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Fisheries
Lili Xing, Lingyu Wang, Femke Roos, Michelle Lee, Gregory A. Wray
Summary: Sea urchins are important mariculture species and model organisms in developmental biology. Cis-regulatory elements control development and physiology by regulating gene expression. Mutations affecting these sequences contribute to phenotypic diversity. Cis-regulatory targets offer new breeding potential for the future.
Article
Biology
Yushi Wu, Arun Devotta, Diana S. Jose-Edwards, Jamie E. Kugler, Lenny J. Negron-Pineiro, Karina Braslavskaya, Jermyn Addy, Jean-Pierre Saint-Jeannet, Anna Di Gregorio
Summary: Gene regulatory networks play a crucial role in coordinating the formation of organs and structures in different organisms. In this study, we investigated the regulatory interaction between Xbp1 and Brachyury in the development of the notochord. Our findings suggest that Brachyury and Xbp1 form a crucial subcircuit in the gene regulatory network of the notochord, which has been conserved during chordate evolution.
Article
Developmental Biology
Nicolas Lonfat, Su Wang, ChangHee Lee, Mauricio Garcia, Jiho Choi, Peter J. Park, Connie Cepko
Summary: The study identified the important role of transcription factors Otx2 and Oc1 in coordinating cone development and function, and discovered many new cis-regulatory modules (CRMs) that could potentially be used as useful reagents for gene therapy of cone diseases.
Article
Biochemistry & Molecular Biology
Petra Vande Zande, Patricia J. Wittkopp
Summary: This study uses expression and fitness data from Saccharomyces cerevisiae gene deletion strains to show that cis-acting mutations tend to have lower pleiotropy and trans-acting mutations are more deleterious. These findings provide strong support for the role of pleiotropy in the preferential fixation of cis-regulatory alleles over evolutionary time.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Jian Ming Khor, Charles A. Ettensohn, Kathryn Song Eng Cheah
Summary: This study dissects the transcriptional control region of the KirrelL gene in echinoderms, uncovering its role in the gene regulatory network underlying skeletogenesis. The study also identifies key cis-regulatory elements and transcription factor inputs that regulate KirrelL expression, as well as the conservation of these regulatory regions across echinoderm species. Furthermore, the study establishes a paradigm for the direct linkage between a developmental gene regulatory network and an effector gene controlling cell behavior.
Article
Plant Sciences
Julien Roziere, Cecile Guichard, Veronique Brunaud, Marie-Laure Martin, Sylvie Coursol
Summary: This study explores preferentially located motifs (PLMs) in the cis-regulatory regions of Arabidopsis thaliana and Zea mays genes using a genome-wide de novo approach. The study identifies three groups of PLMs, with a focus on conserved PLMs in both species, particularly in the 3'-gene-proximal region. Comparison with transcription factor and microRNA binding sites reveals that a significant portion of the identified PLMs are unassigned and show functional predictions that differ from known binding sites.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Developmental Biology
Jian Ming Khor, Jennifer Guerrero-Santoro, Charles A. Ettensohn
Summary: Multinucleated cells or syncytia are common in various taxa, and their biological function is related to the compartmentalization of biochemical or cellular activities. This study reveals that transcription factors and biomineralization proteins have restricted mobility within the syncytium of sea urchin embryonic skeleton, and identifies motifs that limit their mobility.
Review
Biology
Marketa Kaucka
Summary: The extensive morphological variation in mammals stems from their diverse ecological adaptations. The craniofacial region exhibits the highest morphological diversity, primarily determined by the bony skull. Mammalian craniofacial development relies on complex multistep processes governed by conserved genes that require precise spatio-temporal control. The understanding of the origin, divergence, and function of cis-regulatory elements deepens our comprehension of morphological novelty and provides insights into the principles of morphological evolution.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Immunology
Xunyi Long, Chen Luo, Zhengming Zhu
Summary: This article provides an overview of the regulation mechanisms involved in the differentiation and maintenance of CD4(+) T cell subsets, focusing on the function of conserved cis-regulatory elements and their role in the conversion of T regulatory cells to T helper 17 cells.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Developmental Biology
Majed Layous, Lama Khalaily, Tsvia Gildor, Smadar Ben-Tabou de-Leon
Summary: The tolerance to hypoxic conditions changes between different developmental stages of sea urchin embryos, possibly due to the structure of gene regulatory networks. Hypoxia applied during early development strongly affects the activity of certain pathways, while pathways are largely unaffected by hypoxia applied after DV-axis formation.
Article
Genetics & Heredity
David Gokhman, Rachel M. Agoglia, Maia Kinnebrew, Wei Gordon, Danqiong Sun, Vivek K. Bajpai, Sahin Naqvi, Coral Chen, Anthony Chan, Chider Chen, Dmitri A. Petrov, Nadav Ahituv, Honghao Zhang, Yuji Mishina, Joanna Wysocka, Rajat Rohatgi, Hunter B. Fraser
Summary: The study of human-chimpanzee hybrid induced pluripotent stem cells reveals evidence of lineage-specific selection on the hedgehog signaling pathway, which may have contributed to the unique craniofacial morphology of humans. This approach offers a new perspective on understanding gene expression differences between species.
Article
Environmental Sciences
Periklis Paganos, Clemens Vinzenz Ullmann, Daniela Gaglio, Marcella Bonanomi, Noemi Salmistraro, Maria Ina Arnone, Eva Jimenez-Guri
Summary: Microplastics pollution is a serious problem in all seas, and the effects of plastic leachates on the embryonic development of marine animals are poorly understood. In this study, we investigated the developmental effects of plastic leachates on sea urchins and found severe and specific abnormalities, including radialization and malformation of various cells. Our findings suggest that the high concentrations of zinc in plastic leachates are the likely cause of these defects and highlight the detrimental effects of marine plastic pollution on echinoderm development.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Cell Biology
Trine V. Dam, Nicolaj I. Toft, Lars Grontved
Summary: The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing rapidly. There are difficulties in diagnosing and treating NAFLD. Further insight into disease mechanisms and gene regulatory mechanisms associated with tissue remodeling is needed. Mapping the cis-regulatory genome and single-cell analysis are emerging technologies that provide more possibilities for research.
Article
Biochemistry & Molecular Biology
Katya L. Mack, Tyler A. Square, Bin Zhao, Craig T. Miller, Hunter B. Fraser
Summary: This study reveals the importance of gene regulatory evolution in the adaptation of threespine sticklebacks to freshwater habitats, especially concerning tissue-specific differences. The findings suggest that cis-regulatory changes play a significant role in gene divergence, with most of the differences occurring in specific tissues between freshwater and marine environments. The study also identified selective processes, particularly within the Wnt signaling pathway in dental tissues, indicating the role of specific genes in adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Biochemistry & Molecular Biology
Seungsoo Kim, Joanna Wysocka
Summary: Uncovering the cis-regulatory code that governs gene transcription in a given genome and cellular state remains a central goal of biology. This review discusses the different layers of regulation that influence transcriptional outputs, including the binding of transcription factors to specific DNA sequences, the role of cofactors in facilitating their function, and the complex interplay within regulatory landscapes. The authors propose that a quantitative, mechanistically informed model of transcriptional regulation is essential for ultimately understanding the cis-regulatory code.
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