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Proteomes
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Latest Discoveries and Proteomics-Based Methods in Histone Biology
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Latest Discoveries and Proteomics-Based Methods in Histone Biology

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 17703

Special Issue Editors

Dr. Delphine Pflieger

E-Mail Website
Guest Editor
Studying the Dynamics of Proteomes, Large-Scale Biology Laboratory, University Grenoble Alps, CEA, INSERM, BIG-BGE, 38000 Grenoble, France
Interests: histone lysine acylations; histone variants; gametogenesis; brain diseases; integrative omics
Dr. Simone Sidoli

E-Mail Website
Guest Editor
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Interests: chromatin biology; mass spectrometry; proteomics; 3D cell culture models

Special Issue Information

Dear Colleagues,

We are assembling a Special Collection of scientific publications for Proteomes titled “Latest Discoveries and Proteomics-Based Methods in Histone Biology”. Our goal is to put together a Special Issue including research articles, reviews, methods, and commentaries focused on new functional roles of histone post-translational modifications (PTMs) and histone variants, or introduce new approaches to study the crosstalk between histones and the chromatin-reading proteome. We felt the urge to prepare this collection as, even though histones and histone modifications have been studied for decades, the groundbreaking discoveries of the last few months have taught us that chromatin is still a mine of unexplored dimensions. Among others, it is very recent news that the histone H3-H4 tetramer can function as a copper reductase enzyme (https://science.sciencemag.org/content/369/6499/59) and at least 5 novel types of histone modifications were discovered just in the last year (https://pubmed.ncbi.nlm.nih.gov/32498971/). In parallel, advancements in sequencing and proteomics strategies have paved the way to exploring new dimensions on chromatin organization, including crosstalk between modifications, protein and PTM turnover, accessibility and transcription rate of chromatin domains, and locus-specific proteomics using dCAS or other methods. For this reason, we highly encourage the submission of method papers and technical notes that propose new quantitative perspectives for the analysis of the histone language.

We also very much welcome perspective and viewpoint articles presenting unconventional ideas, although obviously all articles will go through a rigorous peer-review processing. In addition, the Guest Editors will select 5 manuscripts as feature papers that will be highlighted in the Special Issue and will be free of charge. Examples of manuscript of high interest are those exploring the role of uncharacterized histone variants or unconventional PTMs such as histone clipping.

We look forward to working with you.

Dr. Delphine Pflieger
Dr. Simone Sidoli
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Histone post-translational modifications
  • Histone variants
  • Chromatin-reading proteins
  • Histone clipping
  • Proteoforms
  • Proteomics

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Published Papers (4 papers)

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Research

15 pages, 2567 KiB  
Article
H2B Type 1-K Accumulates in Senescent Fibroblasts with Persistent DNA Damage along with Methylated and Phosphorylated Forms of HMGA1
by Kévin Contrepois, Carl Mann and François Fenaille
Proteomes 2021, 9(2), 30; https://doi.org/10.3390/proteomes9020030 - 21 Jun 2021
Cited by 5 | Viewed by 3985
Abstract
Cellular senescence is a state of terminal proliferative arrest that plays key roles in aging by preventing stem cell renewal and by inducing the expression of a series of inflammatory factors including many secreted proteins with paracrine effects. The in vivo identification of [...] Read more.
Cellular senescence is a state of terminal proliferative arrest that plays key roles in aging by preventing stem cell renewal and by inducing the expression of a series of inflammatory factors including many secreted proteins with paracrine effects. The in vivo identification of senescent cells is difficult due to the absence of universal biomarkers. Chromatin modifications are key aspects of the senescence transition and may provide novel biomarkers. We used a combined protein profiling and bottom-up mass spectrometry approach to characterize the isoforms and post-translational modifications of chromatin proteins over time in post-mitotic human fibroblasts in vitro. We show that the H2B type 1-K variant is specifically enriched in deep senescent cells with persistent DNA damage. This accumulation was not observed in quiescent cells or in cells induced into senescence without DNA damage by expression of the RAF kinase. Similarly, HMGA1a di-methylated and HMGA1b tri-phosphorylated forms accumulated exclusively in the chromatin of cells in deep senescent conditions with persistent DNA damage. H2B type 1-K and modified HMGA1 may thus represent novel biomarkers of senescent cells containing persistent DNA damage. Full article
(This article belongs to the Special Issue Latest Discoveries and Proteomics-Based Methods in Histone Biology)
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19 pages, 4034 KiB  
Article
Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN
by Gianluca Arauz-Garofalo, Meritxell Jodar, Mar Vilanova, Alberto de la Iglesia Rodriguez, Judit Castillo, Ada Soler-Ventura, Rafael Oliva, Marta Vilaseca and Marina Gay
Proteomes 2021, 9(2), 21; https://doi.org/10.3390/proteomes9020021 - 30 Apr 2021
Cited by 8 | Viewed by 4430
Abstract
Protamines replace histones as the main nuclear protein in the sperm cells of many species and play a crucial role in compacting the paternal genome. Human spermatozoa contain protamine 1 (P1) and the family of protamine 2 (P2) proteins. Alterations in protamine PTMs [...] Read more.
Protamines replace histones as the main nuclear protein in the sperm cells of many species and play a crucial role in compacting the paternal genome. Human spermatozoa contain protamine 1 (P1) and the family of protamine 2 (P2) proteins. Alterations in protamine PTMs or the P1/P2 ratio may be associated with male infertility. Top-down proteomics enables large-scale analysis of intact proteoforms derived from alternative splicing, missense or nonsense genetic variants or PTMs. In contrast to current gold standard techniques, top-down proteomics permits a more in-depth analysis of protamine PTMs and proteoforms, thereby opening up new perspectives to unravel their impact on male fertility. We report on the analysis of two normozoospermic semen samples by top-down proteomics. We discuss the difficulties encountered with the data analysis and propose solutions as this step is one of the current bottlenecks in top-down proteomics with the bioinformatics tools currently available. Our strategy for the data analysis combines two software packages, ProSight PD (PS) and TopPIC suite (TP), with a clustering algorithm to decipher protamine proteoforms. We identified up to 32 protamine proteoforms at different levels of characterization. This in-depth analysis of the protamine proteoform landscape of normozoospermic individuals represents the first step towards the future study of sperm pathological conditions opening up the potential personalized diagnosis of male infertility. Full article
(This article belongs to the Special Issue Latest Discoveries and Proteomics-Based Methods in Histone Biology)
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16 pages, 2224 KiB  
Article
Small Mass but Strong Information: Diagnostic Ions Provide Crucial Clues to Correctly Identify Histone Lysine Modifications
by Alaa Hseiky, Marion Crespo, Sylvie Kieffer-Jaquinod, François Fenaille and Delphine Pflieger
Proteomes 2021, 9(2), 18; https://doi.org/10.3390/proteomes9020018 - 23 Apr 2021
Cited by 8 | Viewed by 4229
Abstract
(1) Background: The proteomic analysis of histones constitutes a delicate task due to the combination of two factors: slight variations in the amino acid sequences of variants and the multiplicity of post-translational modifications (PTMs), particularly those occurring on lysine residues. (2) Methods: To [...] Read more.
(1) Background: The proteomic analysis of histones constitutes a delicate task due to the combination of two factors: slight variations in the amino acid sequences of variants and the multiplicity of post-translational modifications (PTMs), particularly those occurring on lysine residues. (2) Methods: To dissect the relationship between both aspects, we carefully evaluated PTM identification on lysine 27 from histone H3 (H3K27) and the artefactual chemical modifications that may lead to erroneous PTM determination. H3K27 is a particularly interesting example because it can bear a range of PTMs and it sits nearby residues 29 and 31 that vary between H3 sequence variants. We discuss how the retention times, neutral losses and immonium/diagnostic ions observed in the MS/MS spectra of peptides bearing modified lysines detectable in the low-mass region might help validate the identification of modified sequences. (3) Results: Diagnostic ions carry key information, thereby avoiding potential mis-identifications due to either isobaric PTM combinations or isobaric amino acid-PTM combinations. This also includes cases where chemical formylation or acetylation of peptide N-termini artefactually occurs during sample processing or simply in the timeframe of LC-MS/MS analysis. Finally, in the very subtle case of positional isomers possibly corresponding to a given mass of lysine modification, the immonium and diagnostic ions may allow the identification of the in vivo structure. Full article
(This article belongs to the Special Issue Latest Discoveries and Proteomics-Based Methods in Histone Biology)
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18 pages, 6760 KiB  
Article
Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
by Simon Daled, Sander Willems, Bart Van Puyvelde, Laura Corveleyn, Sigrid Verhelst, Laura De Clerck, Dieter Deforce and Maarten Dhaenens
Proteomes 2021, 9(2), 17; https://doi.org/10.3390/proteomes9020017 - 21 Apr 2021
Cited by 5 | Viewed by 4029
Abstract
Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic [...] Read more.
Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment between runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX®, Genovis, Lund, Sweden), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues. Raw data are available via ProteomeXchange with identifier PXD024423. Full article
(This article belongs to the Special Issue Latest Discoveries and Proteomics-Based Methods in Histone Biology)
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