RT Journal Article
SR Electronic
T1 Integrating MNase-seq and RNA-seq time series data to study chromatin and transcription dynamics under cadmium stress
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.28.176545
DO 10.1101/2020.06.28.176545
A1 Trung Q. Tran
A1 Vinay Tripuraneni
A1 Heather K. MacAlpine
A1 David M. MacAlpine
A1 Alexander J. Hartemink
YR 2020
UL http://biorxiv.org/content/early/2020/06/29/2020.06.28.176545.abstract
AB Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists in a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins—including histones, transcription factors (TFs), and polymerases—interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. While gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state is modified and how those modifications connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA binding factors. Using these signatures, we identified associations between chromatin dynamics and transcriptional regulation, not only for known cadmium response genes, but across the entire genome, including antisense transcripts. Those associations allowed us to develop generalizable models that can predict dynamic transcriptional responses on the basis of dynamic chromatin signatures.Competing Interest StatementThe authors have declared no competing interest.