Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks

Jennifer S. Hallinan; Daniel R. Bradley; John S. Mattick; Janet Wiles

doi:10.1109/CEC.2006.1688626

Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks

Jennifer S. Hallinan, Daniel R. Bradley, John S. Mattick, Janet Wiles^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding contribution › peer-review

1 Citation (Scopus)

Abstract

The general assumption in biology is that most genes encode proteins. However, it is now evident that much of the genome of humans and other complex organisms is transcribed into non-protein-coding RNAs. Some of these RNAs are processed into small regulatory RNAs, such as microRNAs, that control many aspects of animal and plant development. It has been suggested that regulatory RNAs represent an additional control layer that was critical to the emergence of complex organisms. We examine this possibility using a model of cell differentiation based on attractors in boolean networks. Our simulation studies show that an additional layer of RNA control modeled as fast temporal links can significantly increase the number of attractors in boolean models of genetic regulatory networks (analogous to the number of cell types in a complex organism). However, it also has the power to simplify the state space structure. We explore the conditions under which these different outcomes occur.

Original language	English
Title of host publication	2006 IEEE Congress on Evolutionary Computation
Place of Publication	Piscataway, N.J.
Publisher	Institute of Electrical and Electronics Engineers (IEEE)
Pages	2551-2555
Number of pages	5
ISBN (Print)	0780394879, 9780780394872
DOIs	https://doi.org/10.1109/CEC.2006.1688626
Publication status	Published - Jul 2006
Externally published	Yes
Event	2006 IEEE Congress on Evolutionary Computation, CEC - 2006 - Vancouver, Canada Duration: 16 Jul 2006 → 21 Jul 2006

Other

Other	2006 IEEE Congress on Evolutionary Computation, CEC - 2006
Country/Territory	Canada
City	Vancouver
Period	16/07/06 → 21/07/06

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10.1109/CEC.2006.1688626

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title = "Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks",

abstract = "The general assumption in biology is that most genes encode proteins. However, it is now evident that much of the genome of humans and other complex organisms is transcribed into non-protein-coding RNAs. Some of these RNAs are processed into small regulatory RNAs, such as microRNAs, that control many aspects of animal and plant development. It has been suggested that regulatory RNAs represent an additional control layer that was critical to the emergence of complex organisms. We examine this possibility using a model of cell differentiation based on attractors in boolean networks. Our simulation studies show that an additional layer of RNA control modeled as fast temporal links can significantly increase the number of attractors in boolean models of genetic regulatory networks (analogous to the number of cell types in a complex organism). However, it also has the power to simplify the state space structure. We explore the conditions under which these different outcomes occur.",

author = "Hallinan, {Jennifer S.} and Bradley, {Daniel R.} and Mattick, {John S.} and Janet Wiles",

year = "2006",

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booktitle = "2006 IEEE Congress on Evolutionary Computation",

publisher = "Institute of Electrical and Electronics Engineers (IEEE)",

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note = "2006 IEEE Congress on Evolutionary Computation, CEC - 2006 ; Conference date: 16-07-2006 Through 21-07-2006",

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Hallinan, JS, Bradley, DR, Mattick, JS & Wiles, J 2006, Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks. in 2006 IEEE Congress on Evolutionary Computation., 1688626, Institute of Electrical and Electronics Engineers (IEEE), Piscataway, N.J., pp. 2551-2555, 2006 IEEE Congress on Evolutionary Computation, CEC - 2006, Vancouver, Canada, 16/07/06. https://doi.org/10.1109/CEC.2006.1688626

Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks. / Hallinan, Jennifer S.; Bradley, Daniel R.; Mattick, John S. et al.
2006 IEEE Congress on Evolutionary Computation. Piscataway, N.J.: Institute of Electrical and Electronics Engineers (IEEE), 2006. p. 2551-2555 1688626.

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding contribution › peer-review

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AB - The general assumption in biology is that most genes encode proteins. However, it is now evident that much of the genome of humans and other complex organisms is transcribed into non-protein-coding RNAs. Some of these RNAs are processed into small regulatory RNAs, such as microRNAs, that control many aspects of animal and plant development. It has been suggested that regulatory RNAs represent an additional control layer that was critical to the emergence of complex organisms. We examine this possibility using a model of cell differentiation based on attractors in boolean networks. Our simulation studies show that an additional layer of RNA control modeled as fast temporal links can significantly increase the number of attractors in boolean models of genetic regulatory networks (analogous to the number of cell types in a complex organism). However, it also has the power to simplify the state space structure. We explore the conditions under which these different outcomes occur.

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Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks

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