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From: Gabriela Novak <>
Subject: Re: [DNA] Epigenetics in latest issue of Nature
Date: Wed, 1 Aug 2007 17:56:47 -0400
References: <46B0FC4A.9030105@comcast.net>
In-Reply-To: <46B0FC4A.9030105@comcast.net>


Thanks, those are nice articles. I like the "The epigenomic era
opens" summary, it is very readable. I just downloaded my copy.
G.

On 1-Aug-07, at 5:34 PM, Bonnie Schrack wrote:

> Curiosity has been expressed on the list about epigenetics. Here is an
> excerpt from an overview that appears in the latest Nature:
>
> *The epigenomic era opens*
>
> Stephen B. Baylin and Kornel E. Schuebel
>
> Readout of information from the genome depends on intricate regulation
> of how DNA is packaged by proteins. The great endeavour to reveal how
> this packaging operates pan-genomically is now under way. A new era is
> opening for biologists involved in understanding cellular systems.
> It is
> exemplified by papers by Mikkelsen et al. (page 553 of this issue) and
> Barski et al. (published in Cell)— they describe the kind of
> unprecedented insights that are emerging from investigations of how a
> single mammalian genome can be regulated to produce different cell
> types.
>
> The technical and biological advances described in these studies
> extend
> the remarkable accomplishments of elucidating the structure, then the
> sequence of the human genome; and they reflect a growing,
> ‘post-genomic’, appreciation of the complexities of genome
> structure and
> function (Fig. 1). The intriguing — and daunting — challenge now is to
> understand the process of how and when specific DNA regions are
> controlled to produce the cellular diversity that underpins the
> development and maintenance of a single organism.
>
> Central to this challenge is the task of enumerating the dizzying
> number
> of proteins interacting with the genome, and the functions they
> subserve. These proteins, called histones, form a combination with DNA
> that is termed chromatin. It is chromatin that provides the software
> packaging for the readout of the DNA hard drive. If alterations in
> genome heritable states occur through a change in the hard drive (that
> is, through a change in the primary sequence of DNA), a genetic
> alteration or mutation has occurred. This contrasts with an epigenetic
> change, which is an alteration in the heritable states of DNA function
> produced by altering the chromatin software. Epigenetic changes lie at
> the heart of how organisms generate different types of tissue under
> different circumstances — in embryonic development, in regulating cell
> renewal in adults, and in the cellular responses of the organism to
> environmental factors and stress. Moreover, disease states such as
> cancer are associated with a combination of both genetic and
> epigenetic
> abnormalities.
>
> . . . .
>
> The papers also provide insights about genomic regions — within genes,
> or between genes — that are unexpectedly marked for expression
> activity.
> These data relate to the
> recent revelations that much more of our genome than previously
> thought
> is engaged in expressing RNA from DNA. The result is production not
> only
> of ‘classical’ messenger RNAs (which produce the proteins defined
> by the
> initial analyses of the genome sequence), but also of a huge number of
> regulatory RNAs (which modulate genome readout by producing multiple
> forms of the same protein or without producing proteins at all).
>
> . . . .
>
> References
> 1. Mikkelsen, T. S. et al. Nature 448, 553–560 (2007).
> 2. Barski, A. et al. Cell 129, 823–837 (2007).
> 3. Watson, J. D. & Crick, F. H. C. Nature 171, 737–738 (1953).
> 4. Lander, E. S. et al. Nature 409, 860–921 (2001).
> 5. Venter, J. C. et al. Science 291, 1304–1351 (2001).
> 6. Li, B., Carey, M. & Workman, J. L. Cell 128, 707–719 (2007).
> 7. Jenuwein, T. & Allis, C. D. Science 293, 1074–1080 (2001).
> 8. Bernstein, B. E., Meissner, A. & Lander, E. S. Cell 128, 669–681
> (2007).
> 9. Kapranov, P. et al. Science 316, 1484–1488 (2007).
> 10. Albiez, H. et al. Chromosome Res. 14, 707–733 (2006).
>
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