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Elliott & Elliott: Biochemistry and Molecular Biology 4e

Chapter 21

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A one-page guide

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Callandine, C. R. and Drew, H. R. (1992). Understanding DNA: the molecule and how it works. Academic Press.
A discussion of DNA structure, supercoiling, and DNA organization in the cell.

Rennie, J. (1993). DNAs new twists. Sci. Am., 266(3), 88-96.
An account of the ?unorthodox? genes - jumping genes, fragile chromosomes, expanded genes, edited mRNA, and nonstandard genetic code in mitochondria and chloroplasts.

Chambers, D. A., Reid, K. B. M., and Cohen, R. L. (1994). DNA: the double helix and the biomedical revolution at 40 years. FASEB J., 8, 1219-26.
Reviews a meeting to mark the 40th anniversary of the double helix. Biochemical nostalgia, but which summarizes the landmarks in the area and looks to the future.

Pennisi, E. (2000). And the gene number is . . . ? Science, 288, 1146-7.
Betting on human gene numbers in 2000. Amusing, but gives perspectives on DNA research.

Dennis, C. and Gallagher, R. (Eds.). (2001). The Human Genome. Nature Publishing Group.

Levine, M. and Tjlan, R. (2003). Transcription regulation and animal diversity. Nature, 424, 147-51 [DOI: 10.1038/nature01763].
Transcriptional complexity may be the answer to why humans have relatively few genes.

Klose, R. J. and Bird, A. P. (2006). Genomic DNA methylation: the mark and its mediators. Trends in Biochem. Sci., 31, 89-97 [DOI: 10.1016/j.tibs.2005.12.008].

Nucleosomes

Hewish, D. R. and Burgoyne, L. A. (1973). Chromatin substructure. The digestion of chromatin DNA at regularly spaced sites by an nuclear deoxyribonuclease. Biochem. Biophys. Res. Commun., 52, 504-10 [DOI: 10.1016/0006-291X(73)90740-7].
Chromatin was found to be digested in a nonrandom manner.

Kornberg, R. D. and Lorsch, Y. (1999). Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 185-94 [DOI: 10.1016/S0092-8674(00)81958-3].
Reviews the nucleosome story

Junk DNA

Riddihough, G. (2002). Three ?Viewpoint? articles, and a review on the other RNA world. Science, 296, 1259-1273 [DOI: 10.1126/science.296.5571.1259].
Papers cover noncoding RNAs and RNA silencing

Gibbs, W. W. (2003). Hidden genes. Sci. Am., 289, 28-33.
Genes that work through RNA rather than protein.

Mattick, J. S. (2003). Challenging the dogma: the hidden layer of nonprotein-coding RNAs in complex organisms. BioEssays, 25, 930-9 [DOI: 10.1002/bies.10332] [PubMed: 14505360].
An early prediction of the importance of RNA in gene control.

Nudler, E. and Mironov, A. S. (2004). The riboswitch control of bacterial metabolism. Trends Biochem. Sci., 29, 11-17 [DOI: 10.1016/j.tibs.2003.11.004].
Summary of the recent progress identifying small RNA aptamers, called ?riboswitches?. Found in the leader sequences of many metabolic genes they can repress or activate their cognate genes at both transcriptional and translational levels.

Gusella, J. F. and MacDonald, M. E. (2006). Huntington?s disease: seeing the pathogenic process through a genetic lens. Trends Biochem. Sci., 31, 533-40 [DOI: 10.1016/j.tibs.2006.06.009].

Greally, J. M. (2007). Genomics: encyclopaedia of humble DNA. Nature, 447, 782-3 [DOI: 10.1038/447782a] [PubMed: 17568731].
Nature News and Views article

No authors quoted. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816 [DOI: 10.1038/nature05874] [PubMed: 17571346].

Pennisi, E. (2007). DNA study forces rethink of what it means to be a gene. Science, 316, 1556-7 [DOI: 10.1126/science.316.5831.1556] [PubMed: 17569836].
A commentary on the ENCODE project results which shows that genes may be far from compact assemblies but have regions scattered around the genome. Highly readable.