Shear, Robert D.2020-09-142020-052020-01-232020Shear, Robert D. 2020. Inferring High Resolution Transcription Elongation Dynamics from Native Elongating Transcript Sequencing (NET-seq). Master's thesis, Harvard Extension School.https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37365034Regulatory phenomena occur in every phase of eukaryotic transcription. Recent improvements in the measurement of nascent RNA measurements have led to insights in elongation dynamics. Native elongating transcript sequencing (NET-seq) reports genome-wide RNA polymerase (RNAP) occupancy at nucleotide level resolution revealing phenomena associated with pausing, the control of anti-sense transcription elongation and others. Here we report that in S. cerevisiae elongation is characterized by regions of constant RNAP occupancy punctuated by abrupt reductions in occupancy. Furthermore, many of these locations are in the vicinity of covalent histone modifications, particularly H3K4 di- and tri-methylation. Additionally, these locations have a characteristic nucleotide type signature.application/pdfchangepoint detectionmathematical modelsNET-seqrna polymearase iisaccharomycestranscription elongationtranscription regulationtranscriptional dynamicsThesis or Dissertation2020-09-140000-0003-2680-267X