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One Base Pair Resolution Histone H1-Nucleosomal DNA Interaction Mapping and 3D Organization of H1 Containing Nucleosome Sajad Hussain Syed

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One Base Pair Resolution Histone H1-Nucleosomal DNA Interaction Mapping and 3D Organization of H1 Containing Nucleosome Sajad Hussain Syed One base pair resolution histone H1-nucleosomal DNA interaction mapping and 3D organization of H1 containing nucleosome Sajad Hussain Syed To cite this version: Sajad Hussain Syed. One base pair resolution histone H1-nucleosomal DNA interaction mapping and 3D organization of H1 containing nucleosome. Biochemistry [q-bio.BM]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00441373 HAL Id: tel-00441373 https://tel.archives-ouvertes.fr/tel-00441373 Submitted on 15 Dec 2009 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Joseph Fourier-Grenoble 1 Chimie et Science du Vivant (Arrêtés ministériels du 5 juillet 1984 et du 30 mars 1992) THÈSE Pour obtenir le titre de Docteur de l’Université Joseph Fourier Discipline Biologie Présentée et soutenue publiquement par SYED Sajad Hussain Le 03 Decembre 2009 One base pair resolution histone H1- nucleosomal DNA interaction mapping and 3D organization of H1 containing nucleosome Jury Dr. Didier TROUCHE Rapporteur Dr. Francesca PALLADINO Rapporteur Pr. Hans GEISELMANN Examinateur Dr. Dimitar ANGELOV Co Directeur de thèse Dr. Stefan DIMITROV Directeur de thèse Thèse préparée au sein du laboratoire Biologie Molécularie et Cellulaire de la Differenciation Unite INSERM U823 Institut Albert Bonniot Universite Joseph Fourier-Grenoble 1 France A mountain is composed of tiny grains of earth. The ocean is made up of tiny drops of water. Even so, life is but an endless series of little details, actions, speeches, and thoughts. And the consequences whether good or bad of even the least of them are far-reaching. Swami Sivananda Saraswati Dedicated to “Abba and Khala” who made the difference!!! ACKNOWLEDGEMENTS The journey of my doctoral studies may not have been so pleasant and full of joy without the help of colleagues and collaborators, both at the Ecole Normale Supérieure de Lyon and Université Joseph Fourier - Grenoble I, coordinated admirably by my mentor Dr. Stefan Dimitrov. I am highly thankful to him for his kind support and involving me in fruitful collaborative works with people from different fields which will have an everlasting influence on my scientific temperament. His enthusiastic, knowledgeable and friendly scientific discussions are the keys to the success of my thesis research, and are deeply appreciated. I am indebted for the personal care he took all along the way. I’m also very grateful to my thesis co-supervisor, Dr. Dimitar Angelov for providing a congenial lab atmosphere and teaching me the chromatin biochemistry. His tireless scientific discussions, tit bits for experimental optimization and thorough result interpretations were essentials for the timely completion of the work. A specials thanks for all his efforts and support, and has been a pleasure to work with him personally as well as scientifically. I would like to thank Prof. Hans Geiselmann, Dr. Didier Trouche and Dr. Francessca Palladino for their time and efforts to evaluate the thesis. I take this opportunity to express my debt of gratitude to Dr. Namita Surolia for her contribution in teaching me the protein biochemistry in the beginning of my research life. I was very lucky to meet Prof. Philippe Bouvet, who actually introduced me to the team of Dr. Stefan Dimitrov and supported me all the way. Thank you very much. Special thanks to the patience and expertise of Dr. Jan Bednar for the long dark room experimental sessions for the Cryo-electron microscopy and the beautiful image galleries. I would also like to thank Dr. Nils Becker, Dr. Ralf Everaers and Sam Meyer for their help in mathematical modeling experiments. I also wish to thank Dr. Cendrine Moskalenko for the Atomic Force Microscopy experiments, Dr. Andrew Travers, Dr. Mathieu Boulard, Dr. Thierry Gautier, Dr. Manu Shukla and Damien Goutte-Gatat for their help in some of my experiments. Manu, Imtiaz and Richi are “not to forget” persons for the wonderful times spent in the lab especially while writing this manuscript. Hats off to all the people of Joliot Curie Laboratory especially Marie-Jo, Fabien Mongelard, Hervé, Fabien Montel, Elsa and Zofia for providing the scientifically vibrant and homely environment. I will miss those afternoon cake parties. My fellow students have helped me in many different ways. I would like to thank Anu, Farhan, Dinil, Aijaz, Mubarak and Sadaf for their interest, their support and their encouragement. My deepest gratitude belongs to my family members and relatives for their love and moral support throughout my life. Finally, I would like to thank the people who actually made the difference. Thanks to Abba (Peer Ghulam Nabi Shah) and Khala (Syeda Hanefa Akhter) for everything. INDEX THÈSE ................................................................................................................................. 1 Acknowledgements ............................................................................................................. 7 INDEX ................................................................................................................................. 9 List of tables and figures ................................................................................................... 14 RESUME DE LA THESE ................................................................................................. 18 Summary of the thesis ....................................................................................................... 20 Information of the laboratories in which the thesis was prepared .................................... 22 list of abbreviations ........................................................................................................... 23 Chapitre I: Chapitre d’Introduction ................................................................................... 24 Chapter I: Introduction ...................................................................................................... 25 I .1 Chromatin introduction ................................................................................... 25 I .2 Chromatin history ........................................................................................... 25 I .2.1 Nobel Prize related to chromatin ..................................................... 27 I .3 Chromatin structure ......................................................................................... 28 I .3.1 DNA ................................................................................................. 29 I .3.2 Nucleosome ...................................................................................... 30 I .3.2.1 Nucleosome core particle .................................................. 31 I .4 Linker histone ................................................................................................. 34 I .4.1 Location of Globular domain on nucleosome .................................. 35 I .4.2 Role of the Carboxy terminus of Histone H1 .................................. 37 I .4.3 Molecular dynamics of Histone H1 ................................................. 39 I .4.4 Linker histone isoforms ................................................................... 41 I .4.4.1 H1.1 – H1.5 ....................................................................... 42 I .4.4.2 H1º/H5 ............................................................................... 43 I .4.4.3 H1x .................................................................................... 43 I .4.4.4 Germ line specific linker histone variants ......................... 43 I .4.5 Linker Histone post translational modifications .............................. 44 I .5 Structure of the 30-nm chromatin fiber ........................................................... 46 I .6 Higher order structures of Chromatin beyond the 30 nm fiber ....................... 49 I .7 Chromatin territories ....................................................................................... 51 I .7.1 Euchromatin ..................................................................................... 51 I .7.2 Heterochromatin ............................................................................... 51 I .8 Chromatin Modifications and Their Function ................................................ 53 I .8.1 Histone post translational modifications .......................................... 53 I .8.1.1 Histone Acetylation ........................................................... 54 I .8.1.2 Histone methylation .......................................................... 54 I .8.1.3 Other covalent histone modifications ............................... 56 I .8.2 Chromatin remodeling ..................................................................... 57 9 I .8.2.1 Different Chromatin remodeling Families ........................ 57 I .8.2.1.1 SWI/SNF family remodelers .............................. 57 I .8.2.1.2 ISWI family remodelers ..................................... 58 I .8.2.1.3 CHD family remodelers ..................................... 59 I .8.2.1.4 INO80 family remodelers .................................
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