
Henikoff, J. G., Belsky, J. A., Krassovsky, K., MacAlpine, D. M. & Henikoff, S. Epigenome characterization at single base-pair resolution. Proc. Natl Acad. Sci. USA 108, 18318–18323 (2011).
pubmed: 22025700 pmcid: 3215028 doi: 10.1073/pnas.1110731108
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
pubmed: 16904174 doi: 10.1016/j.cell.2006.07.024
Soufi, A. et al. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 161, 555–568 (2015).
pubmed: 25892221 pmcid: 4409934 doi: 10.1016/j.cell.2015.03.017
Wesley, N. A. et al. Time resolved-fluorescence resonance energy transfer platform for quantitative nucleosome binding and footprinting. Protein Sci. 31, e4339 (2022).
pubmed: 35634775 pmcid: 9134878 doi: 10.1002/pro.4339
Menet, J. S., Pescatore, S. & Rosbash, M. CLOCK:BMAL1 is a pioneer-like transcription factor. Genes Dev. 28, 8–13 (2014).
pubmed: 24395244 pmcid: 3894415 doi: 10.1101/gad.228536.113
Paquet, E. R., Rey, G. & Naef, F. Modeling an evolutionary conserved circadian cis-element. PLoS Comput. Biol. 4, e38 (2008).
pubmed: 18282089 pmcid: 2242825 doi: 10.1371/journal.pcbi.0040038
Michael, A. K. & Thoma, N. H. Reading the chromatinized genome. Cell 184, 3599–3611 (2021).
pubmed: 34146479 doi: 10.1016/j.cell.2021.05.029
Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061 (2008).
pubmed: 18358816 doi: 10.1016/j.cell.2008.02.039
Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151, 994–1004 (2012).
pubmed: 23159369 pmcid: 3508134 doi: 10.1016/j.cell.2012.09.045
Donovan, B. T. et al. Basic helix–loop–helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions. Mol. Cell 83, 1251–1263 (2023).
pubmed: 36996811 doi: 10.1016/j.molcel.2023.03.006
Polach, K. J. & Widom, J. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258, 800–812 (1996).
pubmed: 8637011 doi: 10.1006/jmbi.1996.0288
Mirny, L. A. Nucleosome-mediated cooperativity between transcription factors. Proc. Natl Acad. Sci. USA 107, 22534–22539 (2010).
pubmed: 21149679 pmcid: 3012490 doi: 10.1073/pnas.0913805107
Ngo, T. T., Zhang, Q., Zhou, R., Yodh, J. G. & Ha, T. Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. Cell 160, 1135–1144 (2015).
pubmed: 25768909 pmcid: 4409768 doi: 10.1016/j.cell.2015.02.001
Moyle-Heyrman, G., Tims, H. S. & Widom, J. Structural constraints in collaborative competition of transcription factors against the nucleosome. J. Mol. Biol. 412, 634–646 (2011).
pubmed: 21821044 pmcid: 3534743 doi: 10.1016/j.jmb.2011.07.032
Swinstead, E. E., Paakinaho, V., Presman, D. M. & Hager, G. L. Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: a new perspective: multiple transcription factors can effect chromatin pioneer functions through dynamic interactions with ATP-dependent chromatin remodeling factors. Bioessays 38, 1150–1157 (2016).
pubmed: 27633730 pmcid: 6319265 doi: 10.1002/bies.201600137
Fierz, B. & Poirier, M. G. Biophysics of chromatin dynamics. Annu. Rev. Biophys. 48, 321–345 (2019).
pubmed: 30883217 doi: 10.1146/annurev-biophys-070317-032847
Hall, M. A. et al. High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat. Struct. Mol. Biol. 16, 124–129 (2009).
pubmed: 19136959 pmcid: 2635915 doi: 10.1038/nsmb.1526
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
pubmed: 32881101 doi: 10.1002/pro.3943
Osakabe, A. et al. Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome. Sci. Rep. 5, 16330 (2015).
pubmed: 26573481 pmcid: 4648065 doi: 10.1038/srep16330
Kujirai, T. et al. Methods for preparing nucleosomes containing histone variants. Methods Mol. Biol. 1832, 3–20 (2018).
pubmed: 30073519 doi: 10.1007/978-1-4939-8663-7_1
Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23–44 (2004).
pubmed: 14870657 doi: 10.1016/S0076-6879(03)75002-2
Abdulrahman, W. et al. A set of baculovirus transfer vectors for screening of affinity tags and parallel expression strategies. Anal. Biochem. 385, 383–385 (2009).
pubmed: 19061853 doi: 10.1016/j.ab.2008.10.044
Wang, Z., Wu, Y., Li, L. & Su, X. D. Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix–loop–helix domains with E-box DNA. Cell Res. 23, 213–224 (2013).
pubmed: 23229515 doi: 10.1038/cr.2012.170
Elegheert, J. et al. Lentiviral transduction of mammalian cells for fast, scalable and high-level production of soluble and membrane proteins. Nat. Protoc. 13, 2991–3017 (2018).
pubmed: 30455477 pmcid: 6364805 doi: 10.1038/s41596-018-0075-9
Zakeri, B. et al. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc. Natl Acad. Sci. USA 109, E690–E697 (2012).
pubmed: 22366317 pmcid: 3311370 doi: 10.1073/pnas.1115485109
Sievers, Q. et al. Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science 362, eaat0572 (2018).
pubmed: 30385546 pmcid: 6326779 doi: 10.1126/science.aat0572
Kilic, S., Bachmann, A. L., Bryan, L. C. & Fierz, B. Multivalency governs HP1α association dynamics with the silent chromatin state. Nat. Commun. 6, 7313 (2015).
pubmed: 26084584 doi: 10.1038/ncomms8313
Aggarwal, T., Materassi, D., Davison, R., Hays, T. & Salapaka, M. Detection of steps in single molecule data. Cell. Mol. Bioeng. 5, 14–31 (2012).
pubmed: 23956798 doi: 10.1007/s12195-011-0188-5
Gaidatzis, D., Lerch, A., Hahne, F. & Stadler, M. B. QuasR: quantification and annotation of short reads in R. Bioinformatics 31, 1130–1132 (2015).
pubmed: 25417205 doi: 10.1093/bioinformatics/btu781
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
pubmed: 19261174 pmcid: 2690996 doi: 10.1186/gb-2009-10-3-r25
Liu, F., Lossl, P., Scheltema, R., Viner, R. & Heck, A. J. R. Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nat. Commun. 8, 15473 (2017).
pubmed: 28524877 pmcid: 5454533 doi: 10.1038/ncomms15473
Schmidt, J. M. et al. A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC.DNA.Cdc6. Nat. Commun. 13, 1059 (2022).
pubmed: 35217664 pmcid: 8881611 doi: 10.1038/s41467-022-28695-w
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).
pubmed: 19029910 doi: 10.1038/nbt.1511
Elias, J. E. & Gygi, S. P. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 604, 55–71 (2010).
pubmed: 20013364 pmcid: 2922680 doi: 10.1007/978-1-60761-444-9_5
Combe, C. W., Fischer, L. & Rappsilber, J. xiNET: cross-link network maps with residue resolution. Mol. Cell. Proteomics 14, 1137–1147 (2015).
pubmed: 25648531 pmcid: 4390258 doi: 10.1074/mcp.O114.042259
Lagerwaard, I. M., Albanese, P., Jankevics, A. & Scheltema, R. A. Xlink Mapping and AnalySis (XMAS)—smooth integrative modeling in ChimeraX. Preprint at bioRxiv https://doi.org/10.1101/2022.04.21.489026 (2022).
Kahraman, A, Malmstrom, L. & Aebersold, R. Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics 27, 2163–2164 (2011).
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022).
pubmed: 34723319 doi: 10.1093/nar/gkab1038
Stark, H. GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methods Enzymol. 481, 109–126 (2010).
pubmed: 20887855 doi: 10.1016/S0076-6879(10)81005-5
Schenk, A. D., Cavadini, S., Thomä, N. H. & Genoud, C. Live analysis and reconstruction of single-particle cryo-electron microscopy data with CryoFLARE. J. Chem. Inf. Model. 60, 2561–2569 (2020).
pubmed: 32233514 doi: 10.1021/acs.jcim.9b01102
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
pubmed: 30412051 pmcid: 6250425 doi: 10.7554/eLife.42166
Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
pubmed: 26592709 pmcid: 4711343 doi: 10.1016/j.jsb.2015.11.003
Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).
pubmed: 31240256 pmcid: 6584505 doi: 10.1038/s42003-019-0437-z
Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife 7, e35383 (2018).
pubmed: 29513216 pmcid: 5854467 doi: 10.7554/eLife.35383
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
pubmed: 23000701 pmcid: 3690530 doi: 10.1016/j.jsb.2012.09.006
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473 doi: 10.1038/nmeth.4169
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
pubmed: 14568533 doi: 10.1016/j.jmb.2003.07.013
Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013).
pubmed: 23872039 pmcid: 3834153 doi: 10.1016/j.ultramic.2013.06.004
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
pubmed: 20124702 pmcid: 2815670 doi: 10.1107/S0907444909052925
Jakobi, A. J., Wilmanns, M. & Sachse, C. Model-based local density sharpening of cryo-EM maps. eLife 6, e27131 (2017).
pubmed: 29058676 pmcid: 5679758 doi: 10.7554/eLife.27131
Burnley, T., Palmer, C. M. & Winn, M. Recent developments in the CCP-EM software suite. Acta Crystallogr. D 73, 469–477 (2017).
doi: 10.1107/S2059798317007859
de la Rosa-Trevin, J. M. et al. Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013).
pubmed: 24075951 doi: 10.1016/j.jsb.2013.09.015
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
pubmed: 20383002 pmcid: 2852313 doi: 10.1107/S0907444910007493
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).
doi: 10.1107/S2059798318006551
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
doi: 10.1107/S2059798318002425
Wang, R. Y. et al. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5, e17219 (2016).
pubmed: 27669148 pmcid: 5115868 doi: 10.7554/eLife.17219
Marze, N. A., Burman, S. S. R., Sheffler, W. & Gray, J. J. Efficient flexible backbone protein–protein docking for challenging targets. Bioinformatics 34, 3461–3469 (2018).
Afonine, P. V. et al. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr. D 74, 814–840 (2018).
doi: 10.1107/S2059798318009324
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
pubmed: 29067766 doi: 10.1002/pro.3330
Matsumoto, S. et al. DNA damage detection in nucleosomes involves DNA register shifting. Nature 571, 79–84 (2019).
pubmed: 31142837 pmcid: 6611726 doi: 10.1038/s41586-019-1259-3
Girardot, C., Scholtalbers, J., Sauer, S., Su, S.-Y. & Furlong, E. E. M. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinf. 17, 419 (2016).
doi: 10.1186/s12859-016-1284-2
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286 pmcid: 3322381 doi: 10.1038/nmeth.1923
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943 pmcid: 2723002 doi: 10.1093/bioinformatics/btp352
Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).
pubmed: 21330290 pmcid: 3065696 doi: 10.1093/bioinformatics/btr064
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
pubmed: 20513432 pmcid: 2898526 doi: 10.1016/j.molcel.2010.05.004
Serizay, J. VplotR: set of tools to make V-plots and compute footprint profiles. R version 1.8.0. https://github.com/js2264/VplotR (2022).
Menet, J. S., Rodriguez, J., Abruzzi, K. C. & Rosbash, M. Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. eLife 1, e00011 (2012).
pubmed: 23150795 pmcid: 3492862 doi: 10.7554/eLife.00011
Sonmezer, C. et al. Molecular co-occupancy identifies transcription factor binding cooperativity in vivo. Mol. Cell 81, 255–267 (2021).
pubmed: 33290745 doi: 10.1016/j.molcel.2020.11.015
Li, T. & Zhu, S. On clustering binary data. in Proc. 2005 SIAM International Conference on Data Mining (SDM) (eds Kargupta, H. et al.) 526–530 (2005).
Xu, H. et al. Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C terminus. Nat. Struct. Mol. Biol. 22, 476–484 (2015).
pubmed: 25961797 pmcid: 4456216 doi: 10.1038/nsmb.3018
Crosby, P., Hoyle, N. P. & O’Neill, J. S. Flexible measurement of bioluminescent reporters using an automated longitudinal luciferase imaging gas- and temperature-optimized recorder (ALLIGATOR). J. Vis. Exp. 130, e56623 (2017).
Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 (2021).
pubmed: 33542510 pmcid: 8183613 doi: 10.1038/s41592-020-01049-4
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
pubmed: 21988835 pmcid: 3261699 doi: 10.1038/msb.2011.75
Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).
pubmed: 19151095 pmcid: 2672624 doi: 10.1093/bioinformatics/btp033

Auteurs

Alicia K Michael (AK)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
University of Basel, Basel, Switzerland.
ORCID: 0000-0002-6080-839X

Lisa Stoos (L)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
University of Basel, Basel, Switzerland.

Priya Crosby (P)

Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.

Nikolas Eggers (N)

Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany.
ORCID: 0000-0002-0256-1982

Xinyu Y Nie (XY)

Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX, USA.

Kristina Makasheva (K)

Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
ORCID: 0000-0002-0645-6848

Martina Minnich (M)

Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
ORCID: 0000-0003-4677-3300

Kelly L Healy (KL)

Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, USA.

Joscha Weiss (J)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
University of Basel, Basel, Switzerland.
ORCID: 0000-0002-4149-0478

Georg Kempf (G)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Simone Cavadini (S)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Lukas Kater (L)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Jan Seebacher (J)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Luca Vecchia (L)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Deyasini Chakraborty (D)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
University of Basel, Basel, Switzerland.

Luke Isbel (L)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
ORCID: 0000-0002-5270-4347

Ralph S Grand (RS)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Florian Andersch (F)

Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.

Jennifer L Fribourgh (JL)

Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.

Dirk Schübeler (D)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
University of Basel, Basel, Switzerland.

Johannes Zuber (J)

Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
Medical University of Vienna, Vienna, Austria.
ORCID: 0000-0001-8810-6835

Andrew C Liu (AC)

Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, USA.
ORCID: 0000-0003-1927-0900

Peter B Becker (PB)

Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany.
ORCID: 0000-0001-7186-0372

Beat Fierz (B)

Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
ORCID: 0000-0002-2991-3044

Carrie L Partch (CL)

Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.
ORCID: 0000-0002-4677-2861

Jerome S Menet (JS)

Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX, USA.
ORCID: 0000-0002-7682-0967

Nicolas H Thomä (NH)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. thoman@fmi.ch.
ORCID: 0000-0003-2685-906X

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Facteurs de transcription à motif basique hélice-boucle-hélice › Facteurs de transcription ARNTL › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Facteurs de transcription à motif basique hélice-boucle-hélice › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Éléments structuraux des protéines › Motifs à hélice-boucle-hélice › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Histone › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Nucléosomes › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Métabolisme › Liaison aux protéines › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Facteurs de transcription à motif basique hélice-boucle-hélice › Protéines CLOCK › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Facteurs de transcription à motif basique hélice-boucle-hélice › Protéines proto-oncogènes c-myc › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Régulation allostérique › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Éléments structuraux des protéines › Glissières à leucine › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Facteurs de transcription à domaine POU › Facteurs de transcription Oct › Facteur de transcription Oct-3 › Cooperation between bHLH transcription factors...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Multimérisation de protéines › Cooperation between bHLH transcription factors...