scholarly journals Histone modifications during the life cycle of the brown alga Ectocarpus

2020 ◽  
Author(s):  
Simon Bourdareau ◽  
Leila Tirichine ◽  
Bérangère Lombard ◽  
Damarys Loew ◽  
Delphine Scornet ◽  
...  
Keyword(s):  
Life Cycle ◽  
Brown Algae ◽  
Land Plant ◽  
Chromatin Modifications ◽  
Post Translational Modifications ◽  
Transcription Start Sites ◽  
Histone Ptms ◽  
Genomic Regions ◽  
Active Genes

AbstractBackgroundBrown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here we have focused on mechanisms of epigenetic regulation involving post-translational modifications (PTMs) of histone proteins.ResultsA total of 47 histone PTMs were identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identified PTMs associated with transcription start sites (TSSs) and gene bodies of active genes, and with transposons. H3K79me2 exhibited an unusual pattern, often marking large genomic regions spanning several genes. TSSs of closely spaced divergently transcribed gene pairs shared a common nucleosome depleted region and exhibited shared histone PTM peaks. Overall, patterns of histone PTMs were stable through the life cycle. Analysis of histone PTMs at generation-biased genes identified a correlation between the presence of specific chromatin marks and the level of gene expression.ConclusionsThe overview of histone PTMs in the brown algae presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.

scholarly journals Histone modifications during the life cycle of the brown alga Ectocarpus

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Simon Bourdareau ◽  
Leila Tirichine ◽  
Bérangère Lombard ◽  
Damarys Loew ◽  
Delphine Scornet ◽  
...  
Keyword(s):  
Life Cycle ◽  
Histone Modifications ◽  
Brown Alga ◽  
Land Plant ◽  
Transcription Start ◽  
Post Translational Modifications ◽  
Transcription Start Sites ◽  
Genomic Regions ◽  
Active Genes

Abstract Background Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. Results A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. Conclusions The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.

scholarly journals A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Simone Sidoli ◽  
Mariana Lopes ◽  
Peder J. Lund ◽  
Naomi Goldman ◽  
Maria Fasolino ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Chemical Properties ◽  
Chromatin Accessibility ◽  
Metabolic Labeling ◽  
Post Translational Modifications ◽  
Histone Ptms ◽  
Active Transcription ◽  
Or Gene ◽  
Histone Codes

Abstract Histone post-translational modifications (PTMs) contribute to chromatin accessibility due to their chemical properties and their ability to recruit enzymes responsible for DNA readout and chromatin remodeling. To date, more than 400 different histone PTMs and thousands of combinations of PTMs have been identified, the vast majority with still unknown biological function. Identification and quantification of histone PTMs has become routine in mass spectrometry (MS) but, since raising antibodies for each PTM in a study can be prohibitive, lots of potential is lost from MS datasets when uncharacterized PTMs are found to be significantly regulated. We developed an assay that uses metabolic labeling and MS to associate chromatin accessibility with histone PTMs and their combinations. The labeling is achieved by spiking in the cell media a 5x concentration of stable isotope labeled arginine and allow cells to grow for at least one cell cycle. We quantified the labeling incorporation of about 200 histone peptides with a proteomics workflow, and we confirmed that peptides carrying PTMs with extensively characterized roles in active transcription or gene silencing were in highly or poorly labeled forms, respectively. Data were further validated using next-generation sequencing to assess the transcription rate of chromatin regions modified with five selected PTMs. Furthermore, we quantified the labeling rate of peptides carrying co-existing PTMs, proving that this method is suitable for combinatorial PTMs. We focus on the abundant bivalent mark H3K27me3K36me2, showing that H3K27me3 dominantly represses histone swapping rate even in the presence of the more permissive PTM H3K36me2. Together, we envision this method will help to generate hypotheses regarding histone PTM functions and, potentially, elucidate the role of combinatorial histone codes.

scholarly journals Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

2018 ◽  
Author(s):  
Jun Zheng ◽  
Erliang Zeng ◽  
Yicong Du ◽  
Cheng He ◽  
Ying Hu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Sequence Data ◽  
Expression Profiles ◽  
Regulatory Role ◽  
Chromatin Modifications ◽  
Small Nuclear Rnas ◽  
Genome Copy Number ◽  
Rna Expression Profiling ◽  
Genomic Regions

AbstractSmall RNAs (sRNAs) are short noncoding RNAs that play roles in many biological processes, including drought responses in plants. However, how the expression of sRNAs dynamically changes with the gradual imposition of drought stress in plants is largely unknown. We generated time-series sRNA sequence data from maize seedlings under drought stress and under well-watered conditions at the same time points. Analyses of length, functional annotation, and abundance of 736,372 non-redundant sRNAs from both drought and well-watered data, as well as genome copy number and chromatin modifications at the corresponding genomic regions, revealed distinct patterns of abundance, genome organization, and chromatin modifications for different sRNA classes of sRNAs. The analysis identified 6,646 sRNAs whose regulation was altered in response to drought stress. Among drought-responsive sRNAs, 1,325 showed transient down-regulation by the seventh day, coinciding with visible symptoms of drought stress. The profiles revealed drought-responsive microRNAs, as well as other sRNAs that originated from ribosomal RNAs (rRNAs), splicing small nuclear RNAs, and small nucleolar RNAs (snoRNA). Expression profiles of their sRNA derivers indicated that snoRNAs might play a regulatory role through regulating stability of rRNAs and splicing small nuclear RNAs under drought condition.

scholarly journals A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress

2020 ◽  
Vol 48 (7) ◽  
pp. 3455-3475
Author(s):  
Cristina Viéitez ◽  
Gerard Martínez-Cebrián ◽  
Carme Solé ◽  
René Böttcher ◽  
Clement M Potel ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Growth Conditions ◽  
Proof Of Concept ◽  
Transcriptional Program ◽  
Post Translational Modifications ◽  
Transcriptional Reprogramming ◽  
Histone Ptms ◽  
Response To Stress ◽  
State Growth

Abstract Cells have the ability to sense, respond and adapt to environmental fluctuations. Stress causes a massive reorganization of the transcriptional program. Many examples of histone post-translational modifications (PTMs) have been associated with transcriptional activation or repression under steady-state growth conditions. Comparatively less is known about the role of histone PTMs in the cellular adaptive response to stress. Here, we performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress. Of note, we observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a ‘personalized’, rather than general, subset of histone requirements for each chromatin context. In addition, we identified a number of new residues that unexpectedly serve to regulate transcription. As a proof of concept, we characterized the function of the histone residues H4-S47 and H4-T30 in response to osmotic and heat stress, respectively. Our results uncover novel roles for the kinases Cla4 and Ste20, yeast homologs of the mammalian PAK2 family, and the Ste11 MAPK as regulators of H4-S47 and H4-T30, respectively. This study provides new insights into the role of histone residues in transcriptional regulation under stress conditions.

scholarly journals Functional redundancy of variant and canonical histone H3 lysine 9 modification in Drosophila

2017 ◽  
Author(s):  
Taylor J.R. Penke ◽  
Daniel J. McKay ◽  
Brian D. Strahl ◽  
A. Gregory Matera ◽  
Robert J. Duronio
Keyword(s):  
Gene Activation ◽  
Histone H3 ◽  
Histone Variants ◽  
Protein Coding ◽  
Post Translational Modifications ◽  
Histone Ptms ◽  
Repressive Chromatin ◽  
Expression Of Genes ◽  
Canonical Histone

ABSTRACTHistone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for “active” histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin. To determine the functions of K9 modification on variant versus canonical H3, we compared the phenotypes caused by engineering H3.3K9R and H3K9R mutant genotypes in Drosophila melanogaster. Whereas most H3.3K9R and a small number of H3K9R mutant animals are capable of completing development and do not have substantially altered protein coding transcriptomes, all H3.3K9RH3K9R combined mutants die soon after embryogenesis and display decreased expression of genes enriched for K9ac. These data suggest that the role of K9ac in gene activation during development can be provided by either H3 or H3.3. Conversely, we found that H3.3K9 is methylated at telomeric transposons, and this mark contributes to repressive chromatin architecture, supporting a role for H3.3 in heterochromatin that is distinct from that of H3. Thus, our genetic and molecular analyses demonstrate that K9 modification of variant and canonical H3 have overlapping roles in development and transcriptional regulation, though to differing extents in euchromatin and heterochromatin.

ASPECTS IN BUILDING A COMPANY WEB-SITE AND ITS ROLE FOR THE DEVELOPMENT OF BUSINESS

2018 ◽  
pp. 117-124
Author(s):  
Petar Halachev ◽  
Victoria Radeva ◽  
Albena Nikiforova ◽  
Miglena Veneva
Keyword(s):  
Life Cycle ◽  
Web Site ◽  
The Internet ◽  
A Company ◽  
The Web ◽  
Design Construction ◽  
Made In ◽  
Site Types

This report is dedicated to the role of the web site as an important tool for presenting business on the Internet. Classification of site types has been made in terms of their application in the business and the types of structures in their construction. The Models of the Life Cycle for designing business websites are analyzed and are outlined their strengths and weaknesses. The stages in the design, construction, commissioning, and maintenance of a business website are distinguished and the activities and requirements of each stage are specified.

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