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1. A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait

   https://doi.org/10.1371/journal.pgen.1010653  

   Weinstein, Michael L.; Jaenke, Chad M.; Asma, Hasiba; Spangler, Matthew; Kohnen, Katherine A.; Konys, Claire C.; Williams, Melissa E.; Williams, Ashley V.; Rebeiz, Mark; Halfon, Marc S.; et al (February 2023, PLOS Genetics)

   Kopp, Artyom (Ed.)

   Animal traits develop through the expression and action of numerous regulatory and realizator genes that comprise a gene regulatory network (GRN). For each GRN, its underlying patterns of gene expression are controlled by cis -regulatory elements (CREs) that bind activating and repressing transcription factors. These interactions drive cell-type and developmental stage-specific transcriptional activation or repression. Most GRNs remain incompletely mapped, and a major barrier to this daunting task is CRE identification. Here, we used an in silico method to identify predicted CREs (pCREs) that comprise the GRN which governs sex-specific pigmentation of Drosophila melanogaster . Through in vivo assays, we demonstrate that many pCREs activate expression in the correct cell-type and developmental stage. We employed genome editing to demonstrate that two CREs control the pupal abdomen expression of trithorax , whose function is required for the dimorphic phenotype. Surprisingly, trithorax had no detectable effect on this GRN’s key trans -regulators, but shapes the sex-specific expression of two realizator genes. Comparison of sequences orthologous to these CREs supports an evolutionary scenario where these trithorax CREs predated the origin of the dimorphic trait. Collectively, this study demonstrates how in silico approaches can shed novel insights on the GRN basis for a trait’s development and evolution. 

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2. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance

   https://doi.org/10.3389/fgene.2021.652189  

   Gupta, Chirag; Ramegowda, Venkategowda; Basu, Supratim; Pereira, Andy (June 2021, Frontiers in Genetics)

   null (Ed.)

   Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice ( Oryza sativa ). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties. 

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3. The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in Mimulus

   https://doi.org/10.1093/genetics/iyaa036  

   Zheng, Xingyu; Om, Kuenzang; Stanton, Kimmy A; Thomas, Daniel; Cheng, Philip A; Eggert, Allison; Simmons, Emily; Yuan, Yao-Wu; Conradi Smith, Gregory D; Puzey, Joshua R; et al (February 2021, Genetics)

   Bomblies, K (Ed.)

   Abstract Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use sequence and expression analysis, followed by transgenic manipulation of gene expression, to identify MYB5a—orthologous to the NEGAN transcriptional activator from M. lewisii—as the gene responsible for the transition to anthocyanin-pigmented petals in M. l. variegatus. In other monkeyflower taxa, MYB5a/NEGAN is part of a reaction-diffusion network that produces semi-repeating spotting patterns, such as the array of spots in the nectar guides of both M. lewisii and M. guttatus. Its co-option for the evolution of an apparently non-patterned trait—the solid petal lobe pigmentation of M. l. variegatus—illustrates how reaction-diffusion can contribute to evolutionary novelty in non-obvious ways. Transcriptome sequencing of a MYB5a RNAi line of M. l. variegatus reveals that this genetically simple change, which we hypothesize to be a regulatory mutation in cis to MYB5a, has cascading effects on gene expression, not only on the enzyme-encoding genes traditionally thought of as the targets of MYB5a but also on all of its known partners in the anthocyanin regulatory network. 

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4. Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)

   https://doi.org/10.3390/plants12112146  

   Naithani, Sushma; Mohanty, Bijayalaxmi; Elser, Justin; D’Eustachio, Peter; Jaiswal, Pankaj (June 2023, Plants)

   Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene–gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene–gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene–gene, gene–protein, and protein–protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement. 

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5. Genetic Mapping of a new Hippo allele, HpoN.1.2, in Drosophila melanogaster

   https://doi.org/000383  

   Siders, JL; Bieser, KL; Hamill, DR; Acosta, EC; Alexander, OK; Ali, HI; Anderson, MJ; Arrasmith, HR; Azam, M; Beeman, NJ; et al (April 2021, microPublication biology)

   null (Ed.)

   Genetic screens provide a mechanism to identify genes involved with different cellular and organismal processes. Using a Flp/FRT screen in the Drosophila eye we identified mutations that result in alterations and de-regulation of cell growth and division. From this screen a group of undergraduate researchers part of the Fly-CURE consortium mapped and characterized a new allele of the gene Hippo, HpoN.1.2. 

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