Team:UCSF/Project

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Project Summary

The goals of synthetic biology are 1) to gain a deeper understanding of native biological systems, and 2) to develop new ones. In doing so, most devices and systems have been constructed by co-opting traditional genetic elements, where transcriptional activators and/or repressors modulate the expression of genes. While this has proved useful and reliable for many synthetic systems, there are additional mechanisms for transcriptional regulation that synthetic biologists have yet to harness.

This year, our team is attempting to engineer epigenetic control of gene expression. In eukaryotic cells, DNA is wound around nucleosomes, protein "spools" that consist of an octamer of histones. The DNA and protein together, termed chromatin, can be tightly packgaged (heterochromatin) or more loosely arranged (eucharomatin). The density of nucleosomal packaging is signaled by a host of histone modifying enzymes, and enforced by chromatin remodeling complexes. Euchromatin is accessible to the transcriptional machinery (active) while heterochromatin is inaccessible, and refractory to transcription (silenced).

In nature, the modulation of gene expression via the alteration of DNA structure is an incredibly powerful form of cellular memory. Indeed, epigenetic changes regulating genome-wide expression patterns can persist through multiple rounds of cell division and remain for the lifetime of the cell. This mechanism allows embryonic stem cells to differentiate into myriad cell types in higher eukaryotes.

For our project, we are establishing, characterizing and standardizing methods to engineer epigenetic control in the eukaryotic yeast Saccharomyces cerevisiae. To do so, we are taking endogenous proteins known to modify chromatin structure, such as Sir2, an NAD+ dependent histone deacetylase, and devising methods to control and direct their activity. We are concentrating on generating a chromatin toolkit that can:

silence (or “close”) euchromatin
operate in a promoter/orientation-independent manner
operate regionally (spread to silence one or more genes)
retain memory (i.e. persistence past a transient stimulus)
initiate silencing or activation through various extracellular cues
link changes in heterochromatin to distinct biological outputs

We believe that the ability to control the structure of chromatin will allow synthetic biologists to engineer robust systems with novel and predictable behaviors. We look forward to introducing and discussing these ideas in November!

(Very) Selected Heterochromatin References:

Hecht, A., Strahl-Bolsinger, S., and M. Grunstein, Spreading of transcriptional repressor Sir3 from telomoeric heterochromatin. Nature, 1996. 383: p. 92-96.

Howitz, KT., Bitterman, KJ., Cohen, HY., Lamming, DW., Lavu, S., Wood, JG., Zipkin, R.E., Chung, P., Kisielewski, A., Zhang, LL., Scherer, B., and DA. Sinclair, Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature, 2003. 425(6954): p.191-6.

Kornberg, R.D. and Y. Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell, 1999. 98(3): p. 285-94.

Jenuwein, T. and C.D. Allis, Translating the histone code. Science, 2001. 293(5532): p. 1074-80.

Rusche, L.N., A.L. Kirchmaier, and J. Rine, The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem, 2003. 72: p. 481-516.

Moazed, D., Common themes in mechanisms of gene silencing. Mol Cell, 2001. 8(3): p. 489-98.

Pirrotta, V. and D.S. Gross, Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol Cell, 2005. 18(4): p. 395-8.

Home	The Team	The Project	Parts Submitted to the Registry	Modeling	Human Practices	Notebooks

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+== '''Project Summary''' ==
+The goals of synthetic biology are 1) to gain a deeper understanding of native biological systems, and 2) to develop new ones.  In doing so, most devices and systems have been constructed by co-opting traditional genetic elements, where transcriptional activators and/or repressors modulate the expression of genes.  While this has proved useful and reliable for many synthetic systems, there are additional mechanisms for transcriptional regulation that synthetic biologists have yet to harness.
+'''This year, our team is attempting to engineer epigenetic control of gene expression.'''  In eukaryotic cells, DNA is wound around nucleosomes, protein "spools" that consist of an octamer of histones. The DNA and protein together, termed chromatin, can be tightly packgaged (heterochromatin) or more loosely arranged (eucharomatin). The density of nucleosomal packaging is signaled by a host of histone modifying enzymes, and enforced by chromatin remodeling complexes.  Euchromatin is accessible to the transcriptional machinery (active) while heterochromatin is inaccessible, and refractory to transcription (silenced).
-== '''Overall project''' ==
+In nature, the modulation of gene expression via the alteration of DNA structure is an incredibly powerful form of cellular memory. Indeed, epigenetic changes regulating genome-wide expression patterns can persist through multiple rounds of cell division and remain for the lifetime of the cell.  This mechanism allows embryonic stem cells to differentiate into myriad cell types in higher eukaryotes.
-The goals of synthetic biology have been framed to both gain a deeper understanding of the endogenous biological systems, as well as to develop new ones.  In doing so, most exogenous devices and systems have been constructed using traditional genetic elements, where transcriptional activators and/or repressors modulate the transcription of protein encoding regions.  While this has proved useful and reliable for synthetic systems, other biological mechanisms provide additionally robust behaviors that synthetic biologists have yet to explore and take advantage of.
+For our project, we are establishing, characterizing and standardizing methods to engineer epigenetic control in the eukaryotic yeast ''Saccharomyces cerevisiae''.  To do so, we are taking endogenous proteins known to modify chromatin structure, such as Sir2, an NAD+ dependent histone deacetylase, and devising methods to control and direct their activity.  We are concentrating on generating a chromatin toolkit that can:
-'''This year, our team is attempting to engineer the epigenetic control of gene expression.'''  In eukaryotic cells, DNA is wound and organized with histone proteins into chromatin units called nucleosomes.  The density of nucleosomal packaging is regulated by a host of histone modifying enzymes, chromatin remodeling complexes, and, frequently, DNA methylation.  DNA located in loosely packed chromatin, or euchromatin, is generally more easily accessed by transcriptional machinery and thus more easily transcribed (active), while in tightly packed and highly ordered heterochromatin, it is inaccessible for transcription (silenced).
-Endogenously, the modulation of gene expression via the alteration of the physical structure of DNA creates an incredibly powerful form of cellular memory—these changes may last through multiple rounds of cell division and remain for the lifetime of the cell.  This mechanism is what allows a single totipotent zygote to differentiate into myriad cell types in higher eukaryotes.
-For our project, we are establishing, characterizing and standardizing methods to engineer cellular memory in the eukaryotic yeast ''Saccharomyces cerevisiae''.  To do so, we are taking endogenous proteins known to modify chromatin structure, such as Sir2, an NAD+ dependent histone deacetylase, and engineering methods to control and direct their activity.  We are concentrating on generating a chromatin toolkit that can:
 *silence (or “close”) euchromatin
-*activate (or “open”) heterochromatin
+*operate in a promoter/orientation-independent manner
-*create silencing/activation with complete permanence
+*operate regionally (spread to silence one or more genes)
-*control and measure the regional space of synthetic remodeling
+*retain memory (i.e. persistence past a transient stimulus)
 *initiate silencing or activation through various extracellular cues
-*link this to distinct biological outputs
+*link changes in heterochromatin to distinct biological outputs
 '''We believe that the ability to control the structure of chromatin will allow synthetic biologists to engineer robust systems with novel and predictable behaviors.  We look forward to introducing and discussing these ideas in November!'''
-== Project Details==
+[[Team:UCSF/Synthetic_Chromatin_Design|More on Synthetic Chromatin]]
+== '''(Very) Selected Heterochromatin References:''' ==
+Hecht, A., Strahl-Bolsinger, S., and M. Grunstein, Spreading of transcriptional repressor Sir3 from telomoeric heterochromatin. Nature, 1996. 383: p. 92-96.
+Howitz, KT., Bitterman, KJ., Cohen, HY., Lamming, DW., Lavu, S., Wood, JG., Zipkin, R.E., Chung, P., Kisielewski, A., Zhang, LL., Scherer, B., and DA. Sinclair, Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature, 2003. 425(6954): p.191-6.
+Kornberg, R.D. and Y. Lorch, Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell, 1999. 98(3): p. 285-94.
+Jenuwein, T. and C.D. Allis, Translating the histone code. Science, 2001. 293(5532): p. 1074-80.
+Rusche, L.N., A.L. Kirchmaier, and J. Rine, The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem, 2003. 72: p. 481-516.
+Moazed, D., Common themes in mechanisms of gene silencing. Mol Cell, 2001. 8(3): p. 489-98.
+Pirrotta, V. and D.S. Gross, Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol Cell, 2005. 18(4): p. 395-8.
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 !align="center"|[[Team:UCSF|Home]]
 !align="center"|[[Team:UCSF/Team|The Team]]
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 !align="center"|[[Team:UCSF/Parts|Parts Submitted to the Registry]]
 !align="center"|[[Team:UCSF/Modeling|Modeling]]
-!align="center"|[[Team:UCSF/Notebook|Notebook]]
+!align="center"|[[Team:UCSF/Human Practices|Human Practices]]
+!align="center"|[[Team:UCSF/Notebook|Notebooks]]
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-(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')