Open Questions: Gene Expression and Regulation

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Prerequisites: Molecular biology and genetics

See also: RNA biology -- Developmental biology -- Genetics and genomics -- Systems Biology

Introduction

Gene promoters

Transcription factors

RNA splicing

RNA interference and microRNA

Epigenetics

DNA methylation

Histone acetylation

Heterochromatin

Evolution of gene regulation


Recommended references: Web sites

Recommended references: Magazine/journal articles

Recommended references: Books

Introduction



Recommended references: Web sites

Site indexes

Science Functional Genomics Resources: Epigenetics
Very good annotated list of resources.


Sites with general resources

Human Epigenome Project
Web site of a consortium which will attempt to map how genes are switched on and off. More specifically, the project intends to catalog how methyl groups attached to DNA affect gene expression.
Histone.com
"This site is intended to keep you up to date on significant developments within the field of Chromatin research, specifically those involving histone modifications and enzymes which deposit those modifications."


Surveys, overviews, tutorials

Gene regulatory network
Article from Wikipedia. See also Gene expression, Transcription factor, Epigenetics, Imprinting, Chromatin, Histone.
Gene Regulatory Networks
Good, concise overview, from the Genomics: GTL site.
How epigenetics is changing our fight with disease
October 2009 article. "Sequencing the human genome was supposed to answer our questions about the genetic origins of disease but the burgeoning science of epigenetics is telling us it's a whole lot more complicated."
Epigenetics
A ScienceWeek "symposium" consisting of excerpts and summaries of articles from various sources.
It's not all in our genes
November 1999 news article about how individuals with identical genotypes may have differing phenotypes.


Recommended references: Magazine/journal articles

Environmental Impact
David Berreby
The Scientist, March 2011
Research in behavioral epigenetics is seeking evidence that links experience to biochemistry to gene expression and back out again.
The Mark of Faith
Robert E. Kingston
The Scientist, March 2011
Testing a central tenet of epigenetic regulation.
Epigenetic suicide note
Elie Dolgin
The Scientist, August 2009
Recently, Moshe Szyf, a McGill University epigeneticist, performed a series of experiments indicating that chemical marks on people’s brain cells can reveal suicidal tendencies long before these people consider taking their own lives.
The Shape of Heredity
Susan M. Gasser
The Scientist, July 2009, p. 34
Tracking the dance of DNA and structural proteins within the nucleus shows that placement makes the difference between gene activity and silence.
Regulating Evolution: How Gene Switches Make Life
Sean B. Carroll; Nicolas Gompel; Benjamin Prudhomme
Scientific American, May 2008
Dad's Hidden Influence
Tina Hesman Saey
Science News, March 29, 2008
A father's legacy to a child's health may start before conception and last generations.
Is It a Code: The Debate
Bryan M. Turner; Steven Henikoff
The Scientist, May 2006
Yes: An epigenetic histone code may allow for unprecedented predictive power. No: Histone modifications, although diverse, do not constitute a complex code of chromatin states.
The Nucleosome Untangled
Brendan Maher
The Scientist, May 2006
Histones serve as slates to a dizzying array of modifications, but researchers are confident they can decipher the epigenetic puzzle.
Computing Gene Regulation
David Secko
The Scientist, December 2004
Researchers take a statistical glimpse at how gene expression is controlled.
The Hidden Genetic Program of Complex Organisms
John S. Mattick
Scientific American, October 2004
Evolution Encoded
Stephen J. Freeland; Laurence D. Hurst
Scientific American, April 2004
Code Breakers
John Travis
Science News, February 14, 2004
Scientists tease out the secrets of proteins that DNA wraps around.
The Unseen Genome: Beyond DNA
W. Wayt Gibbs
Scientific American, December 2003
The Unseen Genome: Gems among the Junk
W. Wayt Gibbs
Scientific American, November 2003
Molecular Machines that Control Genes
Robert Tjian
Scientific American, February 1995, pp. 54-61
Genes provide the instructions for making proteins within cells, but most are inactive at any given time. "Transcription factors" consisting of protein complexes control when and how genes become active.


Recommended references: Books

Eric H. Davidson -- Genomic Regulatory Systems: Development and Evolution
Academic Press, 2001
Davidson's career has been focused on understanding how the development of an organism is encoded in its DNA and how, as a result, animal evolution unfolded. The book gives a thorough and rigorous account of what he has learned. It assumes some understanding of the molecular biology of gene expression without going into detail. One is stimulated to wonder about the evolutionary steps that led the process of gene expression to work the way it does.
Walter J. Gehring -- Master Control Genes in Development and Evolution: The Homeobox Story
Yale University Press, 1998
Evolutionary theory, molecular biology, and developmental biology have come together in a fascinating synthesis which exposes how the mechanisms that control gene expression have evolved, and how the traces of this evolution remain in the way that the sequence of gene expression governs the development of individual organisms. Gehring, whose laboratory discovered the "homeobox genes" which play a key role in this synthesis, provides an excellent account of his research, full of details and real meat.

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