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https://www.readbyqxmd.com/read/28547993/conformational-heterogeneity-and-dna-recognition-by-the-morphogen-bicoid
#1
Ramkrishna Adhikary, Yun Xuan Tan, Jian Liu, Jörg Zimmermann, Matthew Holcomb, Carolyn Yvellez, Philip E Dawson, Floyd E Romesberg
The morphogenic activity of the Drosophila transcription factor bicoid (Bcd), the first morphogenic protein identified, is controlled by its DNA binding homeodomain. Homeodomains mediate developmental processes in all multicellular organisms, but the Bcd homeodomain appears to be unique as it can bind multiple DNA sequences and even RNA. All homeodomain proteins adopt a three-helix fold, with residues of the third helix mediating recognition of the nucleic acid target via interactions with the major groove...
May 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28507987/pitx2-in-embryonic-and-adult-myogenesis
#2
REVIEW
Francisco Hernandez-Torres, Lara Rodríguez-Outeiriño, Diego Franco, Amelia E Aranega
Skeletal muscle is a heterogeneous tissue that represents between 30 and 38% of the human body mass and has important functions in the organism, such as maintaining posture, locomotor impulse, or pulmonary ventilation. The genesis of skeletal muscle during embryonic development is a process controlled by an elaborate regulatory network combining the interplay of extrinsic and intrinsic regulatory mechanisms that transform myogenic precursor cells into functional muscle fibers through a finely tuned differentiation program...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28437444/transcriptional-bursting-in-drosophila-development-stochastic-dynamics-of-eve-stripe-2-expression
#3
David M Holloway, Alexander V Spirov
Anterior-posterior (AP) body segmentation of the fruit fly (Drosophila) is first seen in the 7-stripe spatial expression patterns of the pair-rule genes, which regulate downstream genes determining specific segment identities. Regulation of pair-rule expression has been extensively studied for the even-skipped (eve) gene. Recent live imaging, of a reporter for the 2nd eve stripe, has demonstrated the stochastic nature of this process, with 'bursts' in the number of RNA transcripts being made over time. We developed a stochastic model of the spatial and temporal expression of eve stripe 2 (binding by transcriptional activators (Bicoid and Hunchback proteins) and repressors (Giant and Krüppel proteins), transcriptional initiation and termination; with all rate parameters constrained by features of the experimental data) in order to analyze the noisy experimental time series and test hypotheses for how eve transcription is regulated...
2017: PloS One
https://www.readbyqxmd.com/read/28401018/otx2-expression-contributes-to-proliferation-and-progression-in-myc-amplified-medulloblastoma
#4
REVIEW
Yining Lu, Collin M Labak, Neha Jain, Ian J Purvis, Maheedhara R Guda, Sarah E Bach, Andrew J Tsung, Swapna Asuthkar, Kiran K Velpula
Medulloblastoma is one of the most prevalent pediatric brain malignancies, accounting for approximately 20% of all primary CNS tumors in children under the age of 19. OTX2 is the member of a highly conserved family of bicoid-like homeodomain transcription factors responsible for the regulation of cerebellar development and of current investigational interest in the tumorigenesis of medulloblastoma. Recent studies have revealed that Group 3 and Group 4 medulloblastomas show marked overexpression of OTX2 with a concurrent amplification of the MYC and MYCN oncogenes, respectively, correlating with anaplasticity and unfavorable patient outcomes...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28299188/genome-wide-measurement-of-spatial-expression-in-patterning-mutants-of-drosophila-melanogaster
#5
Peter A Combs, Michael B Eisen
Patterning in the Drosophila melanogaster embryo is affected by multiple maternal factors, but the effect of these factors on spatial gene expression has not been systematically analyzed. Here we characterize the effect of the maternal factors Zelda, Hunchback and Bicoid by cryosectioning wildtype and mutant blastoderm stage embryos and sequencing mRNA from each slice. The resulting atlas of spatial gene expression highlights the intersecting roles of these factors in regulating spatial patterns, and serves as a resource for researchers studying spatial patterning in the early embryo...
2017: F1000Research
https://www.readbyqxmd.com/read/28296637/correction-bicoid-gradient-formation-and-function-in-the%C3%A2-drosophila-pre-syncytial-blastoderm
#6
Zehra Ali-Murthy, Thomas B Kornberg
No abstract text is available yet for this article.
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28197917/sumo-in-drosophila-development
#7
Joseph Cao, Albert J Courey
The ubiquitin -like protein SUMO is conjugated covalently to hundreds of target proteins in organisms throughout the eukaryotic domain. Genetic and biochemical studies using the model organism Drosophila melanogaster are beginning to reveal many essential functions for SUMO in cell biology and development. For example, SUMO regulates multiple signaling pathways such as the Ras/MAPK, Dpp, and JNK pathways. In addition, SUMO regulates transcription through conjugation to many transcriptional regulatory proteins, including Bicoid, Spalt , Scm, and Groucho...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28158178/dynamic-maternal-gradients-control-timing-and-shift-rates-for-drosophila-gap-gene-expression
#8
Berta Verd, Anton Crombach, Johannes Jaeger
Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28054512/the-effect-of-reactions-on-the-formation-and-readout-of-the-gradient-of-bicoid
#9
Emiliano Perez Ipiña, Silvina Ponce Dawson
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites...
February 8, 2017: Physical Biology
https://www.readbyqxmd.com/read/27791980/bicoid-mrna-localises-to-the-drosophila-oocyte-anterior-by-random-dynein-mediated-transport-and-anchoring
#10
Vítor Trovisco, Katsiaryna Belaya, Dmitry Nashchekin, Uwe Irion, George Sirinakis, Richard Butler, Jack J Lee, Elizabeth R Gavis, Daniel St Johnston
bicoid mRNA localises to the Drosophila oocyte anterior from stage 9 of oogenesis onwards to provide a local source for Bicoid protein for embryonic patterning. Live imaging at stage 9 reveals that bicoid mRNA particles undergo rapid Dynein-dependent movements near the oocyte anterior, but with no directional bias. Furthermore, bicoid mRNA localises normally in shot(2A2), which abolishes the polarised microtubule organisation. FRAP and photo-conversion experiments demonstrate that the RNA is stably anchored at the anterior, independently of microtubules...
October 28, 2016: ELife
https://www.readbyqxmd.com/read/27616358/transcriptional-activity-of-the-short-gastrulation-primary-enhancer-in-the-ventral-midline-requires-its-early-activity-in-the-presumptive-neurogenic-ectoderm
#11
Dong-Hyeon Shin, Joung-Woo Hong
The short gastrulation (sog) shadow enhancer directs early and late sog expression in the neurogenic ectoderm and the ventral midline of the developing Drosophila embryo, respectively. Here, evidence is presented that the sog primary enhancer also has both activities, with the late enhancer activity dependent on the early activity. Computational analyses showed that the sog primary enhancer contains five Dorsal (Dl)-, four Zelda (Zld)-, three Bicoid (Bcd)-, and no Single-minded (Sim)-binding sites. In contrast to many ventral midline enhancers, the primary enhancer can direct lacZ expression in the ventral midline as well as in the neurogenic ectoderm without a canonical Simbinding site...
October 2016: BMB Reports
https://www.readbyqxmd.com/read/27528040/the-short-gastrulation-shadow-enhancer-employs-dual-modes-of-transcriptional-synergy
#12
Dong-Hyeon Shin, Joung-Woo Hong
It remains unclear how a limited amount of maternal transcription factor Dorsal (Dl) directs broad expression of short gastrulation (sog) throughout the presumptive neurogenic ectoderm in the Drosophila early embryo. Here, we present evidence that the sog shadow enhancer employs dual modes of transcriptional synergy to produce this broad pattern. Bioinformatics analyses indicated that a minimal enhancer region, systematically mapped in vivo, contains five Dl-, three Zelda (Zld)-, and three Bicoid (Bcd)-binding sites; four of these five Dl-binding sites are closed linked to two Zld- and two Bcd-binding sites...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/27474798/mrna-poly-a-tail-changes-specified-by-deadenylation-broadly-reshape-translation-in-drosophila-oocytes-and-early-embryos
#13
Stephen W Eichhorn, Alexander O Subtelny, Iva Kronja, Jamie C Kwasnieski, Terry L Orr-Weaver, David P Bartel
Because maturing oocytes and early embryos lack appreciable transcription, posttranscriptional regulatory processes control their development. To better understand this control, we profiled translational efficiencies and poly(A)-tail lengths throughout Drosophila oocyte maturation and early embryonic development. The correspondence between translational-efficiency changes and tail-length changes indicated that tail-length changes broadly regulate translation until gastrulation, when this coupling disappears...
July 30, 2016: ELife
https://www.readbyqxmd.com/read/27376588/the-bicoid-mrna-localization-factor-exuperantia-is-an-rna-binding-pseudonuclease
#14
Daniela Lazzaretti, Katharina Veith, Katharina Kramer, Claire Basquin, Henning Urlaub, Uwe Irion, Fulvia Bono
Anterior patterning in Drosophila is mediated by the localization of bicoid (bcd) mRNA at the anterior pole of the oocyte. Exuperantia (Exu) is a putative exonuclease (EXO) associated with bcd and required for its localization. We present the crystal structure of Exu, which reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The catalytic site is degenerate and inactive. Instead, the EXO-like domain mediates dimerization and RNA binding...
August 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27253156/maternal-ap-determinants-in-the-drosophila-oocyte-and-embryo
#15
REVIEW
Jun Ma, Feng He, Gengqiang Xie, Wu-Min Deng
An animal embryo cannot initiate its journey of forming a new life on its own. It must rely on maternally provided resources and inputs to kick-start its developmental process. In Drosophila, the initial polarities of the embryo along both the anterior-posterior (AP) and dorsal-ventral (DV) axes are also specified by maternal determinants. Over the past several decades, genetic and molecular studies have identified and characterized such determinants, as well as the zygotic genetic regulatory networks that control patterning in the early embryo...
September 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27193268/hydrodynamic-modeling-of-bicoid-morphogen-gradient-formation-in-drosophila-embryo
#16
Jun Xie, Guo-Hui Hu
Bicoid is a maternal polarity determinant that mediates the anterior-posterior (AP) patterning in early Drosophila embryo. During oogenesis, its mRNA deposits at the anterior pole of the embryo and then translates to establish the Bicoid morphogen gradient soon after fertilization. Previous investigations indicated that the patterning is induced by the spatial gradient of Bicoid morphogen concentration, where the cytoplasmic convection plays a crucial role. The present study examines the effect of advection transport on the formation of the Bicoid morphogen gradient using direct simulation of the cytoplasmic streaming described by Navier-Stokes equations, in which the cytoplasm behaves as an incompressible Newtonian fluid...
May 19, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27112292/shadow-enhancers-mediate-dynamic-shifts-of-gap-gene-expression-in-the-drosophila-embryo
#17
Ezzat El-Sherif, Michael Levine
Drosophila patterning genes often contain pairs of primary and shadow enhancers that possess overlapping activities [1-5]. It has been suggested that this regulatory "redundancy" helps ensure reliable activation of gene expression under stressful conditions such as increases in temperature [4, 5]. There is also evidence that shadow enhancers help produce sharp on/off boundaries of gene expression in response to small changes in the levels of regulatory factors, such as the maternal Bicoid gradient [6, 7]. Here, we use live-imaging methods to visualize the temporal dynamics of the gap genes Kruppel and knirps, which are essential for the patterning of the thorax and abdomen, respectively [8, 9]...
May 9, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27009473/novel-pitx2-gene-mutations-in-patients-with-axenfeld-rieger-syndrome
#18
Morteza Seifi, Tim Footz, Sherry A M Taylor, Ghada M Elhady, Ebtesam M Abdalla, Michael A Walter
PURPOSE: Mutations in the bicoid-like transcription factor PITX2 gene often result in Axenfeld-Rieger syndrome (ARS), an autosomal-dominant inherited disorder. We report here the discovery and characterization of novel PITX2 deletions in a small kindred with ARS. METHODS: Two familial patients (father and son) from a consanguineous family were examined in the present study. Patient DNA samples were screened for PITX2 mutations by DNA sequencing and for copy number variation by SYBR Green quantitative polymerase chain reaction (PCR) analysis...
November 2016: Acta Ophthalmologica
https://www.readbyqxmd.com/read/26986359/extending-the-dynamic-range-of-transcription-factor-action-by-translational-regulation
#19
Thomas R Sokolowski, Aleksandra M Walczak, William Bialek, Gašper Tkačik
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise...
February 2016: Physical Review. E
https://www.readbyqxmd.com/read/26970001/positional-information-and-cell-fate-determination-in-the-early-drosophila-embryo
#20
REVIEW
Eric Wieschaus
During early development in Drosophila, the spatial information of maternal gradients is translated into discrete transcriptional states determining cell fate. Information transfer depends on reproducibility of the gradients themselves, as well as the ability of cells to accurately measure and utilize morphogen concentrations in biologically meaning ways. In the following essay, these issues are discussed in context of the Bicoid gradient.
2016: Current Topics in Developmental Biology
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