scholarly journals Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis

2018 ◽  
Vol 14 (11) ◽  
pp. 1571-1585 ◽  
Author(s):  
Mengnan He ◽  
Yan Li ◽  
Qianzi Tang ◽  
Diyan Li ◽  
Long Jin ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Structure Changes ◽  
Genome Wide

scholarly journals Chromatin structure changes in Daphnia populations upon exposure to environmental cues – or – The discovery of Wolterecks “Matrix”

2020 ◽  
Author(s):  
Ronaldo de Carvalho AUGUSTO ◽  
Aki Minoda ◽  
Oliver Rey ◽  
Celine Cosseau ◽  
Cristian Chaparro ◽  
...  
Keyword(s):  
Phenotypic Plasticity ◽  
Chromatin Structure ◽  
Biological Material ◽  
Morphological Changes ◽  
Daphnia Pulex ◽  
Experimental System ◽  
Control Treatment ◽  
Open Chromatin ◽  
Structure Changes ◽  
Genome Wide

Abstract Background: This study therefore describes the classical experimental system postulated by Richard Woltereck 100 years ago: the adaptive morphological phenotypic plasticity of daphnia . Phenotypic plasticity is an important feature of biological systems that is likely to play a major role in the adaptation of organisms exposed to an environmental stimulus and it is increasingly related to epigenetic mechanisms. Several studies have started to identify the epigenetic basis of phenotypic plasticity of daphnia including non-coding RNAs, covalent modifications at the histone tails and DNA methylation however no study has yet investigated those effect on the genome-wide chromatin structure. The aim of this work was to study for the first time the overall genome-wide chromatin structure of Daphnia pulex in the context of the iconic complex defense response to predation. We developed a robust and rapid ATAC-seq technique that allows for analyzing chromatin of individual daphnia and show here (i) that this technique can be used with minimal expertise in molecular biology, and (ii) we used it to identify open chromatin structure in daphnia exposed to different environmental cues.Results: Our results encouraged the expected induction of anti-predatory morphological changes in the stress treatment was significantly higher than that of daphnia from the control treatment. The developed ATAC-seq technique can be used to characterize chromatin structures of individuals even those that are small and thus with few biological material, making it possible to determine epigenetic polymorphisms relatively easily and at reasonable cost in full populations. In addition, we deliver evidence that chromatin structure changes upon stimuli from the environment.Conclusion: We report here an extremely fast and straightforward method to map the chromatin status of individuals using small amounts of input biological material. W e show here that changes in the environment, such as predator presence the chromatin structure is profoundly reorganised confirming Woltereck ’s classical postulate.

scholarly journals Chromatin architectural proteins regulate flowering time by precluding gene looping

2021 ◽  
Vol 7 (24) ◽  
pp. eabg3097
Author(s):  
Bo Zhao ◽  
Yanpeng Xi ◽  
Junghyun Kim ◽  
Sibum Sung
Keyword(s):  
Chromatin Structure ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Architectural Proteins ◽  
Floral Repressor ◽  
Flanking Regions ◽  
Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

scholarly journals Chromatin Profiling of the Repetitive and Nonrepetitive Genomes of the Human Fungal Pathogen Candida albicans

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Robert Jordan Price ◽  
Esther Weindling ◽  
Judith Berman ◽  
Alessia Buscaino
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Histone Modifications ◽  
Chromatin Structure ◽  
Fungal Pathogen ◽  
Histone H3 ◽  
Content Type ◽  
Chromatin States ◽  
Genome Wide ◽  
Chromatin Profiling

ABSTRACT Eukaryotic genomes are packaged into chromatin structures that play pivotal roles in regulating all DNA-associated processes. Histone posttranslational modifications modulate chromatin structure and function, leading to rapid regulation of gene expression and genome stability, key steps in environmental adaptation. Candida albicans, a prevalent fungal pathogen in humans, can rapidly adapt and thrive in diverse host niches. The contribution of chromatin to C. albicans biology is largely unexplored. Here, we generated the first comprehensive chromatin profile of histone modifications (histone H3 trimethylated on lysine 4 [H3K4me3], histone H3 acetylated on lysine 9 [H3K9Ac], acetylated lysine 16 on histone H4 [H4K16Ac], and γH2A) across the C. albicans genome and investigated its relationship to gene expression by harnessing genome-wide sequencing approaches. We demonstrated that gene-rich nonrepetitive regions are packaged into canonical euchromatin in association with histone modifications that mirror their transcriptional activity. In contrast, repetitive regions are assembled into distinct chromatin states; subtelomeric regions and the ribosomal DNA (rDNA) locus are assembled into heterochromatin, while major repeat sequences and transposons are packaged in chromatin that bears features of euchromatin and heterochromatin. Genome-wide mapping of γH2A, a marker of genome instability, identified potential recombination-prone genomic loci. Finally, we present the first quantitative chromatin profiling in C. albicans to delineate the role of the chromatin modifiers Sir2 and Set1 in controlling chromatin structure and gene expression. This report presents the first genome-wide chromatin profiling of histone modifications associated with the C. albicans genome. These epigenomic maps provide an invaluable resource to understand the contribution of chromatin to C. albicans biology and identify aspects of C. albicans chromatin organization that differ from that of other yeasts. IMPORTANCE The fungus Candida albicans is an opportunistic pathogen that normally lives on the human body without causing any harm. However, C. albicans is also a dangerous pathogen responsible for millions of infections annually. C. albicans is such a successful pathogen because it can adapt to and thrive in different environments. Chemical modifications of chromatin, the structure that packages DNA into cells, can allow environmental adaptation by regulating gene expression and genome organization. Surprisingly, the contribution of chromatin modification to C. albicans biology is still largely unknown. For the first time, we analyzed C. albicans chromatin modifications on a genome-wide basis. We demonstrate that specific chromatin states are associated with distinct regions of the C. albicans genome and identify the roles of the chromatin modifiers Sir2 and Set1 in shaping C. albicans chromatin and gene expression.

scholarly journals Chromatin structure changes in Daphnia populations upon exposure to environmental cues – or – The discovery of Wolterecks “Matrix”

2019 ◽  
Author(s):  
Ronaldo de Carvalho Augusto ◽  
Aki Minoda ◽  
Oliver Rey ◽  
Céline Cosseau ◽  
Cristian Chaparro ◽  
...  
Keyword(s):  
Phenotypic Plasticity ◽  
Chromatin Structure ◽  
Environmental Gradients ◽  
Gene Mutations ◽  
Reaction Norms ◽  
Environmental Cues ◽  
Global Changes ◽  
Open Chromatin ◽  
Norm Of Reaction ◽  
Structure Changes

AbstractPhenotypic plasticity is an important feature of biological systems that is likely to play a major role in the future adaptation of organisms to the ongoing global changes. It may allow an organism to produce alternative phenotypes in responses to environmental cues. Modifications in the phenotype can be reversible but are sometimes enduring and can even span over generations. The notion of phenotypic plasticity was conceptualized in the early 20th century by Richard Woltereck. He introduced the idea that the combined relations of a phenotypic character and all environmental gradients that influence on it can be defined as “norm of reaction”. Norms of reaction are specific to species and to lineages within species, and they are heritable. He postulated that reaction norms can progressively be shifted over generations depending on the environmental conditions. One of his biological models was the water-flee daphnia. Woltereck proposed that enduring phenotypic modifications and gene mutations could have similar adaptive effects, and he postulated that their molecular bases would be different. Mutations occurred in genes, while enduring modifications were based on something he called the Matrix. He suggested that this matrix (i) was associated with the chromosomes, (ii) that it was heritable, (iii) it changed during development of the organisms, and (iv) that changes of the matrix could be simple chemical substitutions of an unknown, but probably polymeric molecule. We reasoned that the chromatin has all postulated features of this matrix and revisited Woltereck’s classical experiments with daphnia. We developed a robust and rapid ATAC-seq technique that allows for analyzing chromatin of individual daphnia and show here (i) that this technique can be used with minimal expertise in molecular biology, and (ii) we used it to identify open chromatin structure in daphnia exposed to different environmental cues. Our result indicates that chromatin structure changes consistently in daphnia upon this exposure confirming Woltereck’s classical postulate.

scholarly journals Strong replicators associated with open chromatin are sufficient to establish an early replicating domain

2018 ◽  
Author(s):  
Caroline Brossas ◽  
Sabarinadh Chilaka ◽  
Antonin Counillon ◽  
Marc Laurent ◽  
Coralie Goncalves ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Binding Sites ◽  
Replication Origin ◽  
Molecular Mechanisms ◽  
Open Chromatin ◽  
Strongly Correlated ◽  
Topologically Associating Domains ◽  
Genome Wide ◽  
Close Physical Proximity ◽  
Temporal Program

AbstractVertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into topologically associating domains. However, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong replication origin and chromatin modifier binding sites capable of shifting a targeted mid-late replicating region for earlier replication. When inserted side-by-side, these modules acted in cooperation, with similar effects on two late-replicating regions. Targeted insertions of these two modules at two chromosomal sites separated by 30 kb brought these two modules into close physical proximity and induced the formation of an early-replicating domain. Thus, combinations of strong origins and cis-elements capable of opening the chromatin structure are the basic units of early-replicating domains, and are absent from late-replicated regions. These findings are consistent with those of genome-wide studies mapping strong initiation sites and open chromatin marks in vertebrate genomes.

scholarly journals Transcriptional Regulation of Inflammasomes

2020 ◽  
Vol 21 (21) ◽  
pp. 8087
Author(s):  
Maxence Cornut ◽  
Emilie Bourdonnay ◽  
Thomas Henry
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Immune Responses ◽  
Circadian Clock ◽  
Chromatin Structure ◽  
Cell Types ◽  
First Line ◽  
Inflammatory Signals ◽  
Structure Changes ◽  
Different Cell Types

Inflammasomes are multimolecular complexes with potent inflammatory activity. As such, their activity is tightly regulated at the transcriptional and post-transcriptional levels. In this review, we present the transcriptional regulation of inflammasome genes from sensors (e.g., NLRP3) to substrates (e.g., IL-1β). Lineage-determining transcription factors shape inflammasome responses in different cell types with profound consequences on the responsiveness to inflammasome-activating stimuli. Pro-inflammatory signals (sterile or microbial) have a key transcriptional impact on inflammasome genes, which is largely mediated by NF-κB and that translates into higher antimicrobial immune responses. Furthermore, diverse intrinsic (e.g., circadian clock, metabolites) or extrinsic (e.g., xenobiotics) signals are integrated by signal-dependent transcription factors and chromatin structure changes to modulate transcriptionally inflammasome responses. Finally, anti-inflammatory signals (e.g., IL-10) counterbalance inflammasome genes induction to limit deleterious inflammation. Transcriptional regulations thus appear as the first line of inflammasome regulation to raise the defense level in front of stress and infections but also to limit excessive or chronic inflammation.

scholarly journals DNA Methylation Differences Between Zona Pellucida-Bound and Manually Selected Spermatozoa Are Associated With Autism Susceptibility

2021 ◽  
Vol 12 ◽  
Author(s):  
Longda Wang ◽  
Mengxiang Chen ◽  
Gaofeng Yan ◽  
Shuhua Zhao
Keyword(s):  
Dna Methylation ◽  
Candidate Genes ◽  
Zona Pellucida ◽  
Chromatin Structure ◽  
Bisulfite Sequencing ◽  
Nuclear Dna ◽  
Selection Process ◽  
Biological Processes ◽  
Normal Morphology ◽  
Genome Wide

Children conceived through intracytoplasmic sperm injection (ICSI) have been reported to have a higher risk of many abnormalities and disorders, including autism and intellectual disability, which may be due to bypassing of the natural sperm selection process during ICSI. Zona pellucida (ZP)-bound spermatozoa (ZPBS) have normal morphology and nuclear DNA. Using these spermatozoa for ICSI results in better outcomes compared with conventional ICSI. However, differences besides morphology that exist between sperm selected by ZP and by an embryologist and whether these differences affect the risk of autism in offspring after ICSI are unclear. To explore these questions, we compared genome-wide DNA methylation profiles between ZPBS and manually selected spermatozoa (MSS)using single-cell bisulfite sequencing. Global DNA methylation levels were significantly lower in ZPBS than in MSS. Using gene ontology (GO) analysis, genes overlapping differentially methylated regions (DMRs) were enriched in biological processes involving neurogenesis. Furthermore, we found that 47.8% of autism candidate genes were associated with DMRs, compared with 37.1% of matched background genes (P<0.001). This was mainly because of the high proportion of autism candidate genes with bivalent chromatin structure. In conclusion, bivalent chromatin structure results in large differences in the methylation of autism genes between MSS and ZPBS. ICSI using MSS, which increases the risk of methylation mutations compared with ZPBS, may lead to a higher risk of autism in offspring.

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