Abstract
Epigenomic state preserved in museum specimens could be leveraged to provide unique insights into gene regulation trends associated with accelerating environmental change during the Anthropocene. We address the challenges facing museum epigenomics and propose a collaborative framework for researchers and curators to explore this new field.
| Original language | English |
|---|---|
| Pages (from-to) | 295-300 |
| Number of pages | 6 |
| Journal | Trends in Ecology and Evolution |
| Volume | 35 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - Apr 2020 |
| Externally published | Yes |
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In: Trends in Ecology and Evolution, Vol. 35, No. 4, 04.2020, p. 295-300.
Research output: Contribution to journal › Short Survey/Scientific Report › peer-review
TY - JOUR
T1 - Museum Epigenomics
T2 - Charting the Future by Unlocking the Past
AU - Hahn, Erin E.
AU - Grealy, Alicia
AU - Alexander, Marina
AU - Holleley, Clare E.
N1 - Funding Information: The study was supported financially through CSIRO Environomics Future Science Platform funding awarded to C.H. This study was conceived by C.H. All authors contributed to the writing and editing of the manuscript. Figures were prepared by A.G. and E.H. We thank Andrea Wild for providing collections images for Figure 1 and Millie Menzies for assisting with artwork for Figure 2. We thank Olly Berry, Margaret Cawsey, and Leo Joseph for their valuable comments on the manuscript. Funding Information: The study was supported financially through CSIRO Environomics Future Science Platform funding awarded to C.H. This study was conceived by C.H. All authors contributed to the writing and editing of the manuscript. Figures were prepared by A.G. and E.H. We thank Andrea Wild for providing collections images for Figure 1 and Millie Menzies for assisting with artwork for Figure 2 . We thank Olly Berry, Margaret Cawsey, and Leo Joseph for their valuable comments on the manuscript. Bisulfite sequencing bisulfite treatment of DNA converts cytosines to uracils but leaves methylated cytosines (specifically, 5-methylcytosine) unchanged. Sequencing of bisulfite-treated DNA and comparison with untreated DNA reveals sites of DNA methylation. ChIP-Seq ch romatin i mmuno p recipitation followed by seq uencing is used to analyse protein interactions with DNA. In the ChIP procedure, chromatin is crosslinked and antibodies against target proteins are used to enrich for bound DNA, which is then sequenced. Chromatin the complex of DNA and proteins that packages DNA into chromosomes in eukaryotic cells. Crosslinking tissue fixation is typically achieved through treatment with formalin (4% w/v formaldehyde in a buffered salt solution). Formaldehyde induces covalent chemical bonds within and between DNA and proteins. Cytosine deamination removal of an amine group converts cytosine into uracil. This process occurs spontaneously in living cells but is corrected by the cellular machinery. Postmortem deamination accumulates spontaneously as DNA ages. DNA methylation methylation is the addition of a methyl (CH 3 ) group to the nucleotide base cytosine or, less commonly, adenine. Cytosine methylation most commonly occurs at the fifth position in the base’s six atom ring (5-methylcytosine). DNA methylation alters gene expression, however, the extent, placement and effect vary between taxa. Epigenome chemical modifications to the genome that result in changes in gene expression that cannot be explained by changes in DNA sequence. While it is common in other fields to include a dependency upon heritability in a definition of epigenomics, we do not invoke this meaning because dynamic (plastic) changes that are not inherited may still be indicative of an adaptive response to environmental challenges. Histone modifications histones are the predominant protein component of chromatin, acting as spools around which the DNA is wrapped. Chemical modifications are deposited on specific histones to regulate gene expression. Addition of methyl, acetyl, phosphate, and ubiquitin groups on histones can increase or decrease gene expression, depending on position and context. Mass spectrometry a method of characterising proteins based on the mass-to-charge ratio of their molecular subunits. Mass spectrometry can be used to read the amino acid sequence of proteins, characterise protein interactions, and detect chemical modifications. Noncoding RNA functional RNAs that are transcribed from DNA but not translated into protein. These RNAs act to regulate gene expression. Nucleosome the primary packaging unit of DNA, comprised of a stretch of DNA coiled around a complex of eight histones. Positioning of nucleosomes along the DNA strand affects gene expression. Proteome the complement of proteins expressed by a cell, tissue, or organism. The proteome changes as gene expression is up- or downregulated and thus reflects proteins that are present in a given cell, tissue, or organism at a given time. Transcriptome the complement of RNA transcripts expressed by a cell, tissue, or organism. The transcriptome can refer to both coding (messenger) and noncoding RNAs, however, it generally refers only to coding RNAs, those that will be translated into proteins. Voucher specimen a representative sample retained as a reference for an identified taxon and deposited in an accessible and permanent collection facility. Publisher Copyright: © 2019
PY - 2020/4
Y1 - 2020/4
N2 - Epigenomic state preserved in museum specimens could be leveraged to provide unique insights into gene regulation trends associated with accelerating environmental change during the Anthropocene. We address the challenges facing museum epigenomics and propose a collaborative framework for researchers and curators to explore this new field.
AB - Epigenomic state preserved in museum specimens could be leveraged to provide unique insights into gene regulation trends associated with accelerating environmental change during the Anthropocene. We address the challenges facing museum epigenomics and propose a collaborative framework for researchers and curators to explore this new field.
KW - collections
KW - epigenomics
KW - gene regulation
KW - genome
KW - museum
KW - temporal trends
UR - http://www.scopus.com/inward/record.url?scp=85077920502&partnerID=8YFLogxK
U2 - 10.1016/j.tree.2019.12.005
DO - 10.1016/j.tree.2019.12.005
M3 - Short Survey/Scientific Report
C2 - 31955919
AN - SCOPUS:85077920502
SN - 0169-5347
VL - 35
SP - 295
EP - 300
JO - Trends in Ecology and Evolution
JF - Trends in Ecology and Evolution
IS - 4
ER -