Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation

AbstractSuppressor of Hairy wing [Su(Hw)] is an insulator protein that participates in regulating chromatin architecture and gene repression in Drosophila. In previous studies we have shown that Su(Hw) is also required for pre-replication complex (pre-RC) recruitment on Su(Hw)-bound sites (SBSs) in Drosophila S2 cells and pupa. Here, we describe the effect of Su(Hw) on developmentally regulated amplification of 66D and 7F Drosophila amplicons in follicle cells (DAFCs), widely used as models in replication studies. We show Su(Hw) binding co-localizes with all known DAFCs in Drosophila ovaries, whereas disruption of Su(Hw) binding to 66D and 7F DAFCs causes a two-fold decrease in the amplification of these loci. The complete loss of Su(Hw) binding to chromatin impairs pre-RC recruitment to all amplification regulatory regions of 66D and 7F loci at early oogenesis (prior to DAFCs amplification). These changes coincide with a considerable Su(Hw)-dependent condensation of chromatin at 66D and 7F loci. Although we observed the Brm, ISWI, Mi-2, and CHD1 chromatin remodelers at SBSs genome wide, their remodeler activity does not appear to be responsible for chromatin decondensation at the 66D and 7F amplification regulatory regions. We have discovered that, in addition to the CBP/Nejire and Chameau histone acetyltransferases, the Gcn5 acetyltransferase binds to 66D and 7F DAFCs at SBSs and this binding is dependent on Su(Hw). We propose that the main function of Su(Hw) in developmental amplification of 66D and 7F DAFCs is to establish a chromatin structure that is permissive to pre-RC recruitment.

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High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

Nature Communications ◽

10.1038/s41467-021-23213-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sarah E. Pierce ◽

Jeffrey M. Granja ◽

William J. Greenleaf

Keyword(s):

Transcription Factor ◽

Single Cell ◽

Cancer Cells ◽

High Throughput ◽

Regulatory Networks ◽

Temporal Dynamics ◽

Chromatin Accessibility ◽

Regulatory Regions ◽

Factor Binding ◽

Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

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Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Nature Communications ◽

10.1038/s41467-021-23015-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Elisa Oberbeckmann ◽

Vanessa Niebauer ◽

Shinya Watanabe ◽

Lucas Farnung ◽

Manuela Moldt ◽

...

Keyword(s):

Phased Arrays ◽

Stable Steady State ◽

Reference Sites ◽

Chromatin Remodelers ◽

Sliding Direction ◽

Nucleosome Dynamics ◽

Genome Wide ◽

Sequence Elements ◽

Nucleosome Array ◽

Dna Ends

AbstractArrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the ‘ruler’ that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.

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Prediction of genome-wide effects of single nucleotide variants on transcription factor binding

Scientific Reports ◽

10.1038/s41598-020-74793-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sebastian Carrasco Pro ◽

Katia Bulekova ◽

Brian Gregor ◽

Adam Labadorf ◽

Juan Ignacio Fuxman Bass

Keyword(s):

Binding Sites ◽

Cancer Type ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Regulatory Regions ◽

Genome Wide ◽

Transcriptional Regulatory ◽

Gene Regulatory ◽

The Impact ◽

The Relationship

Abstract Single nucleotide variants (SNVs) located in transcriptional regulatory regions can result in gene expression changes that lead to adaptive or detrimental phenotypic outcomes. Here, we predict gain or loss of binding sites for 741 transcription factors (TFs) across the human genome. We calculated ‘gainability’ and ‘disruptability’ scores for each TF that represent the likelihood of binding sites being created or disrupted, respectively. We found that functional cis-eQTL SNVs are more likely to alter TF binding sites than rare SNVs in the human population. In addition, we show that cancer somatic mutations have different effects on TF binding sites from different TF families on a cancer-type basis. Finally, we discuss the relationship between these results and cancer mutational signatures. Altogether, we provide a blueprint to study the impact of SNVs derived from genetic variation or disease association on TF binding to gene regulatory regions.

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Visualization of Drosophila melanogaster chorion genes undergoing amplification.

Molecular and Cellular Biology ◽

10.1128/mcb.8.7.2811 ◽

1988 ◽

Vol 8 (7) ◽

pp. 2811-2821 ◽

Cited By ~ 24

Author(s):

Y N Osheim ◽

O L Miller ◽

A L Beyer

Keyword(s):

Time Frame ◽

Maximum Activity ◽

Follicle Cells ◽

Control Element ◽

Active Gene ◽

Chorion Genes ◽

Temporal Specificity ◽

Preferential Amplification ◽

Essential Region ◽

Large Clusters

We visualized by electron microscopy the preferential amplification of Drosophila chorion genes in late-stage follicle cells. Chromatin spreads revealed large clusters of actively transcribed genes of the appropriate size, spacing, and orientation for chorion genes that were expressed with the correct temporal specificity. Occasionally the active genes were observed within or contiguous with intact replicons and replication forks. In every case, our micrographs are consistent with the hypothesis that the central region of each chorion domain contains a replication origin(s) used during the amplification event. In one case, a small replication bubble was observed precisely at the site of the essential region of the X chromosome amplification control element. The micrographs also suggest that forks at either end of a replicon frequently progress very different distances, presumably due to different times in initiation or different rates of movement. It appears that all chorion genes (even those coding for minor proteins) are transcribed in a "fully on" condition, albeit for varied durations, and that if replication fork passage does inactivate a promoter, it does so very transiently. Furthermore, a DNA segment containing one active gene is likely to have an additional active gene(s). Surprisingly, during the time frame of expected maximum activity, approximately half of the chorion sequences appear transcriptionally inactive.

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ROS induces NETosis by oxidizing DNA and initiating DNA repair

Cell Death Discovery ◽

10.1038/s41420-021-00491-3 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Dhia Azzouz ◽

Meraj A. Khan ◽

Nades Palaniyar

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Polymerase Activity ◽

Neutrophil Activation ◽

Neutrophil Extracellular Trap ◽

Nuclear Antigen ◽

Chromatin Decondensation ◽

Genome Wide ◽

Repair Protein ◽

Dna Repair Protein

AbstractReactive oxygen species (ROS) are essential for neutrophil extracellular trap (NET) formation or NETosis. Nevertheless, how ROS induces NETosis is unknown. Neutrophil activation induces excess ROS production and a meaningless genome-wide transcription to facilitate chromatin decondensation. Here we show that the induction of NADPH oxidase-dependent NETosis leads to extensive DNA damage, and the subsequent translocation of proliferating cell nuclear antigen (PCNA), a key DNA repair protein, stored in the cytoplasm into the nucleus. During the activation of NETosis (e.g., by phorbol myristate acetate, Escherichia coli LPS, Staphylococcus aureus (RN4220), or Pseudomonas aeruginosa), preventing the DNA-repair-complex assembly leading to nick formation that decondenses chromatin causes the suppression of NETosis (e.g., by inhibitors to, or knockdown of, Apurinic endonuclease APE1, poly ADP ribose polymerase PARP, and DNA ligase). The remaining repair steps involving polymerase activity and PCNA interactions with DNA polymerases β/δ do not suppress agonist-induced NETosis. Therefore, excess ROS produced during neutrophil activation induces NETosis by inducing extensive DNA damage (e.g., oxidising guanine to 8-oxoguanine), and the subsequent DNA repair pathway, leading to chromatin decondensation.

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Genome-Wide Association study Identifies a Novel Association Between a Cardiovascular Gene Polymorphism and Superior Athletic Performance

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0111 ◽

2020 ◽

Author(s):

Mohamed Elrayess ◽

Fatima Al-Khelaifi ◽

Noha Yousri ◽

Omar Al-Bagha

Keyword(s):

Athletic Performance ◽

Genome Wide Association Study ◽

Endurance Athlete ◽

Meta Analysis ◽

Significant Snps ◽

Nucleotide Polymorphisms ◽

Replication Studies ◽

Genome Wide ◽

Small Effect Size ◽

Metabolomics Analysis

Research into the genetic predisposition to superior athletic performance has been a hindered by the underpowered studies and the small effect size of identified genetic variants. The aims of this study were to investigate the association of common single-nucleotide polymorphisms (SNPs) with endurance athlete status in a large cohort of elite European athletes using GWAS approach, followed by replication studies in Russian and Japanese elite athletes and functional validation using metabolomics analysis. Results: The association of 476,728 SNPs of Illumina DrugCore Gene chip and endurance athlete status was investigated in 796 European international-level athletes (645 males, 151 females) by comparing allelic frequencies between athletes specialized in sports with high (n=662) and low/moderate (n=134) aerobic component. Validation of results was performed by comparing the frequencies of the most significant SNPs between 242 and 168 elite Russian high and low/moderate aerobic athletes, respectively, and between 60 elite Japanese endurance athletes and 406 controls. A meta-analysis has identified rs1052373 (GG homozygotes) in Myosin Binding Protein (MYBPC3; implicated in cardiac hypertrophic myopathy) gene to be associated with endurance athlete status (P=1.43E-08, odd ratio 2.2). Homozygotes carriers of rs1052373 G allele in Russian athletes had significantly greater VO2max than carriers of the AA+AG (P = 0.005). Subsequent metabolomics analysis revealed several amino acids and lipids associated with rs1052373 G allele (1.82x10-05) including the testosterone precursor androstenediol (3beta, 17beta) disulfate. Conclusion: This is the first report of genome-wide significant SNP and related metabolites associated with elite athlete status. Further investigations of the functional relevance of the identified SNPs and metabolites in relation to enhanced athletic performance are warranted.

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Genome-Wide Association Study of Prevalent and Persistent Cervical High-Risk Human Papillomavirus(HPV) Infection

10.21203/rs.2.16987/v1 ◽

2019 ◽

Author(s):

Sally N. Adebamowo ◽

Adebowale A Adeyemo ◽

Charles N Rotimi ◽

Olayinka Olaniyan ◽

Richard B. Offiong ◽

...

Keyword(s):

Human Papillomavirus ◽

High Risk ◽

Association Study ◽

Genome Wide Association Study ◽

Principal Component ◽

Hpv Infection ◽

Genome Wide Association ◽

Replication Studies ◽

Genome Wide

Abstract Background: Genetic factors may influence the susceptibility to high-risk human papillomavirus (hrHPV) infection and persistence. We conducted the first genome-wide association study (GWAS) to identify variants associated with cervical hrHPV infection and persistence. Methods: Participants were 517 Nigerian women evaluated at baseline and 6 months follow-up visits for HPV. HPV was characterized using SPF10/LiPA25. hrHPV infection was positive if at least one carcinogenic HPV genotype was detected in a sample provided at the baseline visit and persistent if at least one carcinogenic HPV genotype was detected in each of the samples provided at the baseline and follow-up visits. Genotyping was done using the Illumina Multi-Ethnic Genotyping Array (MEGA) and imputation was done using the African Genome Resources Haplotype Reference Panel. Association analysis was done under additive genetic models adjusted for age, HIV status and the first principal component (PC) of the genotypes. Results: The mean (±SD) age of the study participants was 38 (±8) years, 48% were HIV negative, 24% were hrHPV positive and 10% had persistent hrHPV infections. The top three variants associated with hrHPV infections were intronic variants clustered in KLF12 (all OR: 7.06, p=1.43 x 10-6). The top variants associated with cervical hrHPV persistence were in DAP(OR: 6.86, p=7.15 x 10-8), NR5A2(OR: 3.65, p=2.03 x 10-7) and MIR365-2(OR: 7.71, p=2.63 x 10-7) gene regions. Conclusions: This exploratory GWAS yielded novel candidate risk loci for cervical hrHPV infection and persistence. The identified loci have biological annotation and functional data supporting their role in hrHPV infection and persistence. Given our limited sample size, larger discovery and replication studies are warranted to further characterize the reported associations.

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Linkage and evolutionary diversification of developmentally regulated multigene families: tandem arrays of the 401/18 chorion gene pair in silkmoths.

Molecular and Cellular Biology ◽

10.1128/mcb.1.9.814 ◽

1981 ◽

Vol 1 (9) ◽

pp. 814-828 ◽

Cited By ~ 8

Author(s):

C W Jones ◽

F C Kafatos

Keyword(s):

Gene Pair ◽

Single Individual ◽

Developmentally Regulated ◽

Evolutionary Diversification ◽

Repeat Units ◽

Chorion Genes ◽

Restriction Sites ◽

Multiple Copies ◽

Flanking Sequences ◽

Silkmoth Chorion

The coordinately expressed silkmoth chorion genes, 401 and 18, are closely linked as a pair, in divergent orientation. Analysis of overlapping clones (chromosomal "walk") demonstrated that each of the multiple copies of this gene pair is embedded within a larger deoxyribonucleic acid unit, which is tandemly repeated in a few arrays or possibly a single array. Southern analysis and examination of clones from a single individual moth demonstrated that the repeat units are extensively polymorphic in restriction sites, length, and possibly number, no differential amplification was evident during choriogenesis. Intron and 5'-flanking sequences were shown to be specific for the 401/18 gene pair and not to be present elsewhere in the genome. The spatial distribution of variations in the genes and their flanking sequences were examined.

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Abstract 439: Trajectory Analysis of Left Ventricular Dimensions From Biobank Data Uncovers Novel Genetic Associations

Circulation Research ◽

10.1161/res.127.suppl_1.439 ◽

2020 ◽

Vol 127 (Suppl_1) ◽

Author(s):

Tess Pottinger ◽

Megan J Puckelwartz ◽

Lorenzo L Pesce ◽

Anthony Gacita ◽

Isabella Salamone ◽

...

Keyword(s):

Heart Failure ◽

Longitudinal Data ◽

Association Studies ◽

The United States ◽

Left Ventricular ◽

Genome Wide Association Studies ◽

Qtc Interval ◽

Regulatory Regions ◽

Genome Wide ◽

Over Time

Background: Approximately 6 million adults in the United States have heart failure. The progression of heart failure is variable arising from differences in sex, age, genetic background including ancestry, and medication response. Many population-based genetic studies of heart failure have been cross-sectional in nature, failing to gain additional power from longitudinal analyses. As heart failure is known to change over time, using longitudinal data trajectories as a quantitative trait will increase power in genome wide association studies (GWAS). Methods: We used the electronic health record in a racially and ethnically diverse medical biobank from a single, metropolitan US center. We used whole genome data from 896 unrelated participants analyzed, including 494 who had at least 1 electrocardiogram and 324 who had more than 1 echocardiogram (average of 3 observations per person). A mixture model based semiparametric latent growth curve model was used to cluster outcome measures used for genome-wide analyses. Results: GWAS on the trajectory probability of QTc interval identified significant associations with variants in regulatory regions proximal to the WLS gene, which encodes Wntless, a Wnt ligand secretion mediator. WLS was previously associated with QTc and myocardial infarction, thus confirming the power of the method. GWAS on the trajectory probability of left ventricular diameter (LVIDd) identified significant associations with variants in regulatory regions near MYO10 , which encodes unconventional Myosin-10. MYO10 was previously associated with obesity and metabolic syndrome. Conclusions: This is the first study to show an association with variants in or near MYO10 and left ventricular dimension changes over time. Further, we found that using trajectory probabilities can provide increased power to find novel associations with longitudinal data. This reduces the need for larger cohorts, and increases yield from smaller, well-phenotyped cohorts, such as those found in biobanks. This approach should be useful in the study of rare diseases and underrepresented populations.

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Abstract MP171: Transcription Start Site Profiling Defines Promoter and Enhancer Regions for Cardiomyopathy Genes

Circulation Research ◽

10.1161/res.127.suppl_1.mp171 ◽

2020 ◽

Vol 127 (Suppl_1) ◽

Author(s):

Anthony M Gacita ◽

Lisa Dellefave-Castillo ◽

Patrick G Page ◽

David Y Barefield ◽

Andrew Wasserstrom ◽

...

Keyword(s):

Heart Failure ◽

Genetic Variation ◽

Cardiac Tissue ◽

Autosomal Dominant ◽

Gene Promoters ◽

Regulatory Regions ◽

Genome Wide ◽

Reporter Assays ◽

Transcriptional Start Sites ◽

Putative Enhancer

Background: Mutations in more than 100 genes lead to dilated, hypertrophic and other forms of cardiomyopathy. Autosomal dominant mutations in the MYH7 and LMNA genes cause autosomal dominant hypertrophic and dilated cardiomyopathy, respectively. Individual mutations display a range of clinical expression from severe early onset disease to minimal or no symptoms. Genetic variation in noncoding gene regulatory regions including enhancers is expected to modify expression of cardiomyopathy genes and disease expressivity. In addition, heart failure is associated a fetal gene re-expression program, mediated by genetic regulatory regions. The contribution of noncoding genetic variation to cardiomyopathy and heart failure has been hampered by limited genome wide descriptions of human cardiac regulatory regions. Methods and Results: We used C ap A nalysis of G ene E xpression by sequencing (CAGE-seq) to profile the transcriptional start sites in healthy and failed human hearts. CAGE-seq detects the unidirectional signals of gene promoters and the bidirectional signal of transcribed enhancer regions. We identified ~17,000 transcriptional start sites associated with gene promoters and ~1,500 putative enhancer regions active in cardiac tissue. These CAGE-defined regulatory regions carried histone modifications and transcription factor binding properties characteristic of enhancers or promoters. We specifically identified promoter switching and differential enhancer usage between healthy and failed hearts. We intersected CAGE-defined enhancers with additional epigenomic datasets to identify regulatory regions for MYH7 and LMNA genes. We identified 13 putative enhancer regions and validated the functionality of a subset of these regulatory regions using reporter assays and gene editing. Conclusions: This CAGE-seq dataset defines the regulatory environment for heart failure. These promoter and enhancer regions could be used to target heart-failure associated gene expression changes. Additionally, this data can be used to identify enhancer regions regulating cardiomyopathy genes.

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