MASARYKOVA UNIVERZITA Přírodovědecká fakulta Ústav experimentální biologie Oddělení genetiky a molekulární biologie

CHARAKTERIZACE REPETITIVNÍCH SEKVENCÍ U RODU ALLIUM

Diplomová práce

Bc. Roman Gogela

VEDOUCÍ PRÁCE: Mgr. Martina Dvořáčková, Ph.D. Brno 2014

Bibliografický záznam

Autor: Bc. Roman Gogela Přírodovědecká fakulta, Masarykova univerzita Ústav experimentální biologie

Název práce: Charakterizace repetitivních sekvencí u rodu Allium

Studijní program: Experimentální biologie

Studijní obor: Molekulární biologie a genetika

Vedoucí práce: Mgr. Martina Dvořáčková, Ph.D.

Akademický rok: 2013/2014

Počet stran: 117 + 6 stran příloh

Klíčová slova: Allium, Asparagales, GISH, rDNA, repetitivní sekvence, telomery

Bibliographic Entry

Author: Bc. Roman Gogela Faculty of Science, Masaryk University Department of Experimental Biology

Title of Thesis: Characterisation of repetitive sequences in genus Allium

Degree programme: Experimental Biology

Field of Study: Molecular Biology and Genetics

Supervisor: Mgr. Martina Dvořáčková, Ph. D.

Academic Year: 2013/2014

Number of Pages: 117 + 6 pages of appendix

Keywords: Allium, Asparagales, GISH, rDNA, repetitive sequences, telomeres

Abstrakt

Telomery jsou neodmyslitelnou součástí lineárních chromozomů eukaryotických buněk a struktury jim podobné můžeme nalézt i u lineárních chromozomů buněk prokaryotických. Tyto obvykle tandemové repetice nejen kompenzují erozi chromozomů vyvolanou neúplnou replikací, ale zároveň udržují cytogenetickou stabilitu genomu a jsou i regulátory dělivého potenciálu buněk. Od objevu první telomerické sekvence a mechanismu udržování telomer založeném na aktivitě RNA-dependentní DNA-polymerázy (telomerázy) bylo popsáno několik variant „klasické“ telomerické sekvence. Byla také zjištěna existence organismů s telomerami tvořenými jinými sekvencemi a závislými na jiném mechanismu udržování jejich délky. Stále však existují organismy, u kterých není telomerická sekvence známa. Jedněmi z nich jsou zástupci rodu Allium. Diplomové práce je zaměřena na studium lokalizace 45S rDNA a jejích strukturních podjednotek na chromozomech evolučně vzdálených zástupců rodu Allium ve vztahu k předpokládané telomerické úloze této sekvence u zmíněného rodu a dále pak na studium dalších kandidátních sekvencí. Byla provedena i genomová in situ hybridizace mezi modelovými druhy s cílem zjistit, zda sdílí společnou telomerickou sekvenci. Na základě zjištěných výsledků nelze potvrdit telomerickou roli testovaných kandidátních sekvencí. Vzhledem k lokalizaci 45S rDNA lokusů však existuje i nadále možnost, že tato sekvence tvoří telomeru chromozomů, na kterých je lokalizována, případně je zahrnuta v mechanismu jejich udržování. Důležitým zjištěním je objev doposud neznámé sekvence lokalizované na všech koncích chromozomů A. ursinum a sdílené s A. cepa. S velkou pravděpodobností se jedná o sekvenci telomerickou.

Abstract

Telomeres are important parts of linear chromosomes of eukaryotic cells and similar structures can be found at the ends of linear chromosomes of prokaryotic cells too. Telomeres are usually formed as tandem repeats that protect chromosomes against shortening caused by DNA replication. According to their localization, telomeres are involved in the maintenance of genome stability and regulation of cell proliferation capability. Since discovery of the first telomeric sequence and the mechanism of telomere lenght maintenance based on RNA-dependent DNA-polymerase (telomerase), several variants of „classical“ telomeric sequences have been described. Organisms with telomeres formed by other sequences and with different telomere length maintenance were detected. There are still organisms with unknown telomeric sequences, one of them are members of genus Allium. In this thesis, we have studied the localization of 45S rDNA and its subunits in selected species of genus Allium according to predicted role of 45S rDNA as telomeres in this genus. In the following steps, other candidate sequences were tested and genomic in situ hybridization between model species has been done. Based on the acquired results, we were not able to confirm role of the selected candidate sequences as a telomeric sequence within the tested plants from genus Allium According to the localization of the 45rDNA, it is possible that this sequence plays the role of a telomere within these localities, and probably can be involved in the telomere length maintenance process. An important result was the founding of a new sequence which is located on all of the telomeric ends of A. ursinum chromosomes and shared with A. cepa. Probably this sequence is of telomeric origin.

Poděkování

Na tomto místě bych rád poděkoval své vedoucí diplomové práce Mgr. Martině

Dvořáčkové, Ph. D. za odborné vedení, podporu a čas, který mi ochotně věnovala po celou dobu řešení mé diplomové práce.

Dále bych chtěl poděkovat Mgr. Vratislavu Peškovi, Ph. D. za možnost podílet se na projektu studia telomer rodu Allium a odborné rady a konzultace, které mi napomohly osvojit si danou problematiku. V neposlední řadě patří mé velké poděkování také Mgr. Terezii Mandákové, Ph. D. za cenné teoretické i praktické rady na poli rostlinné cytogenetiky. Závěrem chci poděkovat všem kolegů a kolegyním z Oddělení funkční genomiky a proteomiky, se kterými jsem měl čest pracovat, zvláště pak prof. RNDr. Jiřímu Fajkusovi, Csc.

Prohlášení

Prohlašuji, že jsem svoji diplomovou práci vypracoval samostatně s využitím informačních zdrojů, které jsou v práci citovány.

Brno 14. května 2014 ……………………………… Bc. Roman Gogela

Obsah 1. Úvod………………………………………………………………………………...... 13

2. Teoretický úvod………………………………………………………………………...skryto

2.1. Rod Allium……………………………………………………………………….. skryto 2.1.1. Fylogenetické zařazení………………………………………………………..skryto 2.1.2. Morfologické znaky…………………………………………………………. skryto 2.1.3. Oblast rozšíření……………………………………………………………… skryto 2.1.4. Charakteristika genomu……………………………………………………... skryto 2.2. Klasické telomery ...... skryto 2.2.1. Počátky studia telomer...... skryto 2.2.2. Odhalení struktury telomer a mechanismu jejich udržování………………… skryto 2.2.3. Čtyři základní charakteristiky „klasických telomer“...... skryto 2.3. Neobvyklé telomery ...... skryto 2.3.1. Telomerický systém Drosophila ...... skryto

2.3.2. Telomery typu Chironomus………………………………………………….. skryto 2.3.3. Telomery typu Rhynchosciara………………………………………………. skryto 2.3.4. Alternativní způsoby udržování telomer u kvasinek………………………….skryto 2.4. Záhada telomer rodu Allium ...... skryto 2.5. Ribosomální DNA (rDNA)………………………………………………………. skryto 2.5.1. Struktura rDNA a sekvenční konzervovanost………………………………. skryto

2.5.2. 45S rDNA u rodu Allium……………………………………………………. skryto 3. Cíle diplomové práce:………………………………………………………………… skryto

4. Materiál a metody: ……………………………………………………………………. skryto 4.1. Seznam použitých roztoků:...... skryto 4.2. Materiál: ...... skryto

4.2.1. Modelové organismy:...... skryto 4.2.2. Genetický materiál:...... skryto 4.3. Metody:...... skryto 4.3.1. Příprava sond:...... skryto

4.3.2. Příprava preparátů:...... skryto 5. Výsledky:...... skryto 5.1. Lokalizace 45S rDNA u A. ursinum...... skryto 5.2. Genomová in situ hybidizace (GISH)……………………………………………. skryto 5.3. Lokalizace 45S rDNA u A. cepa...... skryto 5.4. Lokalizace kandidátních telomerických sekvencí na chromozomech Allium cepa......

...... skryto

6. Diskuze...... skryto 6.1. Telomery rodu Allium...... skryto 6.1.1. Hypotézy plynoucí z literatury...... skryto 6.1.2. Role 45S rDNA při formování telomer rodu Allium...... skryto

6.1.3. GISH A. cepa a A. ursinum – společná telomerická sekvence?...... skryto 6.1.4. Kandidátní telomerické sekvence – vyhodnocení a možnosti jejich predikce...... skryto 6.2. Variabilita v délce IGS oblasti sekvence 45S rDNA A. ursinum...... skryto 6.3. Variabilita v počtu lokusů 45S rDNA A. cepa a A. ursinum...... skryto 7. Souhrn………………………………………………………………………………... skryto 8. Summary……………………………………………………………………………... skryto 9. Literatura…………………………………………………………………………………. 95

Seznam zkratek

ALT Alternative lengthening of telomeres APG Angiosperm phylogeny group BAC Bacterial artificial chromosome ETS External transcribed spacer FISH Fluorescenční in situ hybridizace gDNA Genomová DNA GISH Genomová in situ hybridizace HAATI Heterochromatin amplification-mediated and telomerase-independent IGS Intergenic spacer ITS Internal transcribed spacer LINE Long interspersed elements non-LTR Non-long terminal repeats NOR Nucleolus organizer region NTS Non-transcribed spacer rDNA Ribosomální DNA RPM Revolutions per minute (otáčky za minutu) SINE Short interspersed elements TER Telomerase RNA TERT Telomerase reverse transcriptase WCSP World Checklist of Selected Plant Families

1. Úvod

Rostliny z rodu Allium (česnek) patří mezi významné kulturní plodiny. Více než dvacet druhů, jako je cibule (Allium cepa), česnek (Allium sativum), pórek (Allium porrum) nebo pažitka (Allium schoeneprasum, Allium tuberosum), je pěstováno, ať už celosvětově či pouze lokálně. Další druhy, jako je například česnek medvědí (Allium ursinum), jsou hojně používané pro vysoký obsah léčivých látek v přírodní medicíně a v neposlední řadě jsou v této skupině hojně zastoupeny i druhy okrasné. Tento druhově velmi bohatý rod však není důležitý pouze z ekonomického hlediska, ale někteří jeho zástupci mají nepopiratelný význam při studiu různých odvětví biologie, především pak v cytogenetice. Allium cepa je jedním z klasických cytogenetických modelových organismů a Allium schorodoprasum bylo po dlouhou dobu využíváno ke studiu B chromosomů. Některé druhy jsou často spojovány s léčbou či prevencí některých onemocnění, proto není divu, že neunikly zájmu moderní medicíny. Druhy jako Allium sativa, Allium macrostemon, nebo Allium victorialis jsou v současnosti studovány s ohledem na jejich farmaceutické využití, převážně kvůli antimikrobiálním, antioxidačním a protinádorovým vlastnostem látek, které syntetizují. Ve své práci se však chci zaměřit na jiný fenomén, který je s těmito rostlinami spojen, a to na doposud nevyjasněnou strukturu jejich telomer. Skutečnost, že telomery těchto rostlin nejsou tvořeny žádnou z doposud známých telomerických sekvencí, byla poprvé popsána v roce 1995, avšak zatím žádná následná studie nepodala uspokojivou odpověď na otázku, o jakou sekvenci se v případě telomer u rostlin rodu Allium jedná. Cílem této práce je proto shrnout dosavadní poznatky o studiu této problematiky a zodpovědět tuto otázku, případně naznačit směr, kterým by se studium struktury telomer u rostlin rodu Allium mohlo dále ubírat.

13

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Příloha 1: Fylogenetický strom Monocotyledonae

Příloha 1. Fylogenetický strom Monocotyledonae. Upraveno podle (APG III, 2009)

Příloha 2: Fylogenetické členění řádu Asparagales

Příloha 2. Fylogenetické členění řádu Asparagales. Upraveno podle (Rodriguez-Enriquez a Grant-Downton, 2013).

Příloha 3: Fylogenetické uspořádání rodu Allium

Druh Sekce Podrod

Druh Sekce Podrod

Druh Sekce Podrod

Druh Sekce Podrod

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