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Comprehensive Annotation of Transcription Factors, Chromatin-Associated Factors, and Basal Transcription Machinery in the Pea Aphid, Acyrthosiphon Pisum, and Development of the Atfdb Database, a Resource for Studies of Transcriptional Regulation

https://doi.org/10.2139/ssrn.4781609
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Inhibition of histone acetylation and deacetylation enzymes affects longevity, development, and fecundity in the pea aphid (Acyrthosiphon pisum)
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The HP1a Disordered C Terminus and Chromo Shadow Domain Cooperate to Select Target Peptide Partners
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Organ specification–growth control connection: New in‐sights from the Drosophila eye–antennal disc
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Evo-Devo Lessons Learned from Aphids
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Differential gene regulatory networks in development and disease
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A conserved function of the zinc finger transcription factor Sp8/9 in allometric appendage growth in the milkweed bug Oncopeltus fasciatus
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The amnioserosa is an apomorphic character of cyclorrhaphan flies
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Suppressor of Hairless, the Drosophila homolog of the mouse recombination signal-binding protein gene, controls sensory organ cell fates
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The activities of two Ets-related transcription factors required for drosophila eye development are modulated by the Ras/MAPK pathway
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Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway
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Computational Strategies for the Genome-Wide Identification of cis-Regulatory Elements and Transcriptional Targets
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Introduction to Transcription Factor Structure and Function
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The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming
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The Hippo Signaling Pathway Coordinately Regulates Cell Proliferation and Apoptosis by Inactivating Yorkie, the Drosophila Homolog of YAP
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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
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Morgan’s Legacy: Fruit Flies and the Functional Annotation of Conserved Genes
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The Human Transcription Factors
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A Comprehensive Drosophila melanogaster Transcription Factor Interactome
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Drosophila HNF4 Regulates Lipid Mobilization and β-Oxidation
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Conserved Role of the Vsx Genes Supports a Monophyletic Origin for Bilaterian Visual Systems
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Keap1/Nrf2 Signaling Regulates Oxidative Stress Tolerance and Lifespan in Drosophila
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The TEAD/TEF Family Protein Scalloped Mediates Transcriptional Output of the Hippo Growth-Regulatory Pathway
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REPTOR and REPTOR-BP Regulate Organismal Metabolism and Transcription Downstream of TORC1
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A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori
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New insight into the RNA interference response against cathepsin-L gene in the pea aphid, Acyrthosiphon pisum: Molting or gut phenotypes specifically induced by injection or feeding treatments
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Transcription factors, chromatin proteins and the diversification of Hemiptera
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An integrated protocol for targeted mutagenesis with CRISPR-Cas9 system in the pea aphid
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Evolutionary divergence of the paralogs Methoprene tolerant (Met) and germ cell expressed (gce) within the genus Drosophila
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Simultaneous profiling of multiple chromatin proteins in the same cells
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Deciphering the multi-scale, quantitative cis-regulatory code
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glial cells missing and gcm2 Cell Autonomously Regulate Both Glial and Neuronal Development in the Visual System of Drosophila
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Evolution of the insect Hox gene cluster: Comparative analysis across 243 species
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Acyrthosiphon pisum
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Drosophila Tbx6-related gene, Dorsocross, mediates high levels of Dpp and Scw signal required for the development of amnioserosa and wing disc primordium
inferredcites →https://doi.org/10.1016/j.ydbio.2007.11.004openalex-extracted
Extraembryonic development in insects and the acrobatics of blastokinesis
inferredcites →https://doi.org/10.1016/j.ydbio.2007.12.037openalex-extracted
Differential requirements for the Pax6(5a) genes eyegone and twin of eyegone during eye development in Drosophila
inferredcites →https://doi.org/10.1016/j.ydbio.2008.01.039openalex-extracted
Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos
inferredcites →https://doi.org/10.1016/j.ydbio.2010.07.010openalex-extracted
Mutual regulatory interactions of the trunk gap genes during blastoderm patterning in the hemipteran Oncopeltus fasciatus
inferredcites →https://doi.org/10.1016/j.ydbio.2011.09.030openalex-extracted
A dissection of the teashirt and tiptop genes reveals a novel mechanism for regulating transcription factor activity
inferredcites →https://doi.org/10.1016/j.ydbio.2013.04.030openalex-extracted
Evolution of the insect terminal patterning system—Insights from the milkweed bug, Oncopeltus fasciatus
inferredcites →https://doi.org/10.1016/j.ydbio.2014.08.021openalex-extracted
Co-regulation of invected and engrailed by a complex array of regulatory sequences in Drosophila
inferredcites →https://doi.org/10.1016/j.ygeno.2020.08.002openalex-extracted
Effect of hepatocyte nuclear factor 4 on the fecundity of Nilaparvata lugens: Insights from RNA interference combined with transcriptomic analysis
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Studying circadian rhythms in Drosophila melanogaster
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marelle Acts Downstream of the Drosophila HOP/JAK Kinase and Encodes a Protein Similar to the Mammalian STATs
inferredcites →https://doi.org/10.1016/s0925-4773(01)00586-xopenalex-extracted
Drosophila MEF2 is a direct regulator of Actin57B transcription in cardiac, skeletal, and visceral muscle lineages
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enok encodes a Drosophila putative histone acetyltransferase required for mushroom body neuroblast proliferation
inferredcites →https://doi.org/10.1038/349175a0openalex-extracted
Base sequence discrimination by zinc-finger DNA-binding domains
inferredcites →https://doi.org/10.1038/385829a0openalex-extracted
pangolinencodes a Lef-1 homologue that acts downstream of Armadillo to transduce the Wingless signal in Drosophila
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Automated protein-DNA interaction screening of Drosophila regulatory elements
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A census of human transcription factors: function, expression and evolution
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Transcription factors: from enhancer binding to developmental control
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Drosophila melanogaster: a simple genetic model of kidney structure, function and disease
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The genes expression difference between winged and wingless bird cherry-oat aphid Rhopalosiphum padi based on transcriptomic data
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maxillopedia is the Tribolium ortholog of proboscipedia
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Properties of developmental gene regulatory networks
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Ultrabithorax is essential for bacteriocyte development
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Bacteriocyte cell death in the pea aphid/ Buchnera symbiotic system
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HLH106, a Drosophila transcription factor with similarity to the vertebrate sterol responsive element binding protein.
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The Rpd3 histone deacetylase is required for segmentation of the Drosophila embryo
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The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene
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Structure of developmental gene regulatory networks from the perspective of cell fate-determining genes
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Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
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A Hepatocyte Nuclear FactorBtabHNF4Mediates Desiccation Tolerance and Fecundity in Whitefly (Bemisia tabaci)
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Distinct mechanisms of E2F regulation by Drosophila RBF1 and RBF2
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Genetic characterization and cloning of mothers against dpp, a gene required for decapentaplegic function in Drosophila melanogaster.
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Sequence of the Tribolium castaneum Homeotic Complex: The Region Corresponding to the Drosophila melanogaster Antennapedia Complex
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FlyBase: a guided tour of highlighted features
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Identification of seven genes essential for male fertility through a genome-wide association study of non-obstructive azoospermia and RNA interference-mediated large-scale functional screening in Drosophila
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The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment
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Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
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Parallel Duplication and Partial Subfunctionalization of -Catenin/Armadillo during Insect Evolution
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Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly
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The Drosophila Fork Head Factor Directly Controls Larval Salivary Gland-Specific Expression of the Glue Protein Gene Sgs3
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Pfam: The protein families database in 2021
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Search and sequence analysis tools services from EMBL-EBI in 2022
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InterPro in 2022
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The Drosophila melanogaster BTB proteins bric a brac bind DNA through a composite DNA binding domain containing a pipsqueak and an AT-Hook motif
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DBD: a transcription factor prediction database
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DBD––taxonomically broad transcription factor predictions: new content and functionality
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Deciphering key features in protein structures with the new ENDscript server
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PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
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The evolution of hexapod engrailed-family genes: evidence for conservation and concerted evolution
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Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bugOncopeltus fasciatus
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Transcriptional activation of hedgehog target genes in Drosophila is mediated directly by the cubitus interruptus protein, a member of the GLI family of zinc finger DNA-binding proteins.
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Control of cell number by Drosophila FOXO: downstream and feedback regulation of the insulin receptor pathway
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The Enok acetyltransferase complex interacts with Elg1 and negatively regulates PCNA unloading to promote the G1/S transition
inferredcites →https://doi.org/10.1101/gad.297374.117openalex-extracted
Physiological/pathological ramifications of transcription factors in the unfolded protein response
inferredcites →https://doi.org/10.1101/gad.4.5.822openalex-extracted
The Drosophila Fos-related AP-1 protein is a developmentally regulated transcription factor.
inferredcites →https://doi.org/10.1101/gad.484208openalex-extracted
dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group silencing
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Control of Drosophila wing and haltere development by the nuclear vestigial gene product.
inferredcites →https://doi.org/10.1101/gad.6.1.50openalex-extracted
Dual Bar homeo box genes of Drosophila required in two photoreceptor cells, R1 and R6, and primary pigment cells for normal eye development.
inferredcites →https://doi.org/10.1101/gad.6.5.715openalex-extracted
apterous, a gene required for imaginal disc development in Drosophila encodes a member of the LIM family of developmental regulatory proteins.
inferredcites →https://doi.org/10.1101/gad.6.6.1030openalex-extracted
The Drosophila sloppy paired locus encodes two proteins involved in segmentation that show homology to mammalian transcription factors.
inferredcites →https://doi.org/10.1101/gad.7.1.42openalex-extracted
Sex-specific transcriptional regulation by the male and female doublesex proteins of Drosophila.
inferredcites →https://doi.org/10.1101/gad.831000openalex-extracted
Orchestrated response: a symphony of transcription factors for gene control
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Comparative validation of the D. melanogaster modENCODE transcriptome annotation
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Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
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Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum : frequent lineage‐specific duplications and losses of developmental genes
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Characterization of the Drosophila Methoprene ‐tolerant gene product
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Myc and Max Homologs in Drosophila
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A transcription factor hierarchy defines an environmental stress response network
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The Transcriptional Repressor dMnt Is a Regulator of Growth in Drosophila melanogaster
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Multiorganismal Insects: Diversity and Function of Resident Microorganisms
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Ecdysone Control of Developmental Transitions: Lessons from Drosophila Research
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Pioneer Transcription Factors Initiating Gene Network Changes
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Transcriptional Coactivator Complexes
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Genetics of Aging in the Fruit Fly,Drosophila melanogaster
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The Drosophila Melanogaster Genome
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BIOLOGY OF BACTERIOCYTE-ASSOCIATED ENDOSYMBIONTS OF PLANT SAP-SUCKING INSECTS
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Transcriptional Regulation of Metabolism
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An overview of the structures of protein-DNA complexes.
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FlyMine: an integrated database for Drosophila and Anopheles genomics
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Spatial expression of transcription factors in Drosophilaembryonic organ development
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Origin and evolution of the enhancer of split complex
inferredcites →https://doi.org/10.1186/s13059-019-1660-0openalex-extracted
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome
inferredcites →https://doi.org/10.1186/s13227-016-0048-4openalex-extracted
Composition and genomic organization of arthropod Hox clusters
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Functional and Evolutionary Genomics in Aphids
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The role of the histone H2A ubiquitinase Sce in Polycomb repression
inferredcites →https://doi.org/10.1242/dev.118.3.719openalex-extracted
The gene tinman is required for specification of the heart and visceral muscles in Drosophila
inferredcites →https://doi.org/10.1242/dev.122.5.1621openalex-extracted
The Drosophila Polycomb group gene Sex comb on midleg (Scm) encodes a zinc finger protein with similarity to polyhomeotic protein
inferredcites →https://doi.org/10.1242/dev.124.18.3471openalex-extracted
ladybird, a new component of the cardiogenic pathway in Drosophila required for diversification of heart precursors
inferredcites →https://doi.org/10.1242/jcs.203612openalex-extracted
The requirement of IRE1 and XBP1 in resolving physiological stress during Drosophila development
inferredcites →https://doi.org/10.1371/journal.pbio.0000021openalex-extracted
Developmental Origin and Evolution of Bacteriocytes in the Aphid–Buchnera Symbiosis
inferredcites →https://doi.org/10.1371/journal.pbio.1000313openalex-extracted
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
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Polycomb Protein SCML2 Regulates the Cell Cycle by Binding and Modulating CDK/CYCLIN/p21 Complexes
inferredcites →https://doi.org/10.1371/journal.pgen.1002426openalex-extracted
Histone H3K9 Trimethylase Eggless Controls Germline Stem Cell Maintenance and Differentiation
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Re-annotation of eightDrosophilagenomes
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Drosophila melanogaster as a versatile model organism to study genetic epilepsies: An overview
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Aphid polyphenisms: trans-generational developmental regulation through viviparity
inferredcites →https://doi.org/10.3389/fphys.2018.01498openalex-extracted
Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum
inferredcites →https://doi.org/10.3389/fphys.2022.982920openalex-extracted
Bacteriocyte plasticity in pea aphids facing amino acid stress or starvation during development
inferredcites →https://doi.org/10.3389/fphys.2023.1248654openalex-extracted
Editorial: Symbiotic organs in insects: development, metabolism, and physiological regulation
inferredcites →https://doi.org/10.3390/cells11030510openalex-extracted
Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution
inferredcites →https://doi.org/10.3390/insects12100884openalex-extracted
The Paramount Role of Drosophila melanogaster in the Study of Epigenetics: From Simple Phenotypes to Molecular Dissection and Higher-Order Genome Organization
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ER Stress Activates the TOR Pathway through Atf6
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