scholarly journals Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

2017 ◽  
Author(s):  
Jenna E. Haines ◽  
Michael B. Eisen
Keyword(s):  
Chromatin Accessibility ◽  
Drosophila Embryo ◽  
Direct Result ◽  
Open Chromatin ◽  
Relative Contribution ◽  
Genome Wide ◽  
Zygotic Transcription ◽  
Early Drosophila Embryo ◽  
Nucleosome Density ◽  
Anterior Posterior

AbstractAs the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of open chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However, it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. Recent work has implicated the ubiquitously expressed, maternal factor Zelda in this process. To assess the relative contribution of activity in the establishment of chromatin accessibility, we have probed chromatin accessibility across the anterior-posterior axis of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is remarkably similar between the two halves. Promoters and enhancers that are active in exclusively one half of the embryo have open chromatin in the other half, demonstrating that chromatin accessibility is not a direct result of activity. However, there is a small skew at enhancers that drive transcription exclusively in either the anterior or posterior half of the embryo, with greater accessibility in the region of activity. Taken together these data support a model in which regions of chromatin accessibility are defined and established by ubiquitous factors, and fine-tuned subsequently by activity.

scholarly journals GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Marissa M Gaskill ◽  
Tyler J Gibson ◽  
Elizabeth D Larson ◽  
Melissa M Harrison
Keyword(s):  
Chromatin Accessibility ◽  
Drosophila Embryo ◽  
Gaga Factor ◽  
Zygotic Transcription ◽  
Early Drosophila Embryo ◽  
Zygotic Gene ◽  
Pioneer Factor ◽  
Pioneer Factors ◽  
Genome Activation ◽  
Development Proceeds

Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.

scholarly journals The pioneer factor GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

2020 ◽  
Author(s):  
Marissa M. Gaskill ◽  
Tyler J. Gibson ◽  
Elizabeth D. Larson ◽  
Melissa M. Harrison
Keyword(s):  
Transcriptional Control ◽  
Chromatin Accessibility ◽  
Drosophila Embryo ◽  
Gaga Factor ◽  
Zygotic Transcription ◽  
Early Drosophila Embryo ◽  
Zygotic Gene ◽  
Pioneer Factor ◽  
Pioneer Factors ◽  
Genome Activation

AbstractFollowing fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are required for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal- to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were necessary for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is needed to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer factors, and we propose that as development proceeds transcriptional control is gradually transferred from Zelda to GAF.

scholarly journals Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient

2017 ◽  
Author(s):  
Colleen E. Hannon ◽  
Shelby A. Blythe ◽  
Eric F. Wieschaus
Keyword(s):  
Target Genes ◽  
Positional Information ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Accessible Chromatin ◽  
Anterior Posterior

ABSTRACTIn Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.

scholarly journals Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells

2020 ◽  
Vol 16 (11) ◽  
pp. e1008422
Author(s):  
Azusa Tanaka ◽  
Yasuhiro Ishitsuka ◽  
Hiroki Ohta ◽  
Akihiro Fujimoto ◽  
Jun-ichirou Yasunaga ◽  
...  
Keyword(s):  
Data Reduction ◽  
Clustering Algorithm ◽  
High Throughput Sequencing ◽  
Hematopoietic Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Genome Wide ◽  
Data Reduction Method ◽  
Effective Analysis

The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards the genome as a string of 1s and 0s based on a set of peaks and calculates the Hamming distances between the strings. This algorithm with the systematically optimized set of peaks enables us to quantitatively evaluate differences between samples of hematopoietic cells and classify cell types, potentially leading to a better understanding of leukemia pathogenesis.

scholarly journals Detecting differential transcription factor activity from ATAC-seq data

2018 ◽  
Author(s):  
Ignacio J. Tripodi ◽  
Mary A. Allen ◽  
Robin D. Dowell
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Nucleotide Polymorphisms ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
Genome Wide ◽  
Recognition Motifs ◽  
Differential Transcription

AbstractTranscription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TF are altered by a perturbation is simple, quick to implement and can be used when biological samples are limited. In the future, we envision this method could be applied to determining which TFs show altered activity in response to a wide variety of drugs and diseases.

scholarly journals Genome-wide Studies Reveal the Essential and Opposite Roles of ARID1A in Controlling Human Cardiogenesis and Neurogenesis from Pluripotent Stem Cells

2020 ◽  
Author(s):  
Juli Liu ◽  
Sheng Liu ◽  
Hongyu Gao ◽  
Lei Han ◽  
Xiaona Chu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Brain Development ◽  
Neural Development ◽  
Pluripotent Stem Cells ◽  
Human Heart ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Neurogenic Genes ◽  
Genome Wide ◽  
Early Human

AbstractBackgroundEarly human heart and brain development simultaneously occur during embryogenesis. Notably, in human newborns, congenital heart defects strongly associate with neurodevelopmental abnormalities, suggesting a common gene/complex underlying both cardiogenesis and neurogenesis. However, due to lack of in vivo studies, the molecular mechanisms that govern both early human heart and brain development remain elusive.ResultsHere, we report ARID1A, which is a DNA-binding-subunit of the SWI/SNF epigenetic complex, controls both neurogenesis and cardiogenesis from human embryonic stem cells (hESCs) via employing distinct mechanisms. Knockout of ARID1A (ARID1A-/-) led to spontaneous differentiation of neural cells together with globally enhanced expression of neurogenic genes in undifferentiated hESCs. Additionally, when compared with WT hESCs, cardiac differentiation from ARID1A-/- hESCs was prominently suppressed, whereas neural differentiation was significantly promoted. Whole genome-wide scRNA-seq, ATAC-seq, and ChIP-seq analyses revealed that ARID1A was required to open chromatin accessibility on promoters of essential cardiogenic genes, and temporally associated with key cardiogenic transcriptional factors T and MEF2C during early cardiac development. However, during early neural development, transcription of most essential neurogenic genes was dependent on ARID1A, which could interact with a known neural restrictive silencer factor REST/NRSF.ConclusionsWe uncovered the opposite roles by ARID1A to govern both early cardiac and neural development from pluripotent stem cells. Global chromatin accessibility on cardiogenic genes is dependent on ARID1A, whereas transcriptional activity of neurogenic genes is under control by ARID1A, possibly through ARID1A-REST/NRSF interaction.

scholarly journals Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Rupinder Sayal ◽  
Jacqueline M Dresch ◽  
Irina Pushel ◽  
Benjamin R Taylor ◽  
David N Arnosti
Keyword(s):  
Drosophila Embryo ◽  
Enhancer Activity ◽  
Genome Wide ◽  
Regulatory Machinery ◽  
A Genome ◽  
Early Drosophila Embryo ◽  
Wide Scale ◽  
Factor Interactions ◽  
Identification And Characterization ◽  
Enhancer Identification

Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models were effective at novel enhancer identification and characterization. Our study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale.

scholarly journals Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

2019 ◽  
Vol 47 (20) ◽  
pp. 10580-10596 ◽  
Author(s):  
Karl J V Nordström ◽  
Florian Schmidt ◽  
Nina Gasparoni ◽  
Abdulrahman Salhab ◽  
Gilles Gasparoni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Experimental Design ◽  
Chromatin Accessibility ◽  
Dnase I ◽  
Open Chromatin ◽  
Functional Interpretation ◽  
Genome Wide ◽  
Show Evidence

Abstract Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often ‘called’ by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in comparison to NOMe-seq, NOMe-seq singles out for its genome-wide coverage allowing to not only detect NDRs but also endogenous DNA methylation and as we show here genome wide segmentation into heterochromatic B domains and local phasing of nucleosomes outside of NDRs. In summary, our comparisons strongly suggest to consider assay specific differences for the experimental design and for generalized and comparative functional interpretations.

scholarly journals Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Theodora Koromila ◽  
Fan Gao ◽  
Yasuno Iwasaki ◽  
Peng He ◽  
Lior Pachter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Accessibility ◽  
Secondary Wave ◽  
Genome Wide ◽  
Zygotic Transcription ◽  
Early Embryos ◽  
Zygotic Gene ◽  
Pioneer Factor ◽  
Pioneer Factors

Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.

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