A synthetic biology approach to probing nucleosome symmetry

Yuichi Ichikawa; Caitlin F. Connelly; Alon Appleboim; Thomas C.R. Miller; Hadas Jacobi; Nebiyu A. Abshiru; Hsin Jung Chou; Yuanyuan Chen; Upasna Sharma; Yupeng Zheng; Paul M. Thomas; Hsuiyi V. Chen; Vineeta Bajaj; Christoph W. Müller; Neil L. Kelleher; Nir Friedman; Daniel N.A. Bolon; Oliver J. Rando; Paul D. Kaufman

doi:10.7554/eLife.28836

A synthetic biology approach to probing nucleosome symmetry

Yuichi Ichikawa, Caitlin F. Connelly, Alon Appleboim, Thomas C.R. Miller, Hadas Jacobi, Nebiyu A. Abshiru, Hsin Jung Chou, Yuanyuan Chen, Upasna Sharma, Yupeng Zheng, Paul M. Thomas, Hsuiyi V. Chen, Vineeta Bajaj, Christoph W. Müller, Neil L. Kelleher, Nir Friedman, Daniel N.A. Bolon, Oliver J. Rando^*, Paul D. Kaufman

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.

Original language	American English
Article number	e28836
Journal	eLife
Volume	6
DOIs	https://doi.org/10.7554/eLife.28836
State	Published - 12 Sep 2017

Bibliographical note

Funding Information:
We thank members of the Rando and Kaufman labs for discussions and critical reading of the manuscript. This work was supported by NIH grant R01GM100164 (OJR and PDK), ERC Grant 340712 (NF), and the ISF I-Core on Chromatin and RNA in Gene Regulation (NF). Proteomics experiments were supported by NIH grants P30CA060553 and P41GM108569. AA is grateful to the Azrieli foundation for the award of an Azrieli Fellowship.

Publisher Copyright:
© Ichikawa et al.

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Ichikawa, Y., Connelly, C. F., Appleboim, A., Miller, T. C. R., Jacobi, H., Abshiru, N. A., Chou, H. J., Chen, Y., Sharma, U., Zheng, Y., Thomas, P. M., Chen, H. V., Bajaj, V., Müller, C. W., Kelleher, N. L., Friedman, N., Bolon, D. N. A., Rando, O. J., & Kaufman, P. D. (2017). A synthetic biology approach to probing nucleosome symmetry. eLife, 6, Article e28836. https://doi.org/10.7554/eLife.28836

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title = "A synthetic biology approach to probing nucleosome symmetry",

abstract = "The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.",

author = "Yuichi Ichikawa and Connelly, {Caitlin F.} and Alon Appleboim and Miller, {Thomas C.R.} and Hadas Jacobi and Abshiru, {Nebiyu A.} and Chou, {Hsin Jung} and Yuanyuan Chen and Upasna Sharma and Yupeng Zheng and Thomas, {Paul M.} and Chen, {Hsuiyi V.} and Vineeta Bajaj and M{\"u}ller, {Christoph W.} and Kelleher, {Neil L.} and Nir Friedman and Bolon, {Daniel N.A.} and Rando, {Oliver J.} and Kaufman, {Paul D.}",

note = "Funding Information: We thank members of the Rando and Kaufman labs for discussions and critical reading of the manuscript. This work was supported by NIH grant R01GM100164 (OJR and PDK), ERC Grant 340712 (NF), and the ISF I-Core on Chromatin and RNA in Gene Regulation (NF). Proteomics experiments were supported by NIH grants P30CA060553 and P41GM108569. AA is grateful to the Azrieli foundation for the award of an Azrieli Fellowship. Publisher Copyright: {\textcopyright} Ichikawa et al.",

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AU - Jacobi, Hadas

AU - Abshiru, Nebiyu A.

AU - Chou, Hsin Jung

AU - Chen, Yuanyuan

AU - Sharma, Upasna

AU - Zheng, Yupeng

AU - Thomas, Paul M.

AU - Chen, Hsuiyi V.

AU - Bajaj, Vineeta

AU - Müller, Christoph W.

AU - Kelleher, Neil L.

AU - Friedman, Nir

AU - Bolon, Daniel N.A.

AU - Rando, Oliver J.

AU - Kaufman, Paul D.

N1 - Funding Information: We thank members of the Rando and Kaufman labs for discussions and critical reading of the manuscript. This work was supported by NIH grant R01GM100164 (OJR and PDK), ERC Grant 340712 (NF), and the ISF I-Core on Chromatin and RNA in Gene Regulation (NF). Proteomics experiments were supported by NIH grants P30CA060553 and P41GM108569. AA is grateful to the Azrieli foundation for the award of an Azrieli Fellowship. Publisher Copyright: © Ichikawa et al.

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N2 - The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.

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A synthetic biology approach to probing nucleosome symmetry

Abstract

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