Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
Innovation in Gene Regulation: The Case of Chromatin Computation
Sonja J. Prohaska, Peter F. Stadler, David C. Krakauer
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Status: Published
J.Theor.Biol. 265: 27-44 (2010)
Abstract
Chromatin regulation is understood to be one of the fundamental modes of
gene regulation in eukaryotic cells. We argue that the basic proteins
that determine the chromatin architecture constitute an evolutionary
ancient layer of transcriptional regulation common to all three domains
of life. We explore phylogenetically, sources of innovation in chromatin
regulation, focusing on protein domains related to chromatin structure
and function, demonstrating a step-wise increase of complexity in
chromatin regulation. Building upon the highly conserved use of variants
of chromosomal architectural proteins to distinguish chromosomal states,
Eukarya secondarily acquired mechanisms for ``writing'' chemical
modifications onto chromatin that constitute persistent signals. The
acquisition of reader domains enabled decoding of these
complex, signal combinations and a decoupling of the signal from
immediate biochemical effects. We show how the coupling of reading and
writing, which is most prevalent in crown-group Eukarya, could have
converted chromatin into a powerful computational device capable of
storing and processing more information than pure cis-regulatory networks.
Keywords
Chromatin, gene regulation, evolution