scholarly journals Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings

2017 ◽  
Author(s):  
Thomas A. Stewart ◽  
Cong Liang ◽  
Justin L. Cotney ◽  
James P. Noonan ◽  
Thomas J. Sanger ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Crown Group ◽  
Ground Plan ◽  
Frame Shift ◽  
Core Set ◽  
Gene Regulatory ◽  
Conserved Gene ◽  
Shift Hypothesis ◽  
Digit Identity

SummaryIn crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits develop with distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digit identities are conserved across amniotes. Transcriptomics of developing limbs shows diversity in the patterns of genetic differentiation of digits, although the anterior-most digit of the pentadactyl limb has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude that only the identity of the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.

scholarly journals Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

2020 ◽  
Author(s):  
Alexander Calderwood ◽  
Jo Hepworth ◽  
Shannon Woodhouse ◽  
Lorelei Bilham ◽  
D. Marc Jones ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Detailed Comparison ◽  
Developmental Time ◽  
Floral Transition ◽  
Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

scholarly journals Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Fredrik Barrenas ◽  
Kevin Raehtz ◽  
Cuiling Xu ◽  
Lynn Law ◽  
Richard R. Green ◽  
...  
Keyword(s):  
Wound Healing ◽  
Expression Profiles ◽  
Healing Process ◽  
Gene Expression Profiles ◽  
Gene Signature ◽  
African Green Monkey ◽  
Wound Healing Process ◽  
Sequencing Data ◽  
Green Monkey ◽  
Conserved Gene

Abstract Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-β and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.

scholarly journals An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles

Gene ◽  
2013 ◽  
Vol 518 (1) ◽  
pp. 17-25 ◽  
Author(s):  
Ryo Araki ◽  
Shigeto Seno ◽  
Yoichi Takenaka ◽  
Hideo Matsuda
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Expression Profiles ◽  
Estimation Method ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Gene Regulatory

scholarly journals Heat Diffusion Kernel Algorithm-Based Interpretation of the Disease Intervention Mechanism for DHA

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 754
Author(s):  
Yuan Quan ◽  
Hong-Yu Zhang ◽  
Jiang-Hui Xiong ◽  
Rui-Feng Xu ◽  
Min Gao
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Heat Diffusion ◽  
Diffusion Kernel ◽  
Significant Gene ◽  
Gene Regulatory ◽  
Core Genes ◽  
Intervention Mechanism

Docosahexaenoic acid (DHA) is effective in the prevention and treatment of cancer, congenital disorders, and various chronic diseases. According to the omnigenic hypothesis, these complex diseases are caused by disordered gene regulatory networks comprising dozens to hundreds of core genes and a mass of peripheral genes. However, conventional research on the disease intervention mechanism of DHA only focused on specific types of genes or pathways instead of examining genes at the network level, resulting in conflicting conclusions. In this study, we used HotNet2, a heat diffusion kernel algorithm, to calculate the gene regulatory networks of connectivity map (cMap)-derived agents (including DHA) based on gene expression profiles, aiming to interpret the disease intervention mechanism of DHA at the network level. As a result, significant gene regulatory networks for DHA and 676 cMap-derived agents were identified respectively. The biological functions of the DHA-regulated gene network provide preliminary insights into the mechanism by which DHA intervenes in disease. In addition, we compared the gene regulatory networks of DHA with those of cMap-derived agents, which allowed us to predict the pharmacological effects and disease intervention mechanism of DHA by analogy with similar agents with clear indications and mechanisms. Some of our analysis results were supported by experimental observations. Therefore, this study makes a significant contribution to research on the disease intervention mechanism of DHA at the regulatory network level, demonstrating the potential application value of this methodology in clarifying the mechanisms about nutrients influencing health.

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