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Linking the dynamics of chromatin occupancy and transcription with predictive models.

Publication ,  Journal Article
Tran, TQ; MacAlpine, HK; Tripuraneni, V; Mitra, S; MacAlpine, DM; Hartemink, AJ
Published in: Genome Res
June 2021

Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within 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. Whereas gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state changes and how those changes 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 predict dynamic transcriptional responses on the basis of dynamic chromatin signatures.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

June 2021

Volume

31

Issue

6

Start / End Page

1035 / 1046

Location

United States

Related Subject Headings

  • Transcription Factors
  • Nucleosomes
  • Histones
  • DNA
  • Chromatin
  • Bioinformatics
  • 3105 Genetics
  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

Citation

APA
Chicago
ICMJE
MLA
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Tran, T. Q., MacAlpine, H. K., Tripuraneni, V., Mitra, S., MacAlpine, D. M., & Hartemink, A. J. (2021). Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Res, 31(6), 1035–1046. https://doi.org/10.1101/gr.267237.120
Tran, Trung Q., Heather K. MacAlpine, Vinay Tripuraneni, Sneha Mitra, David M. MacAlpine, and Alexander J. Hartemink. “Linking the dynamics of chromatin occupancy and transcription with predictive models.Genome Res 31, no. 6 (June 2021): 1035–46. https://doi.org/10.1101/gr.267237.120.
Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Res. 2021 Jun;31(6):1035–46.
Tran, Trung Q., et al. “Linking the dynamics of chromatin occupancy and transcription with predictive models.Genome Res, vol. 31, no. 6, June 2021, pp. 1035–46. Pubmed, doi:10.1101/gr.267237.120.
Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Res. 2021 Jun;31(6):1035–1046.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

June 2021

Volume

31

Issue

6

Start / End Page

1035 / 1046

Location

United States

Related Subject Headings

  • Transcription Factors
  • Nucleosomes
  • Histones
  • DNA
  • Chromatin
  • Bioinformatics
  • 3105 Genetics
  • 11 Medical and Health Sciences
  • 06 Biological Sciences