Browsing by Subject "HOMEOBOX GENE"

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  • Smetana, Ondrej; Mäkilä, Riikka; Lyu, Munan; Amiryousefi, Ali; Rodriguez, Filomeno Sanchez; Wu, Miin-Feng; Sole-Gil, Anna; Gavarron, Marina Leal; Siligato, Riccardo; Miyashima, Shunsuke; Roszak, Pawel; Blomster, Tiina; Reed, Jason W.; Broholm, Suvi; Mähönen, Ari Pekka (2019)
    Wood, a type of xylem tissue, originates from cell proliferation of the vascular cambium. Xylem is produced inside, and phloem outside, of the cambium(1). Morphogenesis in plants is typically coordinated by organizer cells that direct the adjacent stem cells to undergo programmed cell division and differentiation. The location of the vascular cambium stem cells and whether the organizer concept applies to the cambium are currently unknown(2). Here, using lineage-tracing and molecular genetic studies in the roots of Arabidopsis thaliana, we show that cells with a xylem identity direct adjacent vascular cambial cells to divide and function as stem cells. Thus, these xylem-identity cells constitute an organizer. A local maximum of the phytohormone auxin, and consequent expression of CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, promotes xylem identity and cellular quiescence of the organizer cells. Additionally, the organizer maintains phloem identity in a non-cell-autonomous fashion. Consistent with this dual function of the organizer cells, xylem and phloem originate from a single, bifacial stem cell in each radial cell file, which confirms the classical theory of a uniseriate vascular cambium(3). Clones that display high levels of ectopically activated auxin signalling differentiate as xylem vessels; these clones induce cell divisions and the expression of cambial and phloem markers in the adjacent cells, which suggests that a local auxin-signalling maximum is sufficient to specify a stem-cell organizer. Although vascular cambium has a unique function among plant meristems, the stem-cell organizer of this tissue shares features with the organizers of root and shoot meristems.
  • Aykanat, Tutku; Rasmussen, Martin; Ozerov, Mikhail; Niemelä, Eero; Paulin, Lars; Vähä, Juha-Pekka; Hindar, Kjetil; Wennevik, Vidar; Pedersen, Torstein; Svenning, Martin-A.; Primmer, Craig R. (2020)
    1. Animals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction. 2. We aimed to test the hypothesis that heritable resource acquisition variation that covaries with efficiency along the ontogeny would influence maturation timing of individuals. 3. To test this hypothesis, we utilized Atlantic salmon as a model which exhibits a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as stomach fullness and composition) of individuals with different ages, and linked it with genomic regions (haploblocks) that were previously identified to be associated with age-at-maturity. 4. Consistent with the hypothesis, we demonstrated that one of the life-history genomic regions tested (six6) was indeed associated with age-dependent differences in stomach fullness. Prey composition was marginally linked tosix6, and suggestively (but non-significantly) tovgll3genomic regions. We further showed Atlantic salmon switched to the so-called 'feast and famine' strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often. 5. These results suggest genetic variation underlying resource utilization may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food web structures.
  • Aykanat, Tutku; Rasmussen, Martin; Ozerov, Mikhail; Niemelä, Eero; Paulin, Lars; Vähä, Juha-Pekka; Hindar, Kjetil; Wennevik, Vidar; Pedersen, Torstein; Svenning, Martin-A.; Primmer, Craig R. (2020)
    1. Animals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction. 2. We aimed to test the hypothesis that heritable resource acquisition variation that covaries with efficiency along the ontogeny would influence maturation timing of individuals. 3. To test this hypothesis, we utilized Atlantic salmon as a model which exhibits a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as stomach fullness and composition) of individuals with different ages, and linked it with genomic regions (haploblocks) that were previously identified to be associated with age-at-maturity. 4. Consistent with the hypothesis, we demonstrated that one of the life-history genomic regions tested (six6) was indeed associated with age-dependent differences in stomach fullness. Prey composition was marginally linked tosix6, and suggestively (but non-significantly) tovgll3genomic regions. We further showed Atlantic salmon switched to the so-called 'feast and famine' strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often. 5. These results suggest genetic variation underlying resource utilization may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food web structures.
  • Ray, Robert P.; Matamoro-Vidal, Alexis; Ribeiro, Paulo S.; Tapon, Nic; Houle, David; Salazar-Ciudad, Isaac; Thompson, Barry J. (2015)
    How tissues acquire their characteristic shape is a fundamental unresolved question in biology. While genes have been characterized that control local mechanical forces to elongate epithelial tissues, genes controlling global forces in epithelia have yet to be identified. Here, we describe a genetic pathway that shapes appendages in Drosophila by defining the pattern of global tensile forces in the tissue. In the appendages, shape arises from tension generated by cell constriction and localized anchorage of the epithelium to the cuticle via the apical extracellular-matrix protein Dumpy (Dp). Altering Dp expression in the developing wing results in predictable changes in wing shape that can be simulated by a computational model that incorporates only tissue contraction and localized anchorage. Three other wing shape genes, narrow, tapered, and lanceolate, encode components of a pathway that modulates Dp distribution in the wing to refine the global force pattern and thus wing shape.
  • Tachmazidou, Ioanna; Suveges, Daniel; Min, Josine L.; Ritchie, Graham R. S.; Steinberg, Julia; Walter, Klaudia; Iotchkova, Valentina; Schwartzentruber, Jeremy; Huang, Jie; Memari, Yasin; McCarthy, Shane; Crawford, Andrew A.; Bombieri, Cristina; Cocca, Massimiliano; Farmaki, Aliki-Eleni; Gaunt, Tom R.; Jousilahti, Pekka; Kooijman, Marjolein N.; Lehne, Benjamin; Malerba, Giovanni; Mannisto, Satu; Matchan, Angela; Medina-Gomez, Carolina; Metrustry, Sarah J.; Nag, Abhishek; Ntalla, Ioanna; Paternoster, Lavinia; Rayner, Nigel W.; Sala, Cinzia; Scott, William R.; Shihab, Hashem A.; Southam, Lorraine; St Pourcain, Beate; Traglia, Michela; Trajanoska, Katerina; Zaza, Gialuigi; Zhang, Weihua; Artigas, Maria S.; Bansal, Narinder; Benn, Marianne; Chen, Zhongsheng; Danecek, Petr; Lin, Wei-Yu; Locke, Adam; Luan, Jian'an; Manning, Alisa K.; Mulas, Antonella; Sidore, Carlo; Tybjaerg-Hansen, Anne; Perola, Markus; SpiroMeta Consortium; GoT2D Consortium; ArcOGEN Consortium; Understanding Soc Sci Grp; UK10KConsortium (2017)
    Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common-and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. 71% of signals reside within genes and fine mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically relevant discoveries across the frequency spectrum.