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Human mitochondrial transcription factor A (TFAM) distorts DNA into a U-turn, as shown by crystallographic studies. The relevance of this U-turn is associated with transcription initiation at the mitochondrial light strand promoter (LSP). However, it has not been yet discerned whether a tight U-turn or an alternative conformation, such as a V-shape, is formed in solution. Here, single-molecule FRET experiments on freely diffusing TFAM/LSP complexes containing different DNA lengths show that a DNA U-turn is induced by progressive and cooperative binding of the two TFAM HMG-box domains and the linker between them. SAXS studies further show compaction of the protein upon complex formation. Finally, molecular dynamics simulations reveal that TFAM/LSP complexes are dynamic entities, and the HMG boxes induce the U-turn against the tendency of the DNA to adopt a straighter conformation. This tension is resolved by reversible unfolding of the linker, which is a singular mechanism that allows a flexible protein to stabilize a tight bending of DNA., This work was supported by the Ministry of Economy and Competitiveness (MINECO) (BFU2012-33516 and BFU2015-70645-R to M.S., and BIO2012-32868 and BFU2014-61670-EXP to M.O.); Generalitat de Catalunya (SGR2009-1366 and 2014-SGR-997 to M.S., and SGR2009- 1348, 2014 SGR-134 to M.O.); the Instituto Nacional de Bioinforma´tica; the European Union (FP7-HEALTH-2010-261460, FP7-PEOPLE-2011- 290246, and FP7-HEALTH-2012-306029-2 to M.S., and H2020-EINFRA-2015-1-675728 and H2020-EINFRA-2015-676556 to M.O.); and the European Research Council (ERC-2011-ADG_20110209-291433 to M.O.). A.R.-C. was awarded with a ‘‘Junta para la Ampliacio´n de Estudios’’ (Programa JAE) fellowship from Consejo Superior de Investigaciones Cientı´ficas (CSIC). The Structural Biology Unit at IBMB-CSIC is a ‘‘Maria de Maeztu’’ Unit of Excellence awarded by the Ministry of Economy and Competitiveness (MINECO) under MDM-2014-0435. IRB Barcelona is the recipient of a Severo Ochoa Award of Excellence from the Ministry of Economy and Competitiveness (MINECO). The CBS is a member of the French Infrastructure for Integrated Structural Biology (FRISBI), a national infrastructure supported by the French National Research Agency (ANR-10-INBS-05).

DNA accessibility in the cell nucleus depends on its packaging. The stability of the basic compaction unit, the nucleosome, is regulated through the interactions between DNA and histones. Natural sequence variation along the DNA strongly modulates nucleosome stability. Histone variations, mutations and posttranslational modifications alter intra- and internucleosomal interactions. We are investigating interactions which hold nucleosomes together by measuring distances in reconstituted samples using single molecule Forster energy transfer.

Nucleosomes compact the genome and regulate access by wrapping and unwrapping DNA. Here we characterized NaCl-induced opening of mononucleosomes by single-molecule FRET, using donor/acceptor labels on the DNA and various histones. By species-selective fluorescence lifetime and photon distribution analysis we identified new nucleosome opening intermediates and developed a kinetic model [1]. Opening proceeds through a weakening of the H2A-H2B dimer/(H3-H4)2 tetramer interface on a 0.1 ms time scale, then by a slower two-step release of the dimers coupled to DNA unwrapping, extending from several ms to minutes. Nucleosome opening and detachment of histone dimers proceed asymmetrically depending on the DNA sequence.Mutations at the H2A/H3 interface (H2A R81A, R88A, R81A/R88A, R81E/R88E) facilitate the initial opening, confirming the importance of the dimer:tetramer interface for nucleosome stability. This is also supported by molecular dynamics (MD) simulations that show enhanced DNA fluctuations for the mutants. Partially opened states such as described here might be a convenient nucleation point for DNA-recognizing proteins.For characterizing the role of histone tails in nucleosome interaction and stability, we performed MD simulations in explicit and implicit solvent on the H4 tail interacting with the acidic patch of a neighboring nucleosome. The simulations show that H4K16 acetylation decreases the interactions between H4 tail and the acidic patch of the neighboring nucleosome, a process that is central to the regulation of chromatin compaction [2,3].References[1] A. Gansen, A. Valeri, F. Hauger, S. Felekyan, S. Kalinin, K. Toth, J. Langowski, and C. A. M. Seidel. Nucleosome disassembly intermediates characterized by single-molecule FRET. Proc Natl Acad Sci U S A, 106(36):15308-13, Sep 2009.[2] J. Erler, R. Zhang, L. Petridis, X. Cheng, J. C. Smith, and J. Langowski. The role of histone tails in the nucleosome: A computational study. Biophys. J., 107(12):2911-2922, 2014.[3] R. Zhang, J. Erler, J. Langowski. How does histone acetylation regulate chromatin accessibility? A computational study of the role of H4K16 in inter-nucleosome interaction. Biophys. J., under revision.

Histone tails and their posttranslational modifications play a crucial role in controlling genetic activity through alterations of nucleosome structure. Whether or not histone tails regulate DNA accessibility independently of each other or in a concerted fashion is currently under debate. Here we studied the structure-defining properties of selective histone acetylation and point mutations in the H4 tail in a combined bulk FRET - single molecule FRET assay. Nucleosome unwrapping was monitored by FRET between the linker ends of the DNA, while FRET experiments at an internal DNA site in the H2A/H2B binding region reported on nucleosome disassembly.By analysis of nucleosome unwrapping, structural heterogeneity during salt-induced disassembly and dimer exchange between nucleosomes we show that histones H3 and H4 assume significantly different roles in controlling nucleosome architecture. H4-acetylation opposes destabilization by H3-acetylation and reduces linker DNA unwrapping and dimer exchange at higher ionic strength, whereas its influence on nucleosome structure at physiological salt is minute. We found no increase in unwrapping when H3 and H4 were acetylated simultaneously, which challenges the idea of cooperativeness between tails that was observed for truncated H3 and H4. Our data suggest that the effect of lysine acetylation is not cumulative in nature but shows strong histone specificity. The specific role of the H4 tail was finally probed by comparing the effect of point mutations or acetylation of selective lysine residues at positions 5,8,12 and 16.Regardless of the state of acetylation nucleosomes disassemble via an intermediate state, which is suppressed at higher nucleosome concentration, confirming our proposed model of step-wise disassembly.

Nucleosomes, as the basic packing unit of chromatin, regulate DNA accessibility and have significant influence on gene expression. Two copies of each histone protein (H2A, H2B, H3, H4) build up the protein octamer, around which approximately 150 bp of DNA are wrapped.The N-terminal tails of the histones protrude from the nucleosome; they are important for inter- and intranucleosomal interactions. Nucleosome disassembly may be forced in vitro by increasing salt concentration and may be followed by Forster resonance energy transfer (FRET) between fluorophores. We use reconstituted Xenopus laevis nucleosomes, fluorescently labeled on different positions[2] to compare the disassembly of nucleosomes containing mutated histones or modifications to the wild type.Here we focus on the dynamics of the N-tail of H3. Mutated versions of H3 labeled with Alexa488 were used to examine whether there are interactions between the labeled H3 tail and the labeled DNA or other labeled histones. First results show an interaction of the H3 tail and the DNA in vicinity of the dyad axis.The second part is about the functional relevance of a particular region of H2A. Molecular dynamic simulations on ‘tailless’ variants of H3 and H2A have suggested conformational changes affecting two arginines of H2A. Furthermore a conformational change of the protruding part of the DNA was described, which is due to internal conformational changes of H2A[3].From those observations the question arises whether these amino acids are necessary for stable octamers and/or nucleosomes, and how they influence DNA breathing, unwrapping, and stability of entire nucleosomes. To address these questions we generated recombinant H2A proteins incorporating site-specific mutations (R81A, R88A, R81AR88A, R81E, R88E, R81ER88E). Our results show a decreasing stability associated with position (Wt > R88 > R81 > R81R88) and charge (RA > RE) of the amino acids.