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How does an organism extract relevant information from transcription factor concentrations?

How does an organism regulate its genes? The involved regulation typically occurs in terms of a signal processing chain: an externally applied stimulus or a maternally supplied transcription factor leads to the expression of some downstream genes, which, in turn, are transcription factors for furthe...

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Autor principal: Bauer, Marianne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Portland Press Ltd. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704516/
https://www.ncbi.nlm.nih.gov/pubmed/36111776
http://dx.doi.org/10.1042/BST20220333
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author Bauer, Marianne
author_facet Bauer, Marianne
author_sort Bauer, Marianne
collection PubMed
description How does an organism regulate its genes? The involved regulation typically occurs in terms of a signal processing chain: an externally applied stimulus or a maternally supplied transcription factor leads to the expression of some downstream genes, which, in turn, are transcription factors for further genes. Especially during development, these transcription factors are frequently expressed in amounts where noise is still important; yet, the signals that they provide must not be lost in the noise. Thus, the organism needs to extract exactly relevant information in the signal. New experimental approaches involving single-molecule measurements at high temporal precision as well as increased precision in manipulations directly on the genome are allowing us to tackle this question anew. These new experimental advances mean that also from the theoretical side, theoretical advances should be possible. In this review, I will describe, specifically on the example of fly embryo gene regulation, how theoretical approaches, especially from inference and information theory, can help in understanding gene regulation. To do so, I will first review some more traditional theoretical models for gene regulation, followed by a brief discussion of information-theoretical approaches and when they can be applied. I will then introduce early fly development as an exemplary system where such information-theoretical approaches have traditionally been applied and can be applied; I will specifically focus on how one such method, namely the information bottleneck approach, has recently been used to infer structural features of enhancer architecture.
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spelling pubmed-97045162022-12-06 How does an organism extract relevant information from transcription factor concentrations? Bauer, Marianne Biochem Soc Trans Review Articles How does an organism regulate its genes? The involved regulation typically occurs in terms of a signal processing chain: an externally applied stimulus or a maternally supplied transcription factor leads to the expression of some downstream genes, which, in turn, are transcription factors for further genes. Especially during development, these transcription factors are frequently expressed in amounts where noise is still important; yet, the signals that they provide must not be lost in the noise. Thus, the organism needs to extract exactly relevant information in the signal. New experimental approaches involving single-molecule measurements at high temporal precision as well as increased precision in manipulations directly on the genome are allowing us to tackle this question anew. These new experimental advances mean that also from the theoretical side, theoretical advances should be possible. In this review, I will describe, specifically on the example of fly embryo gene regulation, how theoretical approaches, especially from inference and information theory, can help in understanding gene regulation. To do so, I will first review some more traditional theoretical models for gene regulation, followed by a brief discussion of information-theoretical approaches and when they can be applied. I will then introduce early fly development as an exemplary system where such information-theoretical approaches have traditionally been applied and can be applied; I will specifically focus on how one such method, namely the information bottleneck approach, has recently been used to infer structural features of enhancer architecture. Portland Press Ltd. 2022-10-31 2022-09-16 /pmc/articles/PMC9704516/ /pubmed/36111776 http://dx.doi.org/10.1042/BST20220333 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) . Open access for this article was enabled by the participation of Delft University of Technology in an all-inclusive Read & Publish agreement with Portland Press and the Biochemical Society.
spellingShingle Review Articles
Bauer, Marianne
How does an organism extract relevant information from transcription factor concentrations?
title How does an organism extract relevant information from transcription factor concentrations?
title_full How does an organism extract relevant information from transcription factor concentrations?
title_fullStr How does an organism extract relevant information from transcription factor concentrations?
title_full_unstemmed How does an organism extract relevant information from transcription factor concentrations?
title_short How does an organism extract relevant information from transcription factor concentrations?
title_sort how does an organism extract relevant information from transcription factor concentrations?
topic Review Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704516/
https://www.ncbi.nlm.nih.gov/pubmed/36111776
http://dx.doi.org/10.1042/BST20220333
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