A Novel Method to Generate MNase Ladders Reveal Rapid Chromatin Remodeling upon Gametogenesis and Mating in Chlamydomonas

Potdar, Pooja; Pinto, Patrícia; D’Souza, Nicole; Joshi, Prajakta; Malwade, Akshay; Sen, Subhojit

doi:10.1016/j.protis.2018.06.006

Cited by 7 publications

(6 citation statements)

References 41 publications

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“…The estimation of nucleosomal spacing was performed essentially as described by Potdar et al (2018). Briefly, a standard curve was generated using the ladder of molecule markers.…”

Section: Partial Micrococcal Nuclease (Mnase) Digestion Assaymentioning

confidence: 99%

Compensatory replacement of the BigH1 variant histone by canonical H1 supports normal embryonic development in Drosophila

Han

Chen

et al. 2019

Preprint

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Histone variants carry specific functions in addition to those fulfilled by their canonical counterparts. Variants of the linker Histone H1 are prevalent in vertebrates and based on the pattern of their expression, many are presumed to function during germline and the earliest zygotic stages of development.While the existence of multiple H1 variants has hampered their study in vertebrates, a single variant, BigH1, was identified in Drosophila, promising to accelerate our understanding of the biological functions of H1 and H1 variants.Here we uncovered evidence for a compensatory activity that loads maternal H1 onto BigH1-devoid chromatin. Remarkably, this H1-based chromatin state is fully functional in supporting normal embryonic development, suggesting that H1 carries the essential function of the BigH1 molecule under the same developmental context. In addition, we discovered that this compensatory replacement of BigH1 with H1 might be limited to rapidly cycling cells in early embryos.

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“…The estimation of nucleosomal spacing was performed essentially as described by Potdar et al (2018). Briefly, a standard curve was generated using the ladder of molecule markers.…”

Section: Partial Micrococcal Nuclease (Mnase) Digestion Assaymentioning

confidence: 99%

Compensatory replacement of the BigH1 variant histone by canonical H1 supports normal embryonic development in Drosophila

Han

Chen

et al. 2019

Preprint

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“…Omic technologies help drive healthcare decisions toward the uniqueness in each individual. This review reveals the need for new actuators to profile emerging parameters such as chromatin structurebased findings, surfacing as a result of new epigenomic platforms [67,68]. Moreover, there is a great need for designing information workflows directed toward specific cancers that allow translational analysis from appropriate sample source(s).…”

Section: Discussionmentioning

confidence: 99%

Explore & actuate: the future of personalized medicine in oncology through emerging technologies

Babu,

Sen

2024

Current Opinion in Oncology

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Purpose of review The future of medicine is aimed to equip the physician with tools to assess the individual health of the patient for the uniqueness of the disease that separates it from the rest. The integration of omics technologies into clinical practice, reviewed here, would open new avenues for addressing the spatial and temporal heterogeneity of cancer. The rising cancer burden patiently awaits the advent of such an approach to personalized medicine for routine clinical settings. Recent findings To weigh the translational potential, multiple technologies were categorized based on the extractable information from the different types of samples used, to the various omic-levels of molecular information that each technology has been able to advance over the last 2 years. This review uses a multifaceted classification that helps to assess translational potential in a meaningful way toward clinical adaptation. Summary The importance of distinguishing technologies based on the flow of information from exploration to actuation puts forth a framework that allows the clinicians to better adapt a chosen technology or use them in combination to enhance their goals toward personalized medicine.

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“…3.6. In situ MNase digestion of algal chromatin Nanochlorum eucaryotum (SAG 55.87) chromatin was digested with MNase as described by Potdar et al [24]. Briefly, up to 9 × 10 7 N. eucaryotum (SAG 55.87) cells were harvested by centrifugation (2500 × g, royalsocietypublishing.org/journal/rsos R. Soc.…”

Section: Genome Sequencingmentioning

confidence: 99%

Slaying the last unicorn: discovery of histones in the microalga Nanochlorum eucaryotum

Soo

Warnecke

2021

R. Soc. open sci.

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Histones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3 and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga Nanochlorum eucaryotum . If true, derived histone loss in this lineage would constitute an exceptional case that might help us further understand the principles governing eukaryotic gene regulation. To substantiate these earlier reports of histone loss in N. eucaryotum, we sequenced, assembled and quantified its transcriptome. Following a systematic search for histone-fold domains in the assembled transcriptome, we detect orthologues to all four core histones. We also find histone mRNAs to be highly expressed, comparable to the situation in other eukaryotes. Finally, we obtain characteristic protection patterns when N. eucaryotum chromatin is subjected to micrococcal nuclease digestion, indicating widespread formation of nucleosomal complexes in vivo . We conclude that previous reports of missing histones in N. eucaryotum were mistaken. By all indications, Nanochlorum eucaryotum has histone-based chromatin characteristic of most eukaryotes.

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A Novel Method to Generate MNase Ladders Reveal Rapid Chromatin Remodeling upon Gametogenesis and Mating in Chlamydomonas

Cited by 7 publications

References 41 publications

Compensatory replacement of the BigH1 variant histone by canonical H1 supports normal embryonic development in Drosophila

Compensatory replacement of the BigH1 variant histone by canonical H1 supports normal embryonic development in Drosophila

Explore & actuate: the future of personalized medicine in oncology through emerging technologies

Slaying the last unicorn: discovery of histones in the microalga Nanochlorum eucaryotum

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