Nucleosomes are ~147bp DNA wrapped around the histone octamer which are involved in regulating gene transcription. They have the ability to disassemble depending on the process they are involved in and the nucleosome positioning controls the output of the genome. Therefore, it is important to understand the nucleosome positioning and how its positioning affects the binding of transcription factors (TFs) and gene expression thereby regulating the transcription outcome of the genome. Many studies suggest that TFs and nucleosomes compete with each other for genome accessibility. However, the majority of the studies focus on the nucleosome organization rather than underlying DNA sequences and its patterns which might actually be playing an important role in understanding the regulatory role of nucleosomes in gene transcription. This research study focuses on identifying the specific sequence patterns at or around TF binding sites. The study specifically focuses on identifying the fraction of nucleosomes with WW/SS and anti - WW/SS sequence patterns as they might be responsible for maintaining the stability of the nucleosomes. This will provide a new molecular mechanism underlying NDR formation around TF binding sites and pioneer TF-induced chromatin opening.

Library of Congress Subject Headings

Transcription factors; Nucleosomes

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Gregory Babbitt

Advisor/Committee Member

Gary Skuse

Advisor/Committee Member

Feng Cui


RIT – Main Campus

Plan Codes