scholarly journals Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

Development ◽  
2014 ◽  
Vol 141 (4) ◽  
pp. 950-961 ◽  
Author(s):  
K. Rafiq ◽  
T. Shashikant ◽  
C. J. McManus ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins

Development ◽  
2014 ◽  
Vol 141 (12) ◽  
pp. 2542-2542 ◽  
Author(s):  
K. Rafiq ◽  
T. Shashikant ◽  
C. J. McManus ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Sea Urchins ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

Abstract MP208: A Shared Fog2 / Tbx5-dependent Gene Regulatory Network Identified By Transcription Factor-dependent Non-coding RNA Profiling Modulates Cardiac Rhythm

2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Linsin A Smith ◽  
Carlos Perez-Cervantes ◽  
Michael Broman ◽  
Rangarajan Nadadur ◽  
Jeff Steimle ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Cardiac Rhythm ◽  
Association Studies ◽  
Genome Wide Association ◽  
Calcium Handling ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Gene Regulatory ◽  
Atrial Rhythm

Atrial fibrillation (AF) is the most common cardiac arrhythmia, affecting over 33 million individuals throughout the world. AF is highly heritable and recent genome-wide association studies (GWAS) have cumulatively identified over 100 loci associated with AF risk. Genome-wide association studies (GWAS) often identify transcription factor (TF) loci in association with complex human diseases, implying that a significant transcriptional component underlies human disease risk and etiology. The transcription factors ZFPM2 (FOG2), GATA4, and TBX5 have all been implicated in human AF risk by genetic studies. We hypothesized that FOG2, GATA4, and TBX5 functionally interact to regulate a gene regulatory network essential for atrial rhythm control. We generated a novel mouse model of spontaneous AF based on FOG2 overexpression. FOG2 ChIP-seq identified FOG2 genomic localization at loci co-occupied by GATA4, a known FOG2 binding partner. However, we found that FOG2 OE caused gene expression alterations that correlated more highly with TBX5-dependent rather than GATA4-dependent gene expression, including a module of calcium handling genes required for atrial rhythm homeostasis. We applied TF-dependent non-coding transcriptional profiling to examine the FOG2 dependent atrial GRN, which identified 805 candidate regulatory regions with accessible chromatin and FOG2 dependent ncRNAs. TBX5 removal and FOG2 OE caused highly correlated dysregulation of ncRNA expression at open chromatin regions genome-wide, suggesting a functional interaction between TBX5 and FOG2. Furthermore, FOG2 OE only affected enhancer activity by altered ncRNA abundance at locations of TBX5 co-binding. The shared TBX5/FOG2 genomic interaction predicted a potential genetic interaction, and we found that cardiac rhythm abnormalities caused by Tbx5 haploinsufficiency were rescued by Fog2 haploinsufficiency. Taken together, TF-dependent ncRNA-profiling revealed an interconnected cardiac rhythm gene regulatory network (GRN) between FOG2, TBX5 and GATA4. These data nominate a specific model in which FOG2 is recruited by GATA4 to modulate a co-bound TBX5-dependent atrial gene regulatory network for calcium handling and atrial rhythm homeostasis.

scholarly journals Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

2017 ◽  
Author(s):  
David Dylus ◽  
Liisa M. Blowes ◽  
Anna Czarkwiani ◽  
Maurice R. Elphick ◽  
Paola Oliveri
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
De Novo ◽  
Sea Urchins ◽  
Brittle Star ◽  
Stages Of Development ◽  
Sequence Alignments ◽  
Amphiura Filiformis ◽  
Gene Regulatory ◽  
Network Rewiring

ABSTRACTAmongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.Data DepositionsAll sequence reads are available at Genbank SRR4436669 - SRR4436674. Any sequence alignments used are available by the corresponding author upon request.

scholarly journals Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

2020 ◽  
Author(s):  
Xizhi Li ◽  
Min Li ◽  
Beibei Zhou ◽  
Jinlin Bao ◽  
Liang Zhu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Leaf Development ◽  
Regulatory Network ◽  
Leaf Rolling ◽  
Knock Out ◽  
Genome Wide ◽  
Leaf Transcriptome ◽  
Dna Insertion ◽  
Gene Regulatory ◽  
Cuticle Development

Abstract Background SRL1 (SEMI-ROLLED LEAF 1) also named as CLD1 (CURLED LEAF AND DWARF 1), encoding a putative glyphopholipidininol-anchored membrane protein, has been characterized as a gene involved in the regulation of leaf morphology in rice. Mutants of srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit defects in leaf development resulting in a phenotype with adaxially rolled leaves. Results To explore the gene regulatory network of leaf development that controlled by SRL1 in rice, we created a homozygous SRL1 knock out (KO) line by CRISPR/Cas9, which showed defects in leaf development with adaxially rolling. By comparing the leaf transcriptome of a homozygous SRL1 KO line (srl1-KO) with the control, a total number of 3,178 genes were identified as differentially expressed genes, of which 1,216 genes were significantly up regulated, while 1,962 genes were down regulated. Further analyses indicated that, a group of known leaf rolling related genes, which involved in bulliform cells and cuticle development such as OsZHD1, OsLBD3-7, RFS, ACL1, CFL1, SND1, OsCESA5 and OsCESA6 were up or down regulated in the srl1-KO. Conclusions SRL1 might control leaf rolling by regulating a couple of genes that affecting cytological architecture of leaf cells such as bulliforms and cuticle of leaves.

scholarly journals Developmental gene regulatory networks in sea urchins and what we can learn from them

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 203 ◽  
Author(s):  
Megan L. Martik ◽  
Deirdre C. Lyons ◽  
David R. McClay
Keyword(s):  
Transcription Factors ◽  
Gene Regulatory Network ◽  
Sea Urchin ◽  
Network Model ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Sea Urchins ◽  
Cell Types ◽  
Zygotic Transcription ◽  
Gene Regulatory

Sea urchin embryos begin zygotic transcription shortly after the egg is fertilized.  Throughout the cleavage stages a series of transcription factors are activated and, along with signaling through a number of pathways, at least 15 different cell types are specified by the beginning of gastrulation.  Experimentally, perturbation of contributing transcription factors, signals and receptors and their molecular consequences enabled the assembly of an extensive gene regulatory network model.  That effort, pioneered and led by Eric Davidson and his laboratory, with many additional insights provided by other laboratories, provided the sea urchin community with a valuable resource.  Here we describe the approaches used to enable the assembly of an advanced gene regulatory network model describing molecular diversification during early development.  We then provide examples to show how a relatively advanced authenticated network can be used as a tool for discovery of how diverse developmental mechanisms are controlled and work.

scholarly journals Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation

2018 ◽  
Vol 98 (2) ◽  
pp. 209-217 ◽  
Author(s):  
D.G. Michael ◽  
T.J.F. Pranzatelli ◽  
B.M. Warner ◽  
H. Yin ◽  
J.A. Chiorini
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Salivary Gland ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Factors Associated ◽  
Genome Wide ◽  
Gene Regulatory ◽  
Cis And Trans ◽  
Genomic Footprinting

Significant effort has been applied to identify the genome-wide gene expression profiles associated with salivary gland development and pathophysiology. However, relatively little is known about the regulators that control salivary gland gene expression. We integrated data from DNase1 digital genomic footprinting, RNA-seq, and gene expression microarrays to comprehensively characterize the cis- and trans-regulatory components controlling gene expression of the healthy submandibular salivary gland. Analysis of 32 human tissues and 87 mouse tissues was performed to identify the highly expressed and tissue-enriched transcription factors driving salivary gland gene expression. Following RNA analysis, protein expression levels and subcellular localization of 39 salivary transcription factors were confirmed by immunohistochemistry. These expression analyses revealed that the salivary gland highly expresses transcription factors associated with endoplasmic reticulum stress, human T-cell lymphotrophic virus 1 expression, and Epstein-Barr virus reactivation. DNase1 digital genomic footprinting to a depth of 333,426,353 reads was performed and utilized to generate a salivary gland gene regulatory network describing the genome-wide chromatin accessibility and transcription factor binding of the salivary gland at a single-nucleotide resolution. Analysis of the DNase1 gene regulatory network identified dense interconnectivity among PLAG1, MYB, and 13 other transcription factors associated with balanced chromosomal translocations and salivary gland tumors. Collectively, these analyses provide a comprehensive atlas of the cis- and trans-regulators of the salivary gland and highlight known aberrantly regulated pathways of diseases affecting the salivary glands.

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