Genomes and Genes
Experts and Doctors on transcription factors in Eugene, Oregon, United States
Locale: Eugene, Oregon, United States
Topic: transcription factors
- Talbot W, Trevarrow B, Halpern M, Melby A, Farr G, Postlethwait J, et al. A homeobox gene essential for zebrafish notochord development. Nature. 1995;378:150-7 pubmed..We show that floating head is the zebrafish homologue of Xnot, a homeobox gene expressed in the amphibian organizer and notochord. We propose that flh regulates notochord precursor cell fate. ..
- Hans S, Liu D, Westerfield M. Pax8 and Pax2a function synergistically in otic specification, downstream of the Foxi1 and Dlx3b transcription factors. Development. 2004;131:5091-102 pubmed..Combined loss of both factors eliminates all indications of otic specification. We suggest that the Foxi1-Pax8 pathway provides an early 'jumpstart' of otic specification that is maintained by the Dlx3b-Pax2a pathway. ..
- Tanaka M, Hale L, Amores A, Yan Y, Cresko W, Suzuki T, et al. Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes. Dev Biol. 2005;281:227-39 pubmed..This mechanism appears to be different from the mechanism for pelvic loss in stickleback, showing that different taxa can evolve similar phenotypes by different mechanisms...
- Wood Z, Weaver L, Brown P, Beckett D, Matthews B. Co-repressor induced order and biotin repressor dimerization: a case for divergent followed by convergent evolution. J Mol Biol. 2006;357:509-23 pubmed
- Eick G, Thornton J. Evolution of steroid receptors from an estrogen-sensitive ancestral receptor. Mol Cell Endocrinol. 2011;334:31-8 pubmed publisher..The primordial interaction between the ancestral steroid receptor and estrogens may itself have evolved due to an early molecular exploitation event. ..
- Hirono K, Margolis J, Posakony J, Doe C. Identification of hunchback cis-regulatory DNA conferring temporal expression in neuroblasts and neurons. Gene Expr Patterns. 2012;12:11-7 pubmed publisher..Our results provide the necessary foundation for identifying trans-acting factors that establish the Hb early temporal expression domain. ..
- Ryter J, Doe C, Matthews B. Structure of the DNA binding region of prospero reveals a novel homeo-prospero domain. Structure. 2002;10:1541-9 pubmed..We propose that the homeo-prospero domain coordinately regulates Prospero nuclear localization and DNA binding specificity. ..
- Lewis K, Eisen J. Hedgehog signaling is required for primary motoneuron induction in zebrafish. Development. 2001;128:3485-95 pubmed..Our results also suggest that Twhh and Shh are more important for motoneuron development than Ehh. ..
- Tran K, Doe C. Pdm and Castor close successive temporal identity windows in the NB3-1 lineage. Development. 2008;135:3491-9 pubmed publisher..Our results provide a new neuroblast lineage for investigating temporal identity and reveal the importance of Pdm and Cas as timing factors that close temporal identity windows. ..
- Isshiki T, Pearson B, Holbrook S, Doe C. Drosophila neuroblasts sequentially express transcription factors which specify the temporal identity of their neuronal progeny. Cell. 2001;106:511-21 pubmed..We propose that Hunchback and Krüppel control early-born temporal identity in neuroblast cell lineages. ..
- Weaver L, Kwon K, Beckett D, Matthews B. Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator. Proc Natl Acad Sci U S A. 2001;98:6045-50 pubmed..The results suggest that the corepressor of BirA causes a disorder-to-order transition that is a prerequisite to repressor dimerization and DNA binding. ..
- Wakamatsu Y, Maynard T, Jones S, Weston J. NUMB localizes in the basal cortex of mitotic avian neuroepithelial cells and modulates neuronal differentiation by binding to NOTCH-1. Neuron. 1999;23:71-81 pubmed
- Talbot J, Johnson S, Kimmel C. hand2 and Dlx genes specify dorsal, intermediate and ventral domains within zebrafish pharyngeal arches. Development. 2010;137:2507-17 pubmed publisher..Collectively, our work indicates that the expression and function of hand2 and Dlx genes specify major patterning domains along the dorsoventral axis of zebrafish pharyngeal arches...
- Radicella J, Turks D, Chandler V. Cloning and nucleotide sequence of a cDNA encoding B-Peru, a regulatory protein of the anthocyanin pathway in maize. Plant Mol Biol. 1991;17:127-30 pubmed
- McSwiggen J, Bear D, von Hippel P. Interactions of Escherichia coli transcription termination factor rho with RNA. I. Binding stoichiometries and free energies. J Mol Biol. 1988;199:609-22 pubmed..The possible significance of these results for models of rho-dependent transcription termination is discussed in the companion paper. ..
- Ohlendorf D, Anderson W, Takeda Y, Matthews B. High resolution structural studies of Cro repressor protein and implications for DNA recognition. J Biomol Struct Dyn. 1983;1:553-63 pubmed..Crystals have been obtained of complexes of Cro with six-base-pair and nine-basepair DNA oligomers, and X-ray analysis of these co-crystals is in progress. ..
- Yan Y, Talbot W, Egan E, Postlethwait J. Mutant rescue by BAC clone injection in zebrafish. Genomics. 1998;50:287-9 pubmed..We conclude that the injection of large-insert genomic clones will speed the isolation of zebrafish genes disrupted by mutation and hence the identification of gene functions necessary for development of vertebrate embryos. ..
- Halpern M, Hatta K, Amacher S, Talbot W, Yan Y, Thisse B, et al. Genetic interactions in zebrafish midline development. Dev Biol. 1997;187:154-70 pubmed..From these findings we propose that ntl+ plays an early role in cell fate choice at the dorsal midline, mediated by the Ntl protein acting to antagonize floor plate development as well as to promote notochord development. ..
- Van Gilst M, von Hippel P. Assembly of the N-dependent antitermination complex of phage lambda: NusA and RNA bind independently to different unfolded domains of the N protein. J Mol Biol. 1997;274:160-73 pubmed..Thus it appears that N can be described as an unfolded multi-domain protein that becomes ordered in a modular fashion as it encounters its various binding partners within the N-dependent antitermination complex. ..
- Cornell R, Eisen J. Delta/Notch signaling promotes formation of zebrafish neural crest by repressing Neurogenin 1 function. Development. 2002;129:2639-48 pubmed..We propose that temporally distinct episodes of Ngn1 activity in the same precursor population specify these two different types of sensory neurons. ..
- Bruhn L, Sprague G. MCM1 point mutants deficient in expression of alpha-specific genes: residues important for interaction with alpha 1. Mol Cell Biol. 1994;14:2534-44 pubmed
- Miller C, Yelon D, Stainier D, Kimmel C. Two endothelin 1 effectors, hand2 and bapx1, pattern ventral pharyngeal cartilage and the jaw joint. Development. 2003;130:1353-65 pubmed..Together our results reveal two critical edn1 effectors that pattern the vertebrate jaw: hand2 specifies ventral pharyngeal cartilage of the lower jaw and bapx1 specifies the jaw joint. ..
- Yan Y, Willoughby J, Liu D, Crump J, Wilson C, Miller C, et al. A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development. Development. 2005;132:1069-83 pubmed..By contrast, subfunction partitioning between zebrafish co-orthologs of tetrapod genes, such as sox9a and sox9b, can relax pleiotropy and reveal both early and late developmental gene functions. ..
- Kohwi M, Hiebert L, Doe C. The pipsqueak-domain proteins Distal antenna and Distal antenna-related restrict Hunchback neuroblast expression and early-born neuronal identity. Development. 2011;138:1727-35 pubmed publisher..We conclude that Dan/Danr and Svp act in parallel pathways to limit Hb expression and allow neuroblasts to transition from making early-born neurons to late-born neurons at the proper time. ..
- Wilson K, Shewchuk L, Brennan R, Otsuka A, Matthews B. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc Natl Acad Sci U S A. 1992;89:9257-61 pubmed..The structural details of this complex remain an open question, however. ..
- Carney T, Struck A, Doe C. midlife crisis encodes a conserved zinc-finger protein required to maintain neuronal differentiation in Drosophila. Development. 2013;140:4155-64 pubmed publisher..We conclude that Mdlc plays an essential role in maintaining neuronal differentiation, raising the possibility that RNF113A regulates neuronal differentiation in the human CNS. ..
- Gill S, Yager T, von Hippel P. Escherichia coli sigma 70 and NusA proteins. II. Physical properties and self-association states. J Mol Biol. 1991;220:325-33 pubmed..coli core RNA polymerase in solution and as a component of the functional transcription complex. ..
- Liu D, Chu H, Maves L, Yan Y, Morcos P, Postlethwait J, et al. Fgf3 and Fgf8 dependent and independent transcription factors are required for otic placode specification. Development. 2003;130:2213-24 pubmed
- Jovelin R, Phillips P. Evolutionary rates and centrality in the yeast gene regulatory network. Genome Biol. 2009;10:R35 pubmed publisher..A better understanding of how these three cellular networks interact with one another may be needed to fully examine the impact of network structure on the function and evolution of biological systems. ..
- Tran K, Miller M, Doe C. Recombineering Hunchback identifies two conserved domains required to maintain neuroblast competence and specify early-born neuronal identity. Development. 2010;137:1421-30 pubmed publisher..We propose that Hunchback maintains early neuroblast competence by silencing a suite of late-expressed genes. ..
- Brennan R, Roderick S, Takeda Y, Matthews B. Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. Proc Natl Acad Sci U S A. 1990;87:8165-9 pubmed..In contrast to other known protein-DNA complexes, the DNA is not stacked end-to-end. The structure confirms the general features of the model previously proposed for the interaction of Cro with DNA. ..
- Seifried S, Wang Y, von Hippel P. Fluorescent modification of the cysteine 202 residue of Escherichia coli transcription termination factor rho. J Biol Chem. 1988;263:13511-4 pubmed..These fluorescently labeled rho molecules should represent useful probes to study the conformations and inter- and intrasubunit geometries of this termination factor at various stages of its interaction with nascent RNA transcripts. ..
- Maves L, Jackman W, Kimmel C. FGF3 and FGF8 mediate a rhombomere 4 signaling activity in the zebrafish hindbrain. Development. 2002;129:3825-37 pubmed..Taken together, our findings demonstrate a crucial role for FGF-mediated inter-rhombomere signaling in promoting early hindbrain patterning and underscore the significance of organizing centers in patterning the vertebrate neural plate. ..
- Varga Z, Amores A, Lewis K, Yan Y, Postlethwait J, Eisen J, et al. Zebrafish smoothened functions in ventral neural tube specification and axon tract formation. Development. 2001;128:3497-509 pubmed..We propose that smoothened is required for induction of lateral floor plate and a subpopulation of hypothalamic cells and for maintenance of medial floor plate and hypothalamic cells. ..
- Thorpe C, Schlesinger A, Carter J, Bowerman B. Wnt signaling polarizes an early C. elegans blastomere to distinguish endoderm from mesoderm. Cell. 1997;90:695-705 pubmed..Defective mitotic spindle orientations in mom mutant embryos indicate that Wnt signaling influences cytoskeletal polarity in blastomeres throughout the early embryo. ..
- Moens C, Cordes S, Giorgianni M, Barsh G, Kimmel C. Equivalence in the genetic control of hindbrain segmentation in fish and mouse. Development. 1998;125:381-91 pubmed
- Tallafuss A, Gibson D, Morcos P, Li Y, Seredick S, Eisen J, et al. Turning gene function ON and OFF using sense and antisense photo-morpholinos in zebrafish. Development. 2012;139:1691-9 pubmed publisher..Our results suggest that sox10 function might not be critical during neural crest formation. ..
- Puschel A, Westerfield M, Dressler G. Comparative analysis of Pax-2 protein distributions during neurulation in mice and zebrafish. Mech Dev. 1992;38:197-208 pubmed..Our results confirm that Pax genes are highly conserved both in sequences and in expression patterns, indicating that they may have a function during early development that has been conserved during vertebrate evolution. ..
- DeLaurier A, Eames B, Blanco Sanchez B, Peng G, He X, Swartz M, et al. Zebrafish sp7:EGFP: a transgenic for studying otic vesicle formation, skeletogenesis, and bone regeneration. Genesis. 2010;48:505-11 pubmed publisher..This line provides an essential tool for the further study of zebrafish otic vesicle formation and the development and regeneration of the skeleton. ..
- Walker M, Miller C, Coffin Talbot J, Stock D, Kimmel C. Zebrafish furin mutants reveal intricacies in regulating Endothelin1 signaling in craniofacial patterning. Dev Biol. 2006;295:194-205 pubmed
- Maves L, Kimmel C. Dynamic and sequential patterning of the zebrafish posterior hindbrain by retinoic acid. Dev Biol. 2005;285:593-605 pubmed..Our results support a new model of dynamic RA action in the hindbrain, in which a temporally increasing source of RA is required to sequentially initiate progressively more posterior rhombomere identities...
- McDonald J, Holbrook S, Isshiki T, Weiss J, Doe C, Mellerick D. Dorsoventral patterning in the Drosophila central nervous system: the vnd homeobox gene specifies ventral column identity. Genes Dev. 1998;12:3603-12 pubmed..Vertebrate homologs of vnd (Nkx2.1 and 2.2) are similarly expressed in the ventral CNS, raising the possibility that DV patterning within the CNS is evolutionarily conserved. ..
- Moens C, Yan Y, Appel B, Force A, Kimmel C. valentino: a zebrafish gene required for normal hindbrain segmentation. Development. 1996;122:3981-90 pubmed..These results provide genetic evidence for a two-segment periodicity in the hindbrain and suggest that this periodicity arises sequentially, through the specification and later subdivision of a two-rhombomere unit, or 'protosegment'. ..
- Printen J, Sprague G. Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase cascade. Genetics. 1994;138:609-19 pubmed..Finally, we detected an interaction between one of the MAP kinases, Kss1p, and a presumptive target, the transcription factor Ste12p. We failed to detect interactions of Ste4p or Ste20p with any other component of the response pathway. ..
- Baxter S, Gontrum D, Phillips C, Roth A, Dahlquist F. Heterodimerization of the yeast homeodomain transcriptional regulators alpha 2 and a1: secondary structure determination of the a1 homeodomain and changes produced by alpha 2 interactions. Biochemistry. 1994;33:15309-20 pubmed..Relatively minor effects on the resonances from residues in helix 3, the putative DNA-binding helix, were noted upon alpha 2 binding. We have thus located a region of the a1 homeodomain important for specific protein recognition. ..
- Gill S, Weitzel S, von Hippel P. Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J Mol Biol. 1991;220:307-24 pubmed..These results are used to begin to define the basic conformational states and interaction potentials of core polymerase in the various stages of the transcription cycle. ..
- Baird N, Turnbull D, Johnson E. Induction of the heat shock pathway during hypoxia requires regulation of heat shock factor by hypoxia-inducible factor-1. J Biol Chem. 2006;281:38675-81 pubmed publisher..This cross-regulation represents a mechanism by which the low oxygen response pathway has assimilated complex new functions by regulating the key transcriptional activator of the heat shock pathway...
- Rupert P, Daughdrill G, Bowerman B, Matthews B. A new DNA-binding motif in the Skn-1 binding domain-DNA complex. Nat Struct Biol. 1998;5:484-91 pubmed..Skn-1, however, lacks the leucine zipper found in all bZips. Additional contacts with the DNA are made by a short basic segment at the N-terminus of the domain, reminiscent of the 'homeodomain arm'. ..
- Kohwi M, Lupton J, Lai S, Miller M, Doe C. Developmentally regulated subnuclear genome reorganization restricts neural progenitor competence in Drosophila. Cell. 2013;152:97-108 pubmed publisher..We propose that neuroblasts undergo a developmentally regulated subnuclear genome reorganization to permanently silence Hunchback target genes that results in loss of progenitor competence. ..
- Nichols J, Pan L, Moens C, Kimmel C. barx1 represses joints and promotes cartilage in the craniofacial skeleton. Development. 2013;140:2765-75 pubmed publisher..We further show that hand2 feeds back to negatively regulate barx1 expression. We consider the possibility that changes in barx1 function in early vertebrates were among the key innovations fostering the evolution of skeletal joints...
- Tallafuss A, Kelly M, Gay L, Gibson D, Batzel P, Karfilis K, et al. Transcriptomes of post-mitotic neurons identify the usage of alternative pathways during adult and embryonic neuronal differentiation. BMC Genomics. 2015;16:1100 pubmed publisher..This important insight and the lists of enriched genes we have identified will now help pave the way to a better understanding of the mechanisms of embryonic and adult neuronal differentiation and how to manipulate these processes. ..