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https://www.readbyqxmd.com/read/29030151/optimizing-bicoid-signal-extraction
#1
Hossein Hassani, Emmanuel Sirimal Silva, Zara Ghodsi
Signal extraction and analysis is of great importance, not only in fields such as economics and meteorology, but also in genetics and even biomedicine. There exists a range of parametric and nonparametric techniques which can perform signal extractions. However, the aim of this paper is to define a new approach for optimising signal extraction from bicoid gene expression profile. Having studied both parametric and nonparametric signal extraction techniques, we identified the lack of specific criteria enabling users to select the optimal signal extraction parameters...
October 10, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28982761/dense-bicoid-hubs-accentuate-binding-along-the-morphogen-gradient
#2
Mustafa Mir, Armando Reimer, Jenna E Haines, Xiao-Yong Li, Michael Stadler, Hernan Garcia, Michael B Eisen, Xavier Darzacq
Morphogen gradients direct the spatial patterning of developing embryos; however, the mechanisms by which these gradients are interpreted remain elusive. Here we used lattice light-sheet microscopy to perform in vivo single-molecule imaging in early Drosophila melanogaster embryos of the transcription factor Bicoid that forms a gradient and initiates patterning along the anteroposterior axis. In contrast to canonical models, we observed that Bicoid binds to DNA with a rapid off rate throughout the embryo such that its average occupancy at target loci is on-rate-dependent...
September 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28973031/cortical-movement-of-bicoid-in-early-drosophila-embryos-is-actin-and-microtubule-dependent-and-disagrees-with-the-sdd-diffusion-model
#3
Xiaoli Cai, Mira Akber, Alexander Spirov, Stefan Baumgartner
The Bicoid (Bcd) protein gradient in Drosophila serves as a paradigm for gradient formation in textbooks. The SDD model (synthesis, diffusion, degradation) was proposed to explain the formation of the gradient. The SDD model states that the bcd mRNA is located at the anterior pole of the embryo at all times and serves a source for translation of the Bicoid protein, coupled with diffusion and uniform degradation throughout the embryo. Recently, the ARTS model (active RNA transport, synthesis) challenged the SDD model...
2017: PloS One
https://www.readbyqxmd.com/read/28919007/on-the-importance-of-protein-diffusion-in-biological-systems-the-example-of-the-bicoid-morphogen-gradient
#4
REVIEW
Cécile Fradin
Morphogens are proteins that form concentration gradients in embryos and developing tissues, where they act as postal codes, providing cells with positional information and allowing them to behave accordingly. Bicoid was the first discovered morphogen, and remains one of the most studied. It regulates segmentation in flies, forming a striking exponential gradient along the anterior-posterior axis of early Drosophila embryos, and activating the transcription of multiple target genes in a concentration-dependent manner...
September 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28894941/evolutionary-coincidence-of-adaptive-changes-in-exuperantia-and-the-emergence-of-bicoid-in-cyclorrhapha-diptera
#5
Janaina Lima de Oliveira, Iderval Silva Sobrinho-Junior, Samira Chahad-Ehlers, Reinaldo Alves de Brito
The great radiation in the infraorder Cyclorrhapha involved several morphological and molecular changes, including important changes in anterior egg development. During Drosophila oogenesis, exuperantia (exu) is critical for localizing bicoid (bcd) messenger RNA (mRNA) to the anterior region of the oocyte. Because it is phylogenetically older than bcd, which is exclusive to Cyclorrhapha, we hypothesize that exu has undergone adaptive changes to enable this new function. Although exu has been well studied in Drosophila, there is no functional or transcriptional information about it in any other Diptera...
September 11, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28891464/concentration-dependent-chromatin-states-induced-by-the-bicoid-morphogen-gradient
#6
Colleen E Hannon, Shelby A Blythe, Eric F Wieschaus
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context...
September 11, 2017: ELife
https://www.readbyqxmd.com/read/28691901/decoding-temporal-interpretation-of-the-morphogen-bicoid-in-the-early-drosophila-embryo
#7
Anqi Huang, Christopher Amourda, Shaobo Zhang, Nicholas S Tolwinski, Timothy E Saunders
Morphogen gradients provide essential spatial information during development. Not only the local concentration but also duration of morphogen exposure is critical for correct cell fate decisions. Yet, how and when cells temporally integrate signals from a morphogen remains unclear. Here, we use optogenetic manipulation to switch off Bicoid-dependent transcription in the early Drosophila embryo with high temporal resolution, allowing time-specific and reversible manipulation of morphogen signalling. We find that Bicoid transcriptional activity is dispensable for embryonic viability in the first hour after fertilization, but persistently required throughout the rest of the blastoderm stage...
July 10, 2017: ELife
https://www.readbyqxmd.com/read/28547993/conformational-heterogeneity-and-dna-recognition-by-the-morphogen-bicoid
#8
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...
June 6, 2017: Biochemistry
https://www.readbyqxmd.com/read/28507987/pitx2-in-embryonic-and-adult-myogenesis
#9
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
#10
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
#11
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
#12
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
#13
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
#14
REVIEW
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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