Genomic Elements in Health, Disease and Evolution: Junk DNA

319 Pages·2015·6.441 MB·English

by  Kyriacos Felekkis, Konstantinos Voskarides (eds.)

Kyriacos Felekkis
Konstantinos Voskarides E ditors
Genomic
Elements in
Health, Disease
and Evolution
Junk DNA
Genomic Elements in Health, Disease
and Evolution

Kyriacos Felekkis
Konstantinos Voskarides
Editors
Genomic Elements in Health,
Disease and Evolution
Junk DNA
Editors
Kyriacos Felekkis Konstantinos Voskarides
Department of Life and Health Sciences and Department of Biological Sciences
University of Nicosia Medical School Molecular Medicine Research Center
University of Nicosia University of Cyprus
Nicosia , Cyprus Nicosia , Cyprus
ISBN 978-1-4939-3069-2 ISBN 978-1-4939-3070-8 (eBook)
DOI 10.1007/978-1-4939-3070-8
Library of Congress Control Number: 2015950479
Springer New York Heidelberg Dordrecht London
© Springer Science+Business Media New York 2015
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Pref ace
A lthough the term “junk” DNA was used since the early 1960s, the term’s origin
was attributed to Susumo Ohno who offi cially used the term to describe pseudo-
genes’ sequences resulted from gene duplication and subsequent mutagenesis
events. Since then, the term was widely used to describe any non-coding sequence
of the genome. Today, “junk” DNA refers to any genomic sequence that does not
play a functional role in the organism. The use of the term was accompanied by
various unanswered questions: Why do we have so much “junk” DNA in our
genome? Do these non-coding sequences have functional signifi cance? The discov-
ery of novel genomic elements in the recent years was a step forward in an attempt
to address these issues. It appears that the percentage of the non-functional DNA is
being signifi cantly reduced as more and more functions are attributed to those non-
coding regions of the genome. Despite the continuous shrinkage of the non-
functional portion of the genome, it is believed that a signifi cant part of the genome
is indeed non-functional.
In this book, we attempt to provide a thorough review of various non-coding
genomic elements and discuss in depth their role in health, disease and evolution.
We begin our exploration with non-coding RNA molecules, miRNAs, piRNAs,
LncRNAs and transposable elements as these moieties dominate the scientifi c lit-
erature in the last 10 years. We proceed with the discussion of copy number varia-
tion regions, mini- and micro-satellites, and proximal and distal elements of the
genome. The last section of this book focuses on the review of well-known non-
coding regions of the genome, introns, centromeres and telomeres, but enriched
with newly discovered functions. As the vast amount of data in regard to these ele-
ments is attributed to a great degree to the growing technology in the fi eld of bio-
medicine, the last chapter of this book discusses the latest development in the fi eld
of Next Generation Sequence and the potential applications of this technology in the
study of non-coding regions of the genome.
T he original structure of this book was greatly shaped by many conversations
with colleagues in Cyprus and abroad. We are indebted to all the authors contribut-
ing to this publication for their in-depth review of the subject and their excellent
writing. We must also thank all the scientists whose work is included in this book.
v
vi Preface
Special thanks to our respective institutions and colleagues for their support and
critical interventions. The driving force of our inspiration is equivocally our stu-
dents who provide us with the strength and willingness to sit down and write. Last
but not least, we are indebted to our families and friends for their continuous
support and encouragement.
Nicosia, Cyprus Kyriacos Felekkis
Konstantinos Voskarides
Contents
1 MiRNAs’ Function and Role in Evolution:
Under the View of Genomic Enhancement Phenomena ...................... 1
Konstantinos Voskarides and Kyriacos Felekkis
2 MicroRNAs in Disease ............................................................................ 17
Gregory Papagregoriou
3 piRNAs-Transposon Silencing and Germ Line Development ............. 47
Catherine Demoliou
4 Long Non-coding RNA ........................................................................... 83
Monika Gullerova
5 Unveiling Transposable Elements Function to Enrich
Knowledge for Human Physiology and Disease Pathogenesis ............ 109
Ioannis S. Vizirianakis , Elsa P. Amanatiadou , and Sotirios S. Tezias
6 Copy Number Variation in Human Health,
Disease and Evolution ............................................................................. 129
Carolina Sismani , Costas Koufaris , and Konstantinos Voskarides
7 Mini- and Micro-Satellite Markers in Health,
Disease and Evolution ............................................................................. 155
Vasiliki A. Galani , Sofi a Markoula , Leandros Lazaros ,
Paris Ladias , and Ioannis Georgiou
8 Intron Biology, Focusing on Group II Introns,
the Ancestors of Spliceosomal Introns .................................................. 195
María Dolores Molina-Sánchez , Rafael Nisa-Martínez ,
Fernando M. García- Rodriguez , Francisco Martínez-Abarca ,
and Nicolás Toro
9 Centromeres in Health, Disease and Evolution .................................... 221
Thian Thian Beh and Paul Kalitsis
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viii Contents
10 Structure and Functions of Telomeres in Organismal
Homeostasis and Disease ........................................................................ 247
Penelope Kroustallaki and Sarantis Gagos
11 Proximal Regulatory Elements with Emphasis
on CpG Rich Regions.............................................................................. 285
Pavlos Fanis
12 Genomic Analysis Through High-Throughput Sequencing ................ 297
Michalis Hadjithomas
Index ................................................................................................................. 313
Contributors
Elsa P. Amanatiadou , M.Sc. L aboratory of Pharmacology, Department of
Pharmaceutical Sciences , Aristotle University of Thessaloniki , Thessaloniki , Greece
Thian Thian Beh , B.Sc. (Hons.) M urdoch Childrens Research Institute, Royal
Children’s Hospital , Parkville , VIC , Australia
Department of Paediatrics , University of Melbourne , Melbourne , VIC , Australia
Catherine Demoliou , Ph.D. Life and Health Sciences Department, School of
Sciences and Engineering , University of Nicosia , Nicosia , Cyprus
Pavlos Fanis , B.Sc., Ph.D. Molecular Genetics Thalassaemia Department , The
Cyprus Institute of Neurology and Genetics , Nicosia , Cyprus
Kyriacos Felekkis , B.Sc., Ph.D. Department of Life and Health Sciences ,
University of Nicosia Medical School , University of Nicosia, Nicosia , Cyprus
Sarantis Gagos , Ph.D. D epartment of Experimental Medicine and Translational
Research, B iomedical Research Foundation of the Academy of Athens (BRFAA),
Athens , Greece
Vasiliki A. Galani, Ph.D. D epartment of Anatomy – Histology – Embryology,
University of Ioannina , Ioannina , Epirus , Greece
Fernando M. García-Rodriguez , Ph.D. Grupo de Ecología Genética,
Microbiología del Suelo y Sistemas Simbióticos , Estación Experimental del Zaidín/
Consejo Superior de Investigaciones Científi cas , Granada , Spain
Ioannis Georgiou, Ph.D. Division of Reproductive Genetics, Department of
Obstetrics & Gynecology , University of Ioannina , Ioannina , Epirus , Greece
D ivision of Medical Genetics and Clinical Embryology, Department of Obstetrics
& Gynecology , University Hospital of Ioannina , Ioannina , Epirus , Greece
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