scholarly journals The bowfin genome illuminates the developmental evolution of ray-finned fishes

2021 ◽  
Vol 53 (9) ◽  
pp. 1373-1384 ◽  
Author(s):  
Andrew W. Thompson ◽  
M. Brent Hawkins ◽  
Elise Parey ◽  
Dustin J. Wcisel ◽  
Tatsuya Ota ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Order ◽  
Chromatin Accessibility ◽  
Phylogenetic Position ◽  
Developmental Evolution ◽  
Bony Fishes ◽  
Regulatory Loci ◽  
Gene Regulatory ◽  
Amia Calva ◽  
Chromosome Level

AbstractThe bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era.

scholarly journals The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes

2020 ◽  
Author(s):  
Andrew Thompson ◽  
Michael Hawkins ◽  
Elise Parey ◽  
Dustin Wcisel ◽  
Tatsuya Ota ◽  
...  
Keyword(s):  
Skeletal Development ◽  
Chromatin Accessibility ◽  
Respiratory Organ ◽  
Developmental Evolution ◽  
Evolution And Development ◽  
Bony Fishes ◽  
Key Species ◽  
Regulatory Loci ◽  
Gene Regulatory ◽  
Amia Calva

Abstract The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.

scholarly journals Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

2021 ◽  
Author(s):  
Sara A Knaack ◽  
Daniel Conde ◽  
Kelly M Balmant ◽  
Thomas B Irving ◽  
Lucas G Maia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Temporal Change ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Regularized Regression ◽  
Novel Approach ◽  
Regulatory Module ◽  
Gene Regulatory ◽  
Transcriptomic Changes

Rhizobia can establish associations with legumes to provide plants with nitrogen, in a critical symbiosis for agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet the extent of chromatin changes and impact on gene expression is unknown. We combined gene regulatory features and their chromatin accessibility (ATAC-seq) profile to predict the temporal transcriptome (RNA-seq) dynamics of roots treated with rhizobia lipo-chitooligosaccharides. Using a novel approach, Dynamic Regulatory Module Networks, we predicted gene expression as a function of regulatory feature chromatin accessibility. This approach uses regularized regression and identifies the cis-regulatory elements and associated transcription factors that most significantly contribute to transcriptomic changes triggered by lipo-chitooligosaccharides. Regulators involved in auxin (SHY2), ethylene (EIN3), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics.

scholarly journals Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster

2020 ◽  
Author(s):  
Leandro Murgas ◽  
Sebastian Contreras-Riquelme ◽  
J. Eduardo Martínez ◽  
Camilo Villaman ◽  
Rodrigo Santibáñez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Chromatin Accessibility ◽  
Reference Network ◽  
Specific Gene ◽  
Gene Regulatory

AbstractMotivationThe regulation of gene expression is a key factor in the development and maintenance of life in all organisms. This process is carried out mainly through the action of transcription factors (TFs), although other actors such as ncRNAs are involved. In this work, we propose a new method to construct Gene Regulatory Networks (GRNs) depicting regulatory events in a certain context for Drosophila melanogaster. Our approach is based on known relationships between epigenetics and the activity of transcription factors.ResultsWe developed method, Tool for Weighted Epigenomic Networks in D. melanogaster (Fly T-WEoN), which generates GRNs starting from a reference network that contains all known gene regulations in the fly. Regulations that are unlikely taking place are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications, and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from literature. Experimental data files can be generated with several standard procedures and used solely when and if available.Fly T-WEoN is available as a Cytoscape application that permits integration with other tools, and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster.AvailabilityFly T-WEoN, together with its step-by-step guide is available at https://[email protected]

scholarly journals Sc-compReg enables the comparison of gene regulatory networks between conditions using single-cell data

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhana Duren ◽  
Wenhui Sophia Lu ◽  
Joseph G. Arthur ◽  
Preyas Shah ◽  
Jingxue Xin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Chromatin Accessibility ◽  
Lymphocytic Leukemia ◽  
Cell Subpopulation ◽  
Cell Gene Expression ◽  
Healthy Control ◽  
Gene Regulatory

AbstractThe comparison of gene regulatory networks between diseased versus healthy individuals or between two different treatments is an important scientific problem. Here, we propose sc-compReg as a method for the comparative analysis of gene expression regulatory networks between two conditions using single cell gene expression (scRNA-seq) and single cell chromatin accessibility data (scATAC-seq). Our software, sc-compReg, can be used as a stand-alone package that provides joint clustering and embedding of the cells from both scRNA-seq and scATAC-seq, and the construction of differential regulatory networks across two conditions. We apply the method to compare the gene regulatory networks of an individual with chronic lymphocytic leukemia (CLL) versus a healthy control. The analysis reveals a tumor-specific B cell subpopulation in the CLL patient and identifies TOX2 as a potential regulator of this subpopulation.

scholarly journals Genome scans and gene expression microarrays converge to identify gene regulatory loci relevant in schizophrenia

2006 ◽  
Vol 119 (5) ◽  
pp. 558-570 ◽  
Author(s):  
Marquis P. Vawter ◽  
Mary E. Atz ◽  
Brandi L. Rollins ◽  
Kathleen M. Cooper-Casey ◽  
Ling Shao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Scans ◽  
Gene Expression Microarrays ◽  
Regulatory Loci ◽  
Gene Regulatory ◽  
Expression Microarrays

scholarly journals Evolutionary flexibility in flooding response circuitry in angiosperms

Science ◽  
2019 ◽  
Vol 365 (6459) ◽  
pp. 1291-1295 ◽  
Author(s):  
Mauricio A. Reynoso ◽  
Kaisa Kajala ◽  
Marko Bajic ◽  
Donnelly A. West ◽  
Germain Pauluzzi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
High Resolution ◽  
Gene Regulatory Networks ◽  
Wild Species ◽  
Regulatory Networks ◽  
Chromatin Accessibility ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Gene Regulatory

Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergence-activated genes with signatures of overlapping cis regulation by four transcription factor families. Syntenic genes are more highly expressed than nonsyntenic genes, yet both can have the cis motifs and chromatin accessibility associated with submergence up-regulation. Whereas the flexible circuitry spans the eudicot-monocot divide, the frequency of specific cis motifs, extent of chromatin accessibility, and degree of submergence activation are more prevalent in the wetland crop and may have adaptive importance.

scholarly journals Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karolina Stępniak ◽  
Magdalena A. Machnicka ◽  
Jakub Mieczkowski ◽  
Anna Macioszek ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Molecular Mechanisms ◽  
Genome Mapping ◽  
Malignant Gliomas ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Multiple Tumor ◽  
Genes Encoding ◽  
Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

scholarly journals Leveraging epigenetics to enhance the efficacy of immunotherapy

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Jonathan D. Licht ◽  
Richard L. Bennett
Keyword(s):  
Gene Expression ◽  
Clinical Trials ◽  
Antigen Presentation ◽  
Tumor Cells ◽  
Immune Evasion ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Epigenetic Modifications ◽  
Main Body ◽  
Epigenetic Mechanisms

Abstract Background Epigenetic mechanisms regulate chromatin accessibility patterns that govern interaction of transcription machinery with genes and their cis-regulatory elements. Mutations that affect epigenetic mechanisms are common in cancer. Because epigenetic modifications are reversible many anticancer strategies targeting these mechanisms are currently under development and in clinical trials. Main body Here we review evidence suggesting that epigenetic therapeutics can deactivate immunosuppressive gene expression or reprogram tumor cells to activate antigen presentation mechanisms. In addition, the dysregulation of epigenetic mechanisms commonly observed in cancer may alter the immunogenicity of tumor cells and effectiveness of immunotherapies. Conclusions Therapeutics targeting epigenetic mechanisms may be helpful to counter immune evasion and improve the effectiveness of immunotherapies.

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