ALTERATION OF TRANSCRIPTION BY NON-CODING ELEMENTS IN THE HUMAN GENOME A Dissertation Presented to The Academic Faculty By Andrew Conley In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in Bioinformatics in the School of Biology Georgia Institute of Technology August 2012 ALTERATION OF TRANSCRIPTION BY NON-CODING ELEMENTS IN THE HUMAN GENOME Approved by: Dr. I. King Jordan, Advisor Dr. Jung Choi School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Dr. Leonardo Mariño-Ramírez Dr. John McDonald National Center for Biotechnology Information School of Biology National Institutes of Health Georgia Institute of Technology Dr. Roger Wartell School of Biology Georgia Institute of Technology Date Approved: June 25, 2012 To my wife Kathryn and my daughter Charlotte… ACKNOWLEDGEMENTS I must first thank my advisor, Dr. Jordan. He has been an extraordinary teacher and guide throughout my time as his PhD student. I have been extremely fortunate to have his guidance over the years and I have learned most of what I know about the scientific process from him. I am also thankful to my committee members, Jung Choi, Leonardo Mariño-Ramírez, John McDonald, and Roger Wartell, for their help in my research and academic career. Apart from Dr. Jordan himself, the people in the Jordan lab, both past and present members, have been extraordinary in my time as a PhD student. Jittima Piriyapongsa and Ahsan Huda were extraordinarily helpful to me in my early years, while Jianrong Wang has been extremely helpful in the later years. Lee Katz, Eishita Tyagi and Daudi Jjingo have been wonderful friends over the past few years. I am very grateful to my family and all of the support and encouragement that I have received from them. Both of my parents, Jim and Colleen Conley, have instrumental in my education, particularly my mother for encouraging my interest in biology. My mother-in-law Jan and father-in-law David have been extraordinarily encouraging throughout my education, and I wish to thank them as well. More than anyone else, I would like to thank my wife wonderful wife Kathryn. She has been nothing but loving, supportive and understanding throughout a very long PhD process. iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................................................................................ IV LIST OF TABLES ............................................................................................................................................................................. X LIST OF FIGURES .......................................................................................................................................................................... XI LIST OF TERMS ........................................................................................................................................................................... XIV SUMMARY ...................................................................................................................................................................................... XV 1- INTRODUCTION AND LITERATURE REVIEW ............................................................................................................. 1 EUKARYOTIC GENOMES CONTAIN ABUNDANT NON -CODING DNA ........................................................................................ 1 THE HUMAN GENOME CONTAINS MANY FUNCTIONAL NON -CODING ELEMENTS ................................................................. 5 HIGH -THROUGHPUT TECHNIQUES AND MASSIVELY -PARALLEL SEQUENCING AND HAVE DRASTICALLY ALTERED THE STUDY OF GENOME FUNCTION ..................................................................................................................................................... 6 ANTISENSE TRANSCRIPTION IS PERVASIVE IN THE HUMAN GENOME .................................................................................... 8 ALTERNATIVE TRANSCRIPTION TERMINATION HAS ATTRACTED RECENTLY ATTRACTED GREAT INTEREST ................. 8 2 - HUMAN CIS-NATURAL ANTISENSE TRANSCRIPTS INITIATED BY TRANSPOSABLE ELEMENTS ... 10 ABSTRACT ..................................................................................................................................................................................... 10 INTRODUCTION ............................................................................................................................................................................ 10 METHODS ..................................................................................................................................................................................... 11 Identification of TE-TSSs from CAGE data ............................................................................................................ 11 Human genes and TSSs from CAGE data ............................................................................................................... 12 Relative ages of TE-TSSs ............................................................................................................................................... 13 Human-Mouse conservation of TSS ......................................................................................................................... 14 RESULTS AND DISCUSSION ......................................................................................................................................................... 15 Genome-scale identification of cis-NATs ............................................................................................................... 15 v TEs initiate antisense transcription ........................................................................................................................ 16 CONCLUSIONS .............................................................................................................................................................................. 21 3 - RETROVIRAL PROMOTERS IN THE HUMAN GENOME ........................................................................................ 22 ABSTRACT ..................................................................................................................................................................................... 22 INTRODUCTION ............................................................................................................................................................................ 22 METHODS ..................................................................................................................................................................................... 25 RESULTS AND DISCUSSION ......................................................................................................................................................... 26 4 - IDENTIFICATION OF TRANSCRIPTION FACTOR BINDING SITES DERIVED FROM TRANSPOSABLE ELEMENT SEQUENCES USING CHIP-SEQ ......................................................................................................................... 34 ABSTRACT ..................................................................................................................................................................................... 34 INTRODUCTION ............................................................................................................................................................................ 34 Exaptation of Transposable Elements .................................................................................................................... 35 Transposable Elements Evolve Rapidly................................................................................................................. 36 Detection of Functional TE-derived Non-coding sequences ........................................................................ 39 SOFTWARE .................................................................................................................................................................................... 42 METHODS ..................................................................................................................................................................................... 42 Mapping ............................................................................................................................................................................... 43 Read Rescue ....................................................................................................................................................................... 44 Different Methods of Rescue ....................................................................................................................................... 45 Peak Calling ........................................................................................................................................................................ 45 Finding TE-derived TFBS ............................................................................................................................................. 46 EXAMPLE ...................................................................................................................................................................................... 46 Mapping ..............................................................................................................................................................................