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1. Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant.

Author

Earnshaw, WC, Allshire, RC, Black, BE, Bloom, K, Brinkley, BR, Brown, W, Cheeseman, IM, Choo, KHA, Copenhaver, GP, Deluca, JG, Desai, A, Diekmann, S, Erhardt, S, Fitzgerald-Hayes, M, Foltz, D, Fukagawa, T, Gassmann, R, Gerlich, DW, Glover, DM, Gorbsky, GJ, Harrison, SC, Heun, P, Hirota, T, Jansen, LET, Karpen, G, Kops, GJPL, Lampson, MA, Lens, SM, Losada, A, Luger, K, Maiato, H, Maddox, PS, Margolis, RL, Masumoto, H, McAinsh, AD, Mellone, BG, Meraldi, P, Musacchio, A, Oegema, K, O'Neill, RJ, Salmon, ED, Scott, KC, Straight, AF, Stukenberg, PT, Sullivan, BA, Sullivan, KF, Sunkel, CE, Swedlow, JR, Walczak, CE, Warburton, PE, Westermann, S, Willard, HF, Wordeman, L, Yanagida, M, Yen, TJ, Yoda, K, and Cleveland, DW

Subjects
Centromere, Kinetochores, Humans, Scleroderma, Systemic, Chromosomal Proteins, Non-Histone, Histones, Autoantigens, Terminology as Topic, Centromere Protein A, centromere, CENP-A, histone, kinetochore, CenH3, Developmental Biology, Biochemistry and Cell Biology, Genetics
Abstract

The first centromeric protein identified in any species was CENP-A, a divergent member of the histone H3 family that was recognised by autoantibodies from patients with scleroderma-spectrum disease. It has recently been suggested to rename this protein CenH3. Here, we argue that the original name should be maintained both because it is the basis of a long established nomenclature for centromere proteins and because it avoids confusion due to the presence of canonical histone H3 at centromeres.

Published
2013

3. Nucleosome Structure and Function

Author

Chodaparambil, J. V., Edayathumangalam, R. S., Bao, Y., Park, Y. -J., Luger, K., Stock, G., editor, Lessl, M., editor, Berger, S. L., editor, Nakanishi, O., editor, and Haendler, B., editor

Published
2006
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7. In Vitro Chromatin Assembly

Author

Muthurajan, U., primary, Mattiroli, F., additional, Bergeron, S., additional, Zhou, K., additional, Gu, Y., additional, Chakravarthy, S., additional, Dyer, P., additional, Irving, T., additional, and Luger, K., additional

Published
2016
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8. Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant

Author

Earnshaw, W. C., Allshire, R. C., Black, B. E., Bloom, K., Brinkley, B. R., Brown, W., Cheeseman, I. M., Choo, K. H. A., Copenhaver, G. P., DeLuca, J. G., Desai, A., Diekmann, S., Erhardt, S., Fitzgerald-Hayes, M., Foltz, D., Fukagawa, T., Gassmann, R., Gerlich, D. W., Glover, D. M., Gorbsky, G. J., Harrison, S. C., Heun, P., Hirota, T., Jansen, L. E. T., Karpen, G., Kops, G. J. P. L., Lampson, M. A., Lens, S. M., Losada, A., Luger, K., Maiato, H., Maddox, P. S., Margolis, R. L., Masumoto, H., McAinsh, A. D., Mellone, B. G., Meraldi, P., Musacchio, A., Oegema, K., O’Neill, R. J., Salmon, E. D., Scott, K. C., Straight, A. F., Stukenberg, P. T., Sullivan, B. A., Sullivan, K. F., Sunkel, C. E., Swedlow, J. R., Walczak, C. E., Warburton, P. E., Westermann, S., Willard, H. F., Wordeman, L., Yanagida, M., Yen, T. J., Yoda, K., and Cleveland, D. W.

Published
2013
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17. In Vitro Chromatin Assembly: Strategies and Quality Control

Author

Muthurajan U, Francesca Mattiroli, Bergeron S, Zhou K, Gu Y, Chakravarthy S, Dyer P, Irving T, and Luger K

Subjects
Models, Molecular, Protein Folding, DNA, Chromatin Assembly and Disassembly, Microscopy, Atomic Force, Chromatin, Article, Nucleosomes, Histones, Native Polyacrylamide Gel Electrophoresis, X-Ray Diffraction, Scattering, Small Angle, Animals, Humans, Micrococcal Nuclease, Protein Multimerization, Ultracentrifugation, Fluorescent Dyes
Abstract

Chromatin accessibility is modulated by structural transitions that provide timely access to the genetic and epigenetic information during many essential nuclear processes. These transitions are orchestrated by regulatory proteins that coordinate intricate structural modifications and signalling pathways. In vitro reconstituted chromatin samples from defined components are instrumental in defining the mechanistic details of such processes. The bottleneck to appropriate in vitro analysis is the production of high quality, and quality-controlled, chromatin substrates. In this chapter we describe methods for in vitro chromatin reconstitution and quality control. We highlight the strengths and weaknesses of various approaches, and emphasize quality control steps that ensure reconstitution of a bona fide homogenous chromatin preparation. This is essential for optimal reproducibility and reliability of ensuing experiments using chromatin substrates.

Published
2016

19. Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments

Author

Thastrom, A., Gottesfeld, J.M., Luger, K., and Widom, J.

Subjects
DNA binding proteins -- Chemical properties, DNA binding proteins -- Structure, Nucleosomes -- Chemical properties, Nucleosomes -- Structure, Chemistry, Analytic, Biological sciences, Chemistry
Abstract

A method based on quantitative analysis of nucleosome dissociation in dilution experiments that provides a simple practical measure of nucleosome stability was developed recently, and soluble conditions were found, which suggest that this approach might allow absolute equilibrium affinity of the histone chamber for DNA to be measured. The concept that nucleosome assembly/dissembly process is not strictly reversible in these solution conditions is demonstrated, and this implies that equilibrium affinities cannot be obtained from these measurements,

Published
2004

20. A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation

Author

Langowski, J, Zhao, H, Ghirlando, R, Alfonso, C, Arisaka, F, Attali, I, Bain, DL, Bakhtina, MM, Becker, DF, Bedwell, GJ, Bekdemir, A, Besong, TMD, Birck, C, Brautigam, CA, Brennerman, W, Byron, O, Bzowska, A, Chaires, JB, Chaton, CT, Coelfen, H, Connaghan, KD, Crowley, KA, Curth, U, Daviter, T, Dean, WL, Diez, AI, Ebel, C, Eckert, DM, Eisele, LE, Eisenstein, E, England, P, Escalante, C, Fagan, JA, Fairman, R, Finn, RM, Fischle, W, Garcia de la Torre, J, Gor, J, Gustafsson, H, Hall, D, Harding, SE, Hernandez Cifre, JG, Herr, AB, Howell, EE, Isaac, RS, Jao, S-C, Jose, D, Kim, S-J, Kokona, B, Kornblatt, JA, Kosek, D, Krayukhina, E, Krzizike, D, Kusznir, EA, Kwon, H, Larson, A, Laue, TM, Le Roy, A, Leech, AP, Lilie, H, Luger, K, Luque-Ortega, JR, Ma, J, May, CA, Maynard, EL, Modrak-Wojcik, A, Mok, Y-F, Muecke, N, Nagel-Steger, L, Narlikar, GJ, Noda, M, Nourse, A, Obsil, T, Park, CK, Park, J-K, Pawelek, PD, Perdue, EE, Perkins, SJ, Perugini, MA, Peterson, CL, Peverelli, MG, Piszczek, G, Prag, G, Prevelige, PE, Raynal, BDE, Rezabkova, L, Richter, K, Ringel, AE, Rosenberg, R, Rowe, AJ, Rufer, AC, Scott, DJ, Seravalli, JG, Solovyova, AS, Song, R, Staunton, D, Stoddard, C, Stott, K, Strauss, HM, Streicher, WW, Sumida, JP, Swygert, SG, Szczepanowski, RH, Tessmer, I, Toth, RT, Tripathy, A, Uchiyama, S, Uebel, SFW, Unzai, S, Gruber, AV, von Hippel, PH, Wandrey, C, Wang, S-H, Weitzel, SE, Wielgus-Kutrowska, B, Wolberger, C, Wolff, M, Wright, E, Wu, Y-S, Wubben, JM, Schuck, P, Langowski, J, Zhao, H, Ghirlando, R, Alfonso, C, Arisaka, F, Attali, I, Bain, DL, Bakhtina, MM, Becker, DF, Bedwell, GJ, Bekdemir, A, Besong, TMD, Birck, C, Brautigam, CA, Brennerman, W, Byron, O, Bzowska, A, Chaires, JB, Chaton, CT, Coelfen, H, Connaghan, KD, Crowley, KA, Curth, U, Daviter, T, Dean, WL, Diez, AI, Ebel, C, Eckert, DM, Eisele, LE, Eisenstein, E, England, P, Escalante, C, Fagan, JA, Fairman, R, Finn, RM, Fischle, W, Garcia de la Torre, J, Gor, J, Gustafsson, H, Hall, D, Harding, SE, Hernandez Cifre, JG, Herr, AB, Howell, EE, Isaac, RS, Jao, S-C, Jose, D, Kim, S-J, Kokona, B, Kornblatt, JA, Kosek, D, Krayukhina, E, Krzizike, D, Kusznir, EA, Kwon, H, Larson, A, Laue, TM, Le Roy, A, Leech, AP, Lilie, H, Luger, K, Luque-Ortega, JR, Ma, J, May, CA, Maynard, EL, Modrak-Wojcik, A, Mok, Y-F, Muecke, N, Nagel-Steger, L, Narlikar, GJ, Noda, M, Nourse, A, Obsil, T, Park, CK, Park, J-K, Pawelek, PD, Perdue, EE, Perkins, SJ, Perugini, MA, Peterson, CL, Peverelli, MG, Piszczek, G, Prag, G, Prevelige, PE, Raynal, BDE, Rezabkova, L, Richter, K, Ringel, AE, Rosenberg, R, Rowe, AJ, Rufer, AC, Scott, DJ, Seravalli, JG, Solovyova, AS, Song, R, Staunton, D, Stoddard, C, Stott, K, Strauss, HM, Streicher, WW, Sumida, JP, Swygert, SG, Szczepanowski, RH, Tessmer, I, Toth, RT, Tripathy, A, Uchiyama, S, Uebel, SFW, Unzai, S, Gruber, AV, von Hippel, PH, Wandrey, C, Wang, S-H, Weitzel, SE, Wielgus-Kutrowska, B, Wolberger, C, Wolff, M, Wright, E, Wu, Y-S, Wubben, JM, and Schuck, P

Abstract

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.

Published
2015

25. A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin.

Author

Vermeulen, M., Walter, W., Guezennec, X.S. le, Kim, J., Edayathumangalam, R.S., Lasonder, E., Luger, K., Roeder, R.G., Logie, C., Berger, S.L., Stunnenberg, H.G., Vermeulen, M., Walter, W., Guezennec, X.S. le, Kim, J., Edayathumangalam, R.S., Lasonder, E., Luger, K., Roeder, R.G., Logie, C., Berger, S.L., and Stunnenberg, H.G.

Abstract

Contains fulltext : 36160.pdf (publisher's version ) (Closed access), Transcription in eukaryotes is governed in part by histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-containing complexes that are recruited via activators and repressors, respectively. Here, we show that the Sin3/HDAC and N-CoR/SMRT corepressor complexes repress transcription from histone H3- and/or H4-acetylated nucleosomal templates in vitro. Repression of histone H3-acetylated templates was completely dependent on the histone deacetylase activity of the corepressor complexes, whereas this activity was not required to repress H4-acetylated templates. Following deacetylation, both complexes become stably anchored in a repressor-independent manner to nucleosomal templates containing hypoacetylated histone H3, but not H4, resulting in dominance of repression over activation. The observed stable anchoring of corepressor complexes casts doubt on the view of a dynamic balance between readily exchangeable HAT and HDAC activities regulating transcription and implies that pathways need to be in place to actively remove HDAC complexes from hypoacetylated promoters to switch on silent genes.

Published
2006

42. Nucleosome Structure and Function.

Author

Stock, G., Lessl, M., Berger, S. L., Nakanishi, O., Haendler, B., Chodaparambil, J. V., Edayathumangalam, R. S., Bao, Y., Park, Y. -J., and Luger, K.

Abstract

It is now widely recognized that the packaging of genomic DNA, together with core histones, linker histones, and other functional proteins into chromatin profoundly influences nuclear processes such as transcription, replication, DNA repair, and recombination. How chromatin structure modulates the expression of knowledge encoded in eukaryotic genomes, and how these processes take place within the context of a highly complex and compacted genomic chromatin environment remains a major unresolved question in biology. Here we review recent advances in nucleosome structure and dynamics. [ABSTRACT FROM AUTHOR]

Published
2006
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50. Packaging of DNA by shell crosslinked nanoparticles.

Author

Thurmond II, K. Bruce, Remsen, Edward E., Kowalewski, Tomasz, Wooley, Karen L., Choi, S.-K., Felgner, P.L., Thurmond, K.B., Polach, K.J., Studitsky, V.M., Luger, K., Behr, J.-P., Lasic, D.D., Koltover, I., Kabanov, A.V., Yoshikawa, K., Huang, C., Katayose, S., La, S.B., Baker, J.R., and Fritz, H.

Published
1999
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