Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2017 Oct 18

PMID 29038170

Citations 6

Authors

Shuangying Jiang

Yan Liu

Caiyue Xu

Yun Wang

Jianhui Gong

Yue Shen

Qingyu Wu

Jef D Boeke

Junbiao Dai

Affiliations

Soon will be listed here.

Abstract

Using a comprehensive library of histone H2A and H2B mutants, we assessed the biological function of each amino acid residue involved in various stress conditions including exposure to different DNA damage-inducing reagents, different growth temperatures, and other chemicals. H2B N- and H2A C-termini were critical for maintaining nucleosome function and mutations in these regions led to pleiotropic phenotypes. Additionally, two screens were performed using this library, monitoring heterochromatin gene silencing and genome stability, to identify residues that could compromise normal function when mutated. Many distinctive regions within the nucleosome were revealed. Furthermore, we used the barcode sequencing (bar-seq) method to profile the mutant composition of many libraries in one high-throughput sequencing experiment, greatly reducing the labor and increasing the capacity. This study not only demonstrates the applications of the versatile histone library, but also reveals many previously unknown functions of histone H2A and H2B.

Citing Articles

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Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding.

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A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress.

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Structure and function of the Orc1 BAH-nucleosome complex.

De Ioannes P, Leon V, Kuang Z, Wang M, Boeke J, Hochwagen A Nat Commun. 2019; 10(1):2894.

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References

Luger K, Mader A, Richmond R, Sargent D, Richmond T . Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997; 389(6648):251-60. DOI: 10.1038/38444. View

Zheng S, Crickard J, Srikanth A, Reese J . A highly conserved region within H2B is important for FACT to act on nucleosomes. Mol Cell Biol. 2013; 34(3):303-14. PMC: 3911510. DOI: 10.1128/MCB.00478-13. View

Keogh M, Kim J, Downey M, Fillingham J, Chowdhury D, Harrison J . A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature. 2005; 439(7075):497-501. DOI: 10.1038/nature04384. View

Ng H, Ciccone D, Morshead K, Oettinger M, Struhl K . Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc Natl Acad Sci U S A. 2003; 100(4):1820-5. PMC: 149917. DOI: 10.1073/pnas.0437846100. View

Masumoto H, Hawke D, Kobayashi R, Verreault A . A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature. 2005; 436(7048):294-8. DOI: 10.1038/nature03714. View

Tan M, Luo H, Lee S, Jin F, Yang J, Montellier E . Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell. 2011; 146(6):1016-28. PMC: 3176443. DOI: 10.1016/j.cell.2011.08.008. View

Downs J, Lowndes N, Jackson S . A role for Saccharomyces cerevisiae histone H2A in DNA repair. Nature. 2001; 408(6815):1001-4. DOI: 10.1038/35050000. View

Ng T, Lenstra T, Duggan N, Jiang S, Ceto S, Holstege F . Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics. 2013; 195(3):795-807. PMC: 3813865. DOI: 10.1534/genetics.113.152082. View

Yao G, Wan J, Liu Q, Mu C, Wang Y, Sang J . Characterization of Pph3-mediated dephosphorylation of Rad53 during methyl methanesulfonate-induced DNA damage repair in . Biochem J. 2017; 474(7):1293-1306. DOI: 10.1042/BCJ20160889. View

10.

Robzyk K, Recht J, Osley M . Rad6-dependent ubiquitination of histone H2B in yeast. Science. 2000; 287(5452):501-4. DOI: 10.1126/science.287.5452.501. View

11.

Sun Z, Allis C . Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 2002; 418(6893):104-8. DOI: 10.1038/nature00883. View

12.

Dai J, Hyland E, Yuan D, Huang H, Bader J, Boeke J . Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell. 2008; 134(6):1066-78. PMC: 2701395. DOI: 10.1016/j.cell.2008.07.019. View

13.

Keogh M, Kurdistani S, Morris S, Ahn S, Podolny V, Collins S . Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005; 123(4):593-605. DOI: 10.1016/j.cell.2005.10.025. View

14.

Smith A, Heisler L, St Onge R, Farias-Hesson E, Wallace I, Bodeau J . Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res. 2010; 38(13):e142. PMC: 2910071. DOI: 10.1093/nar/gkq368. View

15.

Luo J, Xu X, Hall H, Hyland E, Boeke J, Hazbun T . Histone h3 exerts a key function in mitotic checkpoint control. Mol Cell Biol. 2009; 30(2):537-49. PMC: 2798460. DOI: 10.1128/MCB.00980-09. View

16.

Aguilera J, Randez-Gil F, Prieto J . Cold response in Saccharomyces cerevisiae: new functions for old mechanisms. FEMS Microbiol Rev. 2007; 31(3):327-41. DOI: 10.1111/j.1574-6976.2007.00066.x. View

17.

Kimura H, Cook P . Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J Cell Biol. 2001; 153(7):1341-53. PMC: 2150718. DOI: 10.1083/jcb.153.7.1341. View

18.

Armache K, Garlick J, Canzio D, Narlikar G, Kingston R . Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Å resolution. Science. 2011; 334(6058):977-82. PMC: 4098850. DOI: 10.1126/science.1210915. View

19.

Richards E, Elgin S . Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell. 2002; 108(4):489-500. DOI: 10.1016/s0092-8674(02)00644-x. View

20.

Kawashima S, Nakabayashi Y, Matsubara K, Sano N, Enomoto T, Tanaka K . Global analysis of core histones reveals nucleosomal surfaces required for chromosome bi-orientation. EMBO J. 2011; 30(16):3353-67. PMC: 3160661. DOI: 10.1038/emboj.2011.241. View