DOCSLIB.ORG

And Abdominal-B in Drosqbhilu Melanogaster

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Copyright 0 1995 by the Genetics Society of America and Trans Interactions Between the iab Regulatory Regions and abdominal-A and Abdominal-B in Drosqbhilu melanogaster Jd Eileen Hendrickson and Shigeru Sakonju Department of Human Genetics, Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah 841 12 Manuscript received August 15, 1994 Accepted for publication November 8, 1994 ABSTRACT The infra-abdominal ( iab) elements in the bithorax complex of Drosophila melanogaster regulate the transcription of the homeotic genesabdominal-A ( abd-A) and Abdominal-B ( Abd-B) in cis. Here we describe two unusual aspects of regulation by the iab elements, revealed by an analysis of an unexpected comple- mentation between mutations in the Abd-B transcription unit and these regulatory regions. First,we find that iab-6 and iab7 can regulate Abd-B in trans. This iab trans regulation is insensitive to chromosomal rearrangements that disrupt transvection effects at the nearby Ubx locus. In addition, we show that a transposed Abd-B transcription unitand promoter on the Ychromosomecan be activatedby iabelements located on the third chromosome. These results suggest that the iab regions can regulate their target promoter located ata distant sitein the genomein a manner that is much less dependent on homologue pairing than other transvection effects.The iab regulatory regionsmay have a very strong affinity for the target promoter, allowing them to interactwith each other despite the inhibitory effectsof chromosomal rearrangements. Second, by generating abd-A mutations on rearrangement chromosomes that break in the iab-7 region, we show that these breaks induce theiab elements to switch their target promoter from Abd-B to abd-A. These two unusual aspects of iab regulation are related by the iab7 breakpoint chromo- somes that prevent iab elements from acting onAbd-B and allow them to act on abd-A. We propose that the iab-7 breaks prevent both iab trans regulation and target specificity by disrupting a mechanism that targets the iab regions to the Abd-B promoter. ROPER development of an organism requires precise other chromosome ( ZACHARet al. 1985; CASTELLI-GAIR P regulation of gene expression. Enhancer and si- et al. 1990; GEYERet al. 1990) . lencer elements provide one level of this regulation, The homeotic genes of the bithorax complex, Ubx, activating and suppressing, respectively, the transcrip- abd-A and Abd-B, specify segmental identitiesof overlap- tion of genes in precise temporal and spatial patterns. ping body segments of the fly from parasegments (PS) Enhancer/ silencer elements can regulate the activity 5 through PS 14, corresponding to the third thoracic of specific target promoters from a relatively long dis- (T3) throughthe ninth abdominal segment (A9) tance in cis on the same chromosome (for review see (LEWIS1978; DUNCAN 1987).Genetic analyses have re- ATCHISON1988) . In Drosophila melanogaster a genetic vealed two typesof complementation groups, lethal and phenomenon calledtransvection suggests thaten- nonlethal, within thebithorax complex (Figure 1; hancers and silencers can also regulate promoters in LEWIS1978; SANCHEZ-HERREROet al. 1985) . Lethal com- trans on a homologous chromosome (see JUDD 1988; plementation groups identify the Ubx, abd-A and Abd-B WU and GOLDBERC1989; PIRROTTA1990; TARTOFand transcription units that encode essential DNA-binding HENIKOFF1991; WU 1993 for reviews). This effect was proteins. Abd-Bcomprises two subfunctions, Abd-Bm and originally described for regulatory mutations for the Abd-Br, provided by four overlappingtranscripts encod- Ultrabithmax ( Ubx) gene (LEWIS1954). In a transvec- ing Abd-BI and Abd-BII proteins in PS10-13 and PS14, tion effect chromosomal rearrangements that disrupt respectively (CASANOVA et al. 1986; CASANOVA and pairing between homologous chromosomesenhance or WHITE 1987; DELORENZIet al. 1988; KUZIORA and suppress the phenotype caused by certain regulatory MCGINNIS1988; SANCHEZ-HERREROand CROSBY1988; mutations. Thus, it has been proposed that homologue CELNIKERet al. 1989; ZAVORTINK and SAKONJU1989; pairing allows interaction between a regulatory element DELORENZIand BIENZ1990; BOULETet al. 1991 ) . Non- on one chromosome and its target promoter on an- lethal complementation groups,which affect subsets of Ubx, abd-A and Abd-B expression domains, identify regu- We dedicate this paper to E. B. Lewis, who began it d, on the latory elements for Ubx, abd-A and Abd-B transcription of his 77th birthday. occasion units. The abx, bx, pbx and bxd elements regulate Ubx Corresponding author: Shigeru Sakonju, Howard Hughes Medical Institute, 5200 Eccles Institute, Bldg. 533, University of Utah, Salt transcriptionin PS 5 (T2/T3)and PS 6 (T3/A1) Lake City, UT 841 12. E-mail: [email protected] ( BEACHYet al. 1985; HOGNESSet al. 1985; WHITEand Genetics 139: 835-848 (February, 1995) 836 J. E. Hendrickson and S. Sakonju WILCOX1985) . iab-2, -3 and -4 elements regulate abd- 137 Cs source and crossing them to females carryingthe double A in PS7 (A2), PS8 (A3) and PS9 (A4), respectively mutation Cbx'Ubx'. Cbx'Ubx' heterozygotes show a dominant phenotype of warped and held out wings because Cbx' acts ( KARCH et al. 1990; MACIAS et al. 1990) iab-5-iab-7 ele- . to misexpress Ubx+ on the homologous chromosome via a ments regulate theAbd-B class A transcription unit that transvection effect (LEWIS1955; CABRERAet al. 1985; WHITE codes for the Abd-BI protein in PSlO (A5) through and AKAM 1985; WHITEand WILCOX1985; WTELLI-GAIRet al. PS13 (A8) (CELNIKERet al. 1990; BOULETet al. 1991; 1990). This transvection effect is disrupted by chromosomal SANCHEZ-HERRERO1991 ) . Although specific regulatory rearrangements that break once between Ubxand the centro- mere and once outsidethis region. We recoveredre- mutations affecting the expression of the class A Abd-B arrangement mutations on the Abd-BDi4chromosome that dis- transcriptin PS13 andthe three longer transcripts rupt transvection between Cbx' and Ubx+ by screening for (class B, C and y) that code for the Abd-BII protein Abd-Bfli4/ Cbx'Ubx' F1 progeny with wild-type wings. The re- in PS14 and PS15 have not been found, they are ex- arrangements were mapped by following segregationwith au- pected to identify iab8 and iab9, respectively. tosomal markers. Some mutations were more finely mapped by cytogenetic analysis of larval polytene salivary gland chro- Genetic and molecular evidence indicate thatreg- the mosomes. ulatory elements in these iab regions act in cis. When To isolate abd-A mutations on an iab7 breakpoint chromo- mutations mapping to the transcription units aremade some, i~b-7~~'/TM3 Sbmale flies, aged1-7 days, were irradi- heterozygous with mutationsin regulatory elements, ated with 4000 rad using a I3'Cs source. They were immedi- they partially fail to complement each other. Further- ately mated en masse to TM? Sb/ TM6 Tb 1-7-day-old virgin females. After 7 days the parents were removed. Individual more, expression patterns of Ubx, abd-A and Abd-B tran- i~b7~~'*/TM6 Tb F1 males were allowed to mate with abd- scripts are altered in embryos mutant for these regula- A['"/ TM6 Tb females. i~b7~~'*/TM6 TbF2 progeny from tory elements ( BEACHYet al. 1985; HOGNESSet al. 1985; vials containin no Tb' upae were crossed separately to abd- A MXI , abd-AMx', abd-AMyand abd-AflZ4to confirm that they WHITEand WILCOX 1985;CELNIKER et al. 1990; KARCH carried an abd-A mutation. From 9735 individual matings we et al. 1990; MACIAS et al. 1990; BOULETet al. 1991; Ski- recovered two abd-A mutations, abd-AP' and abdAF2. CHEZ-HERRERO1991 ) , and aspects of correct expression abd-AP' and abd-A.F2 are null for abd-A function based on patterns can be recapitulated by a lacZ reporter under the following criteria. Cuticle preparations of abd-AF'/ abd- the controlof these regulatory elements in transformed ~D24and abd-A./Xz/ ~bd-A')'~embryos show transformation of flies (SIMONet al. 1990; MULLERand BIENZ1991; QIAN ventral denticle belts towardAl, typical of abd-A mutants (Sh- et ul. 1991; BUSTURIAand BIENZ1993). CHEZ-HERREROet al. 1985). abd-AP' homozygotes also show transformations typical of abd-A mutants, but abd-A,'xz homozy- We describe in this paper an analysis of an unex- gotes show a transformation of denticle belts toward T3. abd- pected complementation between mutations in Abd-the AP2/ Ubx embryos show a transformation of A1 toward T3 B transcription unit andits regulatory regions.We show and die before hatching, but abd-AJX2/bx34' animals live to that the iab regulatory elements can regulate the target adulthood and show no obvious transformation. We suspect promoter intrans. Unlike previously described transvec- that the abd-APz deletion includes pbx and bxd but not bx. The deletion may include part of the Ubx promoter, causing tion effects, this trans regulation by the iab elements, an enhanced transvection from bxt that suppresses the b~'~' which we call ITR, is unusually resistant to disruption phenotype ( MARTINEZ-LABORDA et al. 1992). Analysis of abd- by chromosomal rearrangements. We alsoshow that A-"' or abd-AP2 chromosomes reveals no chromosomal abnor- chromosomal rearrangements that separate theiab ele- malities other than the parental i~b7~"inversions. Southern ments from their normal Abd-B target promoter cause blot analysis using fragmentsof genomic clonesL2235, L2255, L2265, L2279, R8004 and R8019 (KARCH et al. 1985) reveals abd-A to substitute for someAbd-B functions, mostlikely that abd-AJX' contains a deletion of 4-6 kb including the abd- by allowing the iab elements that normally act on Abd- A homebox and that abd-AP' is associated witha deletion with B to act on abd-A instead. the right endpoint between abd-A exons 2 and 4. Neither mutation contains lesions in the iab regions to the right of the abd-A transcriptional unit. Neither mutant expresses abd- MATERIALS AND METHODS A transcripts in embryos as assayed by whole mount in situ Fly stocks. Fly stocks were maintained at 25" in a humidi- hybridization.
Recommended publications
  • Generating High Variability of B Chromosomes in Eyprepocnemis Plorans (Grasshopper)

    Generating High Variability of B Chromosomes in Eyprepocnemis Plorans (Grasshopper)

    Heredity 71 (1993) 352—362 Received 5 January 1993 Genetical Society of Great Britain Generating high variability of B chromosomes in Eyprepocnemis plorans (grasshopper) M. D. LOPEZ-LEON, J. CABRERO, M. C. PARDO, E. VISERAS, J. P. M. CAMACHO* & J. L. SANTOSI Departamento de Genética, Facu/tad de Ciencias, Un/versidad de Granada, E- 18071 Granada, Spa/n and tDepartamento de Genét/ca, Facultad de B/o/ogIa, Un/vers/dad Comp/utense de Madrid, E-28040 Madrid, Spa/n Twenty-eightprogeny analyses (PAs) performed on specimens of E. plorans collected from four natural Iberian populations have been informative about the transmission of rare B chromosome types or the de novo origin of some of them. At least ii rare B-types have been found in addition to the predominant ones: B1 in Daimuz, B2 in Jete and Salobreña, and B5 in Fuengirola. The presence in two controlled crosses of one embryo carrying a B-type which was absent in the parents suggests that these B variants (B20 and B )haveoriginated de novo. Eleven other PAs suggest that new B derivatives are recurrently arising in these populations. The most frequent B chromosome mutation was centromere misdivision that originated four different B-types (B2m1,B110,B210 and Bmjnj). Other rearrangements were pericentric inversions (B211, B212 and B213), inverse tandem fusion (B211), centric fusion (B11) and deletions (B2d1andB2d2).Thefour B derivatives produced by centromeric misdivision are significantly eliminated during sexual transmission, most probably owing to deficiencies in the control of chromosome movement by their hemicentromeres. Those derived from translocations showed Mendelian transmission but deletion B variants showed a tendency to elimination.
  • Continuous Variation in Y-Chromosome Structure of Rumex Acetosa

    Continuous Variation in Y-Chromosome Structure of Rumex Acetosa

    Heredity 57 (1986) 247-254 The Genetical Society of Great Britain Received 16 December 1985 Continuous variation in Y-chromosome structure of Rumex acetosa A. S. Wilby and School of Biological Sciences, J. S. Parker Queen Mary College, Mile End Road, London El 4NS. The dioecious angiosperm Rumex acetosa has an XXIXY1Y2sex-chromosomesystem. Each V-chromosome is heterochromatic except for a minute terminal euchromatic pairing segment. The Vs are constant in size but have a variable centromere position. The centromeres can be located anywhere within the central 40 per cent of the chromosome but are excluded from the two distal 30 per cent regions. In a sample of 270 males from 18 different populations 68 distinct variants have been identified on the basis of V-morphology. All populations are highly polymorphic with a minimum of four variants in a sample of ten males. The origin and significance of this massive variability is considered in this paper. Increased mutation rate of the Ys may be implicated in maintenance of this variation. I NTRO DUCTI ON these "inert" Ys has been described (Vana, 1972) variation in their structure has been overlooked. Sex-determinationin animals is usually genic and Extensive heterochroinatic content is a charac- frequently associated with visibly-differentiated teristic of many Y- and W-chromosomes. Indeed, sex-chromosomes. Sex expression in plants, some have argued that the process of hetero- however, is usually more plastic, and is subject to chromatinisation itself was implicated in the initial environmental influences such as temperature and phase of sex-chromosome differentiation (Jones, photoperiod (Heslop-Harrison, 1957).
  • Transvection in 2012: Site-Specific Transgenes Reveal a Plethora of Trans-Regulatory Effects

    Transvection in 2012: Site-Specific Transgenes Reveal a Plethora of Trans-Regulatory Effects

    COMMENTARY Transvection in 2012: Site-Specific Transgenes Reveal a Plethora of Trans-Regulatory Effects Judith A. Kassis1 Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 In this commentary, Judith Kassis discusses Bateman et al., widespread in the Drosophila genome (Bateman et al. 2012; “Comparing Enhancer Action in cis and in trans” and Mellert Mellert and Truman 2012). and Truman “Transvection is Common Throughout the Dro- Both groups of researchers used the phi-C31 system to in- sophila Genome”, which are published in this issue of GENETICS. tegrate transgenes into specific genomic locations to look at the ability of one transgene to activate the expression of another, N Drosophila, homologous chromosomes are paired in so- greatly increasing our knowledge of trans-interactions and sug- Imatic cells (reviewed in McKee 2004), leading to the oppor- gesting many experiments for the future. However, beyond that, tunity for regulatory DNA on one chromosome to influence their approaches to studying transvection and the questions they the expression of a promoter located on the homologous addressed differ. Bateman et al. (2012) used recombination- chromosome (reviewed in Duncan 2002; Kennison and mediated cassette exchange (Bateman et al. 2006) to insert Southworth 2002). Such trans-regulatory interactions were a simple, defined enhancer, the GMR (which consists of five first reported by Ed Lewis (Lewis 1954) who found that binding sites for the eye transcriptional activator Glass) and allelic complementation between particular mutations within adefined promoter driving the expression of either GFP or the bithorax complex did not occur when the pairing of ho- mCherry into three different chromosomal insertion sites to ad- mologous chromosomes was disrupted.
  • Gene Expression Changes Elicited by a Parasitic B Chromosome in the Grasshopper Eyprepocnemis Plorans Are Consistent with Its Phenotypic Effects

    Gene Expression Changes Elicited by a Parasitic B Chromosome in the Grasshopper Eyprepocnemis Plorans Are Consistent with Its Phenotypic Effects

    Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects Beatriz Navarro-Domínguez, María Martín-Peciña, Francisco J. Ruiz-Ruano, Josefa Cabrero, José María Corral, María Dolores López-León, et al. Chromosoma Biology of the Nucleus ISSN 0009-5915 Chromosoma DOI 10.1007/s00412-018-00689-y 1 23 Your article is protected by copyright and all rights are held exclusively by Springer- Verlag GmbH Germany, part of Springer Nature. This e-offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Chromosoma https://doi.org/10.1007/s00412-018-00689-y ORIGINAL ARTICLE Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects Beatriz Navarro-Domínguez1,2 & María Martín-Peciña1 & Francisco J. Ruiz-Ruano1 & Josefa Cabrero1 & José María Corral3,4 & María Dolores López-León1 & Timothy F. Sharbel3,5 & Juan Pedro M. Camacho1 Received: 24 August 2018 /Revised: 20 December 2018 /Accepted: 21 December 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract Parasitism evokes adaptive physiological changes in the host, many of which take place through gene expression changes.
  • Multi-Scale Organization of the Drosophila Melanogaster Genome

    Multi-Scale Organization of the Drosophila Melanogaster Genome

    G C A T T A C G G C A T genes Review Multi-Scale Organization of the Drosophila melanogaster Genome Samantha C. Peterson † , Kaylah B. Samuelson † and Stacey L. Hanlon * Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; [email protected] (S.C.P.); [email protected] (K.B.S.) * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome. Keywords: Drosophila; topologically associating domain; insulator; pairing; transvection; B chromo- some; cytogenetics Citation: Peterson, S.C.; Samuelson, K.B.; Hanlon, S.L.
  • Supernumerary B Chromosomes of Aegilops Speltoides Undergo Precise Elimination in Roots Early in Embryo Development

    Supernumerary B Chromosomes of Aegilops Speltoides Undergo Precise Elimination in Roots Early in Embryo Development

    ARTICLE https://doi.org/10.1038/s41467-020-16594-x OPEN Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development Alevtina Ruban 1,2,6, Thomas Schmutzer 1,3,6, Dan D. Wu1,4, Joerg Fuchs1, Anastassia Boudichevskaia 1,2, Myroslava Rubtsova1,5, Klaus Pistrick 1, Michael Melzer1, Axel Himmelbach1, Veit Schubert1, Uwe Scholz 1 & ✉ Andreas Houben 1 1234567890():,; Not necessarily all cells of an organism contain the same genome. Some eukaryotes exhibit dramatic differences between cells of different organs, resulting from programmed elimina- tion of chromosomes or their fragments. Here, we present a detailed analysis of programmed B chromosome elimination in plants. Using goatgrass Aegilops speltoides as a model, we demonstrate that the elimination of B chromosomes is a strictly controlled and highly efficient root-specific process. At the onset of embryo differentiation B chromosomes undergo elimination in proto-root cells. Independent of centromere activity, B chromosomes demonstrate nondisjunction of chromatids and lagging in anaphase, leading to micro- nucleation. Chromatin structure and DNA replication differ between micronuclei and primary nuclei and degradation of micronucleated DNA is the final step of B chromosome elimination. This process might allow root tissues to survive the detrimental expression, or over- expression of B chromosome-located root-specific genes with paralogs located on standard chromosomes. 1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland OT Gatersleben, Germany. 2 KWS SAAT SE & Co. KGaA, 37574 Einbeck, Germany. 3 Martin Luther University Halle-Wittenberg, Institute for Agricultural and Nutritional Sciences, 06099 Halle (Saale), Germany. 4 Triticeae Research Institute, Sichuan Agricultural University, 611130 Wenjiang, China.
  • 1 the Role of Cask in Neuronal Morphogenesis

    1 the Role of Cask in Neuronal Morphogenesis

    The Role of CASK in Neuronal Morphogenesis and Brain Size in Drosophila: A Genetic Model of Human Intellectual Disability with Microcephaly Item Type text; Electronic Dissertation Authors Tello Vega, Judith Arane Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 29/09/2021 20:08:46 Link to Item http://hdl.handle.net/10150/630252 THE ROLE OF CASK IN NEURONAL MORPHOGENESIS AND BRAIN SIZE IN DROSOPHILA: A GENETIC MODEL OF HUMAN INTELLECTUAL DISABILITY WITH MICROCEPHALY by Judith Arane Tello Vega Copyright © Judith Arane Tello Vega 2018 A Dissertation Submitted to the Faculty of the GRADUATE INTERDISCIPLINARY PROGRAM IN NEUROSCIENCE In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2018 1 2 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of the requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this dissertation are allowable without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department or the Dean of the Graduate College when in his or her judgment the proposed use of the material is in the interests of scholarship.
  • Interallelic Transcriptional Enhancement As an in Vivo Measure of Transvection in Drosophila Melanogaster

    Interallelic Transcriptional Enhancement As an in Vivo Measure of Transvection in Drosophila Melanogaster

    INVESTIGATION Interallelic Transcriptional Enhancement as an in Vivo Measure of Transvection in Drosophila melanogaster Geoffrey P. Noble,*,† Patrick J. Dolph,‡ and Surachai Supattapone*,†,1 *Department of Biochemistry and Cell Biology and †Department of Medicine, Geisel School of Medicine, and ‡Department of Biology, Dartmouth College, Hanover, New Hampshire 03755 ABSTRACT Transvection—pairing-dependent interallelic regulation resulting from enhancer action in KEYWORDS trans—occurs throughout the Drosophila melanogaster genome, likely as a result of the extensive somatic transvection homolog pairing seen in Dipteran species. Recent studies of transvection in Drosophila have demonstrated enhancer important qualitative differences between enhancer action in cis vs. in trans, as well as a modest synergistic somatic pairing effect of cis- and trans-acting enhancers on total tissue transcript levels at a given locus. In the present study, GAL4-UAS we identify a system in which cis- and trans-acting GAL4-UAS enhancer synergism has an unexpectedly large quantitative influence on gene expression, boosting total tissue transcript levels at least fourfold relative to those seen in the absence of transvection. We exploit this strong quantitative effect by using publicly available UAS-shRNA constructs from the TRiP library to assay candidate genes for transvection activity in vivo. The results of the present study, which demonstrate that in trans activation by simple UAS enhancers can have large quantitative effects on gene expression in Drosophila, have important new implications for experimental design utilizing the GAL4-UAS system. The nuclear genome is often pictured to function as a linear arrange- which there is widespread physical interaction between maternal and ment of nucleotides grouped into genes and regulatory elements paternal homologous chromosomes (McKee 2004; Metz 1916; Stevens operating more or less locally in cis .
  • How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

    How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

    G C A T T A C G G C A T genes Review How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes Alevtina Ruban ID , Thomas Schmutzer, Uwe Scholz ID and Andreas Houben * ID Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany; [email protected] (A.R.); [email protected] (T.S.); [email protected] (U.S.) * Correspondence: [email protected]; Tel.: +49-(0)-39482-5486 Received: 28 August 2017; Accepted: 24 October 2017; Published: 25 October 2017 Abstract: Accessory, supernumerary, or—most simply—B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS), their structure comprises fragments of standard (A) chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences. Keywords: B chromosome; supernumerary chromosome; evolution; next generation sequencing 1. Recent Discoveries Related to the Origin and Evolution of B Chromosomes The origin and evolution of the B chromosomes, which appear to make a non-essential contribution to the overall genome, have puzzled cytogeneticists for over a century.
  • Rare Allelic Forms of PRDM9 Associated with Childhood Leukemogenesis

    Rare Allelic Forms of PRDM9 Associated with Childhood Leukemogenesis

    Rare allelic forms of PRDM9 associated with childhood leukemogenesis Julie Hussin1,2, Daniel Sinnett2,3, Ferran Casals2, Youssef Idaghdour2, Vanessa Bruat2, Virginie Saillour2, Jasmine Healy2, Jean-Christophe Grenier2, Thibault de Malliard2, Stephan Busche4, Jean- François Spinella2, Mathieu Larivière2, Greg Gibson5, Anna Andersson6, Linda Holmfeldt6, Jing Ma6, Lei Wei6, Jinghui Zhang7, Gregor Andelfinger2,3, James R. Downing6, Charles G. Mullighan6, Philip Awadalla2,3* 1Departement of Biochemistry, Faculty of Medicine, University of Montreal, Canada 2Ste-Justine Hospital Research Centre, Montreal, Canada 3Department of Pediatrics, Faculty of Medicine, University of Montreal, Canada 4Department of Human Genetics, McGill University, Montreal, Canada 5Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA 6Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA 7Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. *corresponding author : [email protected] SUPPLEMENTARY INFORMATION SUPPLEMENTARY METHODS 2 SUPPLEMENTARY RESULTS 5 SUPPLEMENTARY TABLES 11 Table S1. Coverage and SNPs statistics in the ALL quartet. 11 Table S2. Number of maternal and paternal recombination events per chromosome. 12 Table S3. PRDM9 alleles in the ALL quartet and 12 ALL trios based on read data and re-sequencing. 13 Table S4. PRDM9 alleles in an additional 10 ALL trios with B-ALL children based on read data. 15 Table S5. PRDM9 alleles in 76 French-Canadian individuals. 16 Table S6. B-ALL molecular subtypes for the 24 patients included in this study. 17 Table S7. PRDM9 alleles in 50 children from SJDALL cohort based on read data. 18 Table S8: Most frequent translocations and fusion genes in ALL.
  • Transvection Is Common Throughout the Drosophila Genome

    Transvection Is Common Throughout the Drosophila Genome

    INVESTIGATION Transvection Is Common Throughout the Drosophila Genome David J. Mellert1 and James W. Truman Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147 ABSTRACT Higher-order genome organization plays an important role in transcriptional regulation. In Drosophila, somatic pairing of homologous chromosomes can lead to transvection, by which the regulatory region of a gene can influence transcription in trans.We observe transvection between transgenes inserted at commonly used phiC31 integration sites in the Drosophila genome. When two transgenes that carry endogenous regulatory elements driving the expression of either LexA or GAL4 are inserted at the same integration site and paired, the enhancer of one transgene can drive or repress expression of the paired transgene. These transvection effects depend on compatibility between regulatory elements and are often restricted to a subset of cell types within a given expression pattern. We further show that activated UAS transgenes can also drive transcription in trans. We discuss the implication of these findings for (1) understanding the molecular mechanisms that underlie transvection and (2) the design of experiments that utilize site- specific integration. HOUGH much of transcriptional regulation is due to hypomorphic or loss-of-function alleles of a gene exhibit Tregulatory elements that act in cis, relatively near the pairing-dependent complementation. Because of the low transcriptional start site of a gene, long-range and trans frequency of finding such complementary mutations, work interactions can also affect gene regulation (reviewed in on understanding transvection has focused on test cases in- Henikoff and Comai 1998; Dekker 2008). To understand cluding, but not limited to, the yellow (Geyer et al.
  • Functional Analysis of a New Dominant-Negative Allele of Miranda During CNS Development in Drosophila

    Functional Analysis of a New Dominant-Negative Allele of Miranda During CNS Development in Drosophila

    Functional analysis of a new dominant-negative allele of miranda during CNS development in Drosophila Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf Vorgelegt von Chieko Takizawa aus Tokyo, Japan Düsseldorf, 2006 Gedruckt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf Tag der mündlich Prüfung: 22. Mai 2006 Berichterstatter: Prof. Dr. A. Wodarz Prof. Dr. E. Knust 1 Introduction..................................................................................................... 1 1.1 Generation of cell diversity .............................................................................. 1 1.2 Development of the central nervous system in Drosophila ............................... 2 1.3 Asymmetric cell division of Drosophila neuroblasts......................................... 4 1.4 Proteins involved in the asymmetric cell division of neuroblasts....................... 5 1.4.1 Basally localized proteins .......................................................................... 6 1.4.2 Apically localized proteins......................................................................... 6 1.4.3 Other proteins involved in asymmetric cell division................................... 8 1.5 Control of daughter cell size asymmetry......................................................... 11 1.6 Asymmetric cell division in other systems: common features and differences. 11 1.6.1 Drosophila