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Histone Post-Translational Modifications and Nucleosome Organisation in Transcriptional Regulation: Some Open Questions

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Protein Reviews

Part of the book series: Advances in Experimental Medicine and Biology ((PROTRE,volume 966))

Abstract

The organisation of chromatin is first discussed to conclude that nucleosomes play both structural and transcription-regulatory roles. The presence of nucleosomes makes difficult the access of transcriptional factors to their target sequences and the action of RNA polymerases. The histone post-translational modifications and nucleosome remodelling are first discussed, from a historical point of view, as mechanisms to remove the obstacles imposed by chromatin structure to transcription. Instead of reviewing the state of the art of the whole field, this review is centred on some open questions. First, some “non-classical” histone modifications, such as short-chain acylations other than acetylation, are considered to conclude that their relationship with the concentration of metabolic intermediaries might make of them a sensor of the physiological state of the cells. Then attention is paid to the interest of studying chromatin organisation and epigenetic marks at a single nucleosome level as a complement to genome-wide approaches. Finally, as a consequence of the above questions, the review focuses on the presence of multiple histone post-translational modifications on a single nucleosome. The methods to detect them and their meaning, with special emphasis on bivalent marks, are discussed.

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Abbreviations

BRD:

bromodomain

ChIP:

chromatin immunoprecipitation

HAT:

histone acetyltransferase

HDAC:

histone deacetylase

HP1:

heterochromatin protein 1

MNP:

micrococcal nuclease protection

NFR:

nucleosome-free region

PCR:

polymerase chain reaction

PHD:

plant homeodomain

PTM:

post-translational modification

RT-qPCR:

real time quantitative PCR

TG:

transglutaminase

TPA:

12-O-tetradecanoylphorbol-13-acetate

TSS:

Transcription start site

YEATS:

YNL107w, ENL, AF-9, and TFIIF small subunit

ZMYND8:

zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8

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Acknowledgments

This work was supported by grants from the Spanish Ministerio de Economía y Competitividad (FIS PI12/02110) and from Generalitat Valenciana (PROMETEO 2013–005). We are very indebted to Prof. Juan R. Viña for attracting our attention to the metabolic enzymes that “moonlight” in the nucleus.

Conflict of Interest

The authors declare no conflict of interests.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology and Institute of Health Research INCLIVA, University of Valencia, Valencia, Spain

    Josefa Castillo, Gerardo López-Rodas & Luis Franco

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  1. Josefa Castillo
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  2. Gerardo López-Rodas
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  3. Luis Franco
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Correspondence to Luis Franco .

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  1. Biochem and Mol Biol, Baylor College of Medicine, Houston, Texas, USA

    M. Zouhair Atassi

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Castillo, J., López-Rodas, G., Franco, L. (2017). Histone Post-Translational Modifications and Nucleosome Organisation in Transcriptional Regulation: Some Open Questions. In: Atassi, M. (eds) Protein Reviews. Advances in Experimental Medicine and Biology(), vol 966. Springer, Singapore. https://doi.org/10.1007/5584_2017_58

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