6ne3 › Citations

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome.

<div class='caption-title'>High resolution structure of SNF2h bound to a nucleosome with 60 bp of flanking DNA in the presence of ADP-BeFx and 140 mM KCl.</div>
<div class='caption-title'>Cryo-EM analysis of singly bound SNF2h-nucleosome complexes (140 mM KCl) .</div>
<div class='caption-title'>Cryo-EM Densities of SHL+2 and SHL-2 SNF2h-Nucleosome complexes obtained at 140 mM.</div>
Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y
OpenAccess logo Elife 8 (2019)
Cited: 40 times
EuropePMC logo PMID: 31210637

Abstract

The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.

Reviews - 6ne3 mentioned but not cited (3)

  1. Principles of nucleosome recognition by chromatin factors and enzymes. McGinty RK, Tan S. Curr Opin Struct Biol 71 16-26 (2021)
  2. Chromatin remodelling comes into focus. Sundaramoorthy R, Owen-Hughes T. F1000Res 9 F1000 Faculty Rev-1011 (2020)
  3. BAZ1B the Protean Protein. Sharif SB, Zamani N, Chadwick BP. Genes (Basel) 12 1541 (2021)

Articles - 6ne3 mentioned but not cited (4)

  1. Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features. Li D, Wang Q, Gong NN, Kurolap A, Feldman HB, Boy N, Brugger M, Grand K, McWalter K, Guillen Sacoto MJ, Wakeling E, Hurst J, March ME, Bhoj EJ, Nowaczyk MJM, Gonzaga-Jauregui C, Mathew M, Dava-Wala A, Siemon A, Bartholomew D, Huang Y, Lee H, Martinez-Agosto JA, Schwaibold EMC, Brunet T, Choukair D, Pais LS, White SM, Christodoulou J, Brown D, Lindstrom K, Grebe T, Tiosano D, Kayser MS, Tan TY, Deardorff MA, Song Y, Hakonarson H. Sci Adv 7 eabf2066 (2021)
  2. Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Cell 186 4100-4116.e15 (2023)
  3. Long non-coding RNA lncMGC mediates the expression of TGF-β-induced genes in renal cells via nucleosome remodelers. Kato M, Chen Z, Das S, Wu X, Wang J, Li A, Chen W, Tsark W, Tunduguru R, Lanting L, Wang M, Moore R, Kalkum M, Abdollahi M, Natarajan R. Front Mol Biosci 10 1204124 (2023)
  4. research-article Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking. Chio US, Palovcak E, Autzen AAA, Autzen HE, Muñoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y. bioRxiv 2023.06.20.545796 (2023)


Reviews citing this publication (11)

  1. Moving Mountains-The BRCA1 Promotion of DNA Resection. Densham RM, Morris JR. Front Mol Biosci 6 79 (2019)
  2. INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling. Willhoft O, Wigley DB. Curr Opin Struct Biol 61 50-58 (2020)
  3. The emerging role of ISWI chromatin remodeling complexes in cancer. Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. J Exp Clin Cancer Res 40 346 (2021)
  4. Biophysics of Chromatin Remodeling. Nodelman IM, Bowman GD. Annu Rev Biophys 50 73-93 (2021)
  5. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Clapier CR. Int J Mol Sci 22 5578 (2021)
  6. Multicolor single-molecule FRET for DNA and RNA processes. Feng XA, Poyton MF, Ha T. Curr Opin Struct Biol 70 26-33 (2021)
  7. Sentinels of chromatin: chromodomain helicase DNA-binding proteins in development and disease. Alendar A, Berns A. Genes Dev 35 1403-1430 (2021)
  8. Collaboration through chromatin: motors of transcription and chromatin structure. Gamarra N, Narlikar GJ. J Mol Biol 433 166876 (2021)
  9. Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability. Morgan A, LeGresley S, Fischer C. Int J Mol Sci 22 E76 (2020)
  10. RSF1 in cancer: interactions and functions. Cai G, Yang Q, Sun W. Cancer Cell Int 21 315 (2021)
  11. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Nat Rev Mol Cell Biol (2023)

Articles citing this publication (22)

  1. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Han Y, Reyes AA, Malik S, He Y. Nature 579 452-455 (2020)
  2. Histone dynamics mediate DNA unwrapping and sliding in nucleosomes. Armeev GA, Kniazeva AS, Komarova GA, Kirpichnikov MP, Shaytan AK. Nat Commun 12 2387 (2021)
  3. Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA. Shi X, Prasanna C, Soman A, Pervushin K, Nordenskiöld L. Commun Biol 3 639 (2020)
  4. Structural features of nucleosomes in interphase and metaphase chromosomes. Arimura Y, Shih RM, Froom R, Funabiki H. Mol Cell 81 4377-4397.e12 (2021)
  5. Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome. Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S. Elife 10 e71420 (2021)
  6. Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP. Nat Struct Mol Biol 29 121-129 (2022)
  7. Partial Replacement of Nucleosomal DNA with Human FACT Induces Dynamic Exposure and Acetylation of Histone H3 N-Terminal Tails. Tsunaka Y, Ohtomo H, Morikawa K, Nishimura Y. iScience 23 101641 (2020)
  8. Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome. Nodelman IM, Shen Z, Levendosky RF, Bowman GD. Proc Natl Acad Sci U S A 118 e2014498118 (2021)
  9. DNP-enhanced solid-state NMR spectroscopy of chromatin polymers. Elathram N, Ackermann BE, Debelouchina GT. J Magn Reson Open 10-11 100057 (2022)
  10. Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Wu H, Muñoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y. Science 381 319-324 (2023)
  11. The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells. Klein DC, Troy K, Tripplehorn SA, Hainer SJ. BMC Genomics 24 201 (2023)
  12. Functional crosstalk between the cohesin loader and chromatin remodelers. Muñoz S, Jones A, Bouchoux C, Gilmore T, Patel H, Uhlmann F. Nat Commun 13 7698 (2022)
  13. Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V. Nat Struct Mol Biol 30 1571-1581 (2023)
  14. Single-particle cryo-EM: beyond the resolution. Armache JP, Cheng Y. Natl Sci Rev 6 864-866 (2019)
  15. A Genetically Encoded Approach for Breaking Chromatin Symmetry. Lukasak BJ, Thompson RE, Mitchener MM, Feng VJ, Bagert JD, Muir TW. ACS Cent Sci 8 176-183 (2022)
  16. CHD Chromatin Remodeling Protein Diversification Yields Novel Clades and Domains Absent in Classic Model Organisms. Trujillo JT, Long J, Aboelnour E, Ogas J, Wisecaver JH. Genome Biol Evol 14 evac066 (2022)
  17. H2A-H2B Histone Dimer Plasticity and Its Functional Implications. Kniazeva AS, Armeev GA, Shaytan AK. Cells 11 2837 (2022)
  18. Letter Histone dynamics play a critical role in SNF2h-mediated nucleosome sliding. Gamarra N, Narlikar GJ. Nat Struct Mol Biol 28 548-551 (2021)
  19. Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1. Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S. Nat Commun 15 1000 (2024)
  20. The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families. Zhong Y, Moghaddas Sani H, Paudel BP, Low JKK, Silva APG, Mueller S, Deshpande C, Panjikar S, Reid XJ, Bedward MJ, van Oijen AM, Mackay JP. Nat Commun 13 7524 (2022)
  21. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Biochem J 481 219-244 (2024)
  22. Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study. Oleinikov PD, Fedulova AS, Armeev GA, Motorin NA, Singh-Palchevskaia L, Sivkina AL, Feskin PG, Glukhov GS, Afonin DA, Komarova GA, Kirpichnikov MP, Studitsky VM, Feofanov AV, Shaytan AK. Int J Mol Sci 24 15194 (2023)


Quick links