scholarly journals The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jelena Erceg ◽  
Jumana AlHaj Abed ◽  
Anton Goloborodko ◽  
Bryan R. Lajoie ◽  
Geoffrey Fudenberg ◽  
...  
Keyword(s):  
Computational Approach ◽  
Homologous Chromosomes ◽  
Layered Architecture ◽  
Homolog Pairing ◽  
Genome Wide ◽  
Mammalian Embryos ◽  
Pioneer Factor ◽  
Genome Activation ◽  
Drosophila Embryos ◽  
Zygotic Genome

Abstract Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.

scholarly journals The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos

2018 ◽  
Author(s):  
Jelena Erceg ◽  
Jumana AlHaj Abed ◽  
Anton Goloborodko ◽  
Bryan R. Lajoie ◽  
Geoffrey Fudenberg ◽  
...  
Keyword(s):  
Early Stage ◽  
Chromatin Accessibility ◽  
Homologous Chromosomes ◽  
Layered Architecture ◽  
Homolog Pairing ◽  
Genome Wide ◽  
New Strategy ◽  
Pioneer Factor ◽  
Standing Question ◽  
Drosophila Embryos

AbstractGenome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focused on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first addressed the long-standing question of whether pairing extends genome-wide and, to this end, developed a haplotype-resolved Hi-C approach that uses a new strategy to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This approach revealed striking genome-wide pairing in Drosophila embryos. Moreover, we discovered pairing to be surprisingly structured, with trans-homolog domains and interaction peaks, many coinciding with the positions of analogous cis features. We also found a significant correlation between pairing and the chromatin accessibility mediated by the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered more than a century ago.One Sentence SummaryA robust approach for haplotype-resolved Hi-C reveals highly-structured homolog pairing in early stage Drosophila embryos.

CLAMP regulates Zygotic Genome Activation in Drosophila embryos

Genetics ◽  
2021 ◽  
Author(s):  
Megan M Colonnetta ◽  
Juan E Abrahante ◽  
Paul Schedl ◽  
Daryl M Gohl ◽  
Girish Deshpande
Keyword(s):  
Temporal Dynamics ◽  
Embryonic Patterning ◽  
Zygotic Genome Activation ◽  
Promoter Sequences ◽  
Genome Wide ◽  
Zygotic Transcription ◽  
Pioneer Factor ◽  
Genome Activation ◽  
Drosophila Embryos ◽  
Zygotic Genome

Abstract Embryonic patterning is critically dependent on zygotic genome activation (ZGA). In Drosophila melanogaster embryos, the pioneer factor Zelda directs ZGA, possibly in conjunction with other factors. Here we have explored novel involvement of Chromatin-Linked Adapter for MSL Proteins (CLAMP) during ZGA. CLAMP binds thousands of sites genome-wide throughout early embryogenesis. Interestingly, CLAMP relocates to target promoter sequences across the genome when ZGA is initiated. Although there is a considerable overlap between CLAMP and Zelda binding sites, the proteins display distinct temporal dynamics. To assess whether CLAMP occupancy affects gene expression, we analyzed transcriptomes of embryos zygotically compromised for either clamp or zelda and found that transcript levels of many zygotically-activated genes are similarly affected. Importantly, compromising either clamp or zelda disrupted the expression of critical segmentation and sex determination genes bound by CLAMP (and Zelda). Furthermore, clamp knockdown embryos recapitulate other phenotypes observed in Zelda-depleted embryos, including nuclear division defects, centrosome aberrations, and a disorganized actomyosin network. Based on these data, we propose that CLAMP acts in concert with Zelda to regulate early zygotic transcription.

scholarly journals Cohesin facilitates zygotic genome activation in zebrafish

2017 ◽  
Author(s):  
Michael Meier ◽  
Jenny Grant ◽  
Amy Dowdle ◽  
Amarni Thomas ◽  
Jennifer E. Gerton ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Chromatin Structure ◽  
Cell Cycle Progression ◽  
Zygotic Genome Activation ◽  
Chromosome Architecture ◽  
Genome Wide ◽  
Pioneer Factor ◽  
Cohesin Subunit ◽  
Genome Activation ◽  
Zygotic Genome

At zygotic genome activation (ZGA), changes in chromatin structure are associated with new transcription immediately following the maternal-to-zygotic transition (MZT). The nuclear architectural proteins, cohesin and CCCTC-binding factor (CTCF), contribute to chromatin structure and gene regulation. We show here that normal cohesin function is important for ZGA in zebrafish. Depletion of cohesin subunit Rad21 delays ZGA without affecting cell cycle progression. In contrast, CTCF depletion has little effect on ZGA whereas complete abrogation is lethal. Genome wide analysis of Rad21 binding reveals a change in distribution from pericentromeric satellite DNA, and few locations including the miR-430 locus (whose products are responsible for maternal transcript degradation), to genes, as embryos progress through the MZT. After MZT, a subset of Rad21 binding occurs at genes dysregulated upon Rad21 depletion and overlaps pioneer factor Pou5f3, which activates early expressed genes. Rad21 depletion disrupts the formation of nucleoli and RNA polymerase II foci, suggestive of global defects in chromosome architecture. We propose that Rad21/cohesin redistribution to active areas of the genome is key to the establishment of chromosome organization and the embryonic developmental program.

scholarly journals A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation

2020 ◽  
Author(s):  
Christopher D. R. Wyatt ◽  
Barbara Pernaute ◽  
André Gohr ◽  
Marta Miret-Cuesta ◽  
Lucia Goyeneche ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Transcriptional Control ◽  
Exon Skipping ◽  
Tissue Type ◽  
Zygotic Genome Activation ◽  
Damage Response ◽  
Mammalian Embryos ◽  
Genome Activation ◽  
Zygotic Genome

ABSTRACTThe transition from maternal to embryonic transcriptional control is a crucial step in embryogenesis. However, how alternative splicing is regulated during this process and how it contributes to early development is unknown. Using transcriptomic data from pre-implantation stages of human, mouse and cow, we show that the stage of zygotic genome activation (ZGA) exhibits the highest levels of exon skipping diversity reported for any cell or tissue type. Interestingly, much of this exon skipping is temporary, leads to disruptive non-canonical isoforms, and occurs in genes enriched for DNA damage response in the three species. We identified two core spliceosomal components, Snrpb and Snrpd2, as regulators of these patterns. These genes have low maternal expression at the time of ZGA and increase sharply thereafter. Consistently, microinjection of Snrpb/d2 mRNA into mouse zygotes reduces the levels of temporary exon skipping at ZGA, and leads to an increase in etoposide-induced DNA damage response. Altogether, our results suggest that mammalian embryos undergo an evolutionarily conserved and developmentally programmed specific splicing failure at the time of genome activation that attenuates cellular responses to DNA damage at these early stages.

scholarly journals Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Saurabh J. Pradhan ◽  
Puli Chandramouli Reddy ◽  
Michael Smutny ◽  
Ankita Sharma ◽  
Keisuke Sako ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chromatin Accessibility ◽  
Dna Binding Proteins ◽  
Developmental Transitions ◽  
Pluripotency Factors ◽  
Neural Crest Development ◽  
Genome Wide ◽  
Zebrafish Embryogenesis ◽  
Genome Activation ◽  
Zygotic Genome

AbstractZygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.

scholarly journals Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Isabella V Soluri ◽  
Lauren M Zumerling ◽  
Omar A Payan Parra ◽  
Eleanor G Clark ◽  
Shelby A Blythe
Keyword(s):  
Regulatory Networks ◽  
Embryonic Patterning ◽  
Chromatin States ◽  
Regulatory Modules ◽  
Network Function ◽  
Pioneer Factor ◽  
Gene Regulatory ◽  
Genome Activation ◽  
Drosophila Embryos ◽  
Late Function

Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC-seq on Drosophila embryos during the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of late segmentation network CRMs. opa-driven changes in accessibility are accompanied by equivalent changes in gene expression. Interfering with the timing of opa activity impacts the proper patterning of expression. These results indicate that dynamic systems for chromatin regulation directly impact the reading of embryonic patterning information.

scholarly journals Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis

2020 ◽  
Author(s):  
Saurabh J. Pradhan ◽  
Puli Chandramouli Reddy ◽  
Michael Smutny ◽  
Ankita Sharma ◽  
Keisuke Sako ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Dna Binding ◽  
Chromatin Accessibility ◽  
Dna Binding Proteins ◽  
Developmental Transitions ◽  
Pluripotency Factors ◽  
Neural Crest Development ◽  
Genome Wide ◽  
Genome Activation ◽  
Zygotic Genome

AbstractZygotic genome activation (ZGA) initiates regionalized transcription responsible for the acquisition of distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, whether the tissue-specific transcription is mechanistically linked with the onset of ZGA is unknown. Here, we have addressed the involvement of chromatin organizer SATB2 in orchestrating these processes during vertebrate embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility revealed contrasting molecular functions of maternal and zygotic pools of Satb2. Maternal Satb2 represses zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented. We discuss the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.

scholarly journals Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation

2019 ◽  
Vol 74 (1) ◽  
pp. 185-195.e4 ◽  
Author(s):  
Stephen L. McDaniel ◽  
Tyler J. Gibson ◽  
Katharine N. Schulz ◽  
Meilin Fernandez Garcia ◽  
Markus Nevil ◽  
...  
Keyword(s):  
Zygotic Genome Activation ◽  
Pioneer Factor ◽  
Genome Activation ◽  
Zygotic Genome

scholarly journals Chiffon triggers global histone H3 acetylation and expression of developmental genes in Drosophila embryos

2021 ◽  
Author(s):  
Eliana F. Torres-Zelada ◽  
Smitha George ◽  
Hannah R. Blum ◽  
Vikki M. Weake
Keyword(s):  
Gene Expression ◽  
Histone Acetylation ◽  
Potential Role ◽  
Developmental Genes ◽  
Histone Acetyltransferase Gcn5 ◽  
Genome Activation ◽  
H3 Acetylation ◽  
Drosophila Embryos ◽  
Cell Cycle Kinase ◽  
Zygotic Genome

The histone acetyltransferase Gcn5 is critical for gene expression and development. In Drosophila, Gcn5 is part of four complexes (SAGA, ATAC, CHAT, and ADA) that are essential for fly viability and have key roles in regulating gene expression. Here, we show that while the SAGA, ADA, and CHAT complexes play redundant roles in embryonic gene expression, the insect-specific CHAT complex uniquely regulates expression of a subset of developmental genes. We also identify a substantial decrease in histone acetylation in chiffon mutant embryos that exceeds that observed in ada2b, suggesting broader roles for Chiffon in regulating histone acetylation outside of the Gcn5 complexes. The chiffon gene encodes two independent polypeptides that nucleate formation of either the CHAT or Dbf4-dependent kinase (DDK) complexes. DDK includes the cell cycle kinase Cdc7, which is necessary for maternally-driven DNA replication in the embryo. We identify a temporal switch between the expression of these chiffon gene products during a short window during the early nuclear cycles in embryos that correlates with the onset of zygotic genome activation, suggesting a potential role for CHAT in this process.

scholarly journals Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics

2021 ◽  
Author(s):  
Virginia L Pimmett ◽  
Matthieu Dejean ◽  
Carola Fernandez ◽  
Antonio Trullo ◽  
Edouard Bertrand ◽  
...  
Keyword(s):  
Core Promoter ◽  
Quantitative Imaging ◽  
Tata Box ◽  
Polymerase Pausing ◽  
Multicellular Organisms ◽  
Genome Activation ◽  
The Impact ◽  
Rate Limiting ◽  
Drosophila Embryos ◽  
Zygotic Genome

AbstractGenes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge in transcription is understanding how promoter composition dictates bursting, particularly in multicellular organisms. We investigate two key Drosophila developmental promoter motifs, the TATA box (TATA) and the Initiator (INR). Using live imaging in Drosophila embryos and new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds to minutes. TATA-containing promoters and INR-containing promoters exhibit distinct dynamics, with one or two separate rate-limiting steps respectively. A TATA box is associated with long active states, high rates of polymerase initiation, and short-lived, infrequent inactive states. In contrast, the INR motif leads to two inactive states, one of which relates to promoter-proximal polymerase pausing. Surprisingly, the model suggests pausing is not obligatory, but occurs stochastically for a subset of polymerases. Overall, our results provide a rationale for promoter switching during zygotic genome activation.

Sign in / Sign up

Export Citation Format

Share Document