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Elliott & Elliott: Biochemistry and Molecular Biology 4e

Chapter 25

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ENCODE

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.

MicroRNA

Fire, A. et al. (1998). Potent and specific genetic interference by double-stranded RNA in C elegans. Nature, 391, 806-11 [DOI: 10.1038/35888] [PubMed: 9486653].

Nishikura, K. (2001). A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst. Cell 107, 415-18 [DOI: 10.1016/S0092-8674(01)00581-5] [PubMed: 11719182].
Minireview

Zamore, P. D. (2001). RNA interference: listening to the sound of silence. Nat. Struct. Biol., 8, 746-50 [DOI: 10.1038/nsb0901-746].
Review on gene silencing.

Martinez, J. (2002). Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563-74 [DOI: 10.1016/S0092-8674(02)00908-X] [PubMed: 12230974].

Shi, Y. (2003). Mammalian RNAi for the masses. Trends Genet., 19, 9-12 [DOI: 10.1016/S0168-9525(02)00005-7].
The siRNAs (small interfering RNAs) are easily synthesized chemically. Their sequence specificity means that, in principle, any mRNA can be targeted to silence (or knockdown) expression of specific genes. Deals with potential medical applications.

Lavorgna, G. et al. (2004). In search of antisense. Trends Biochem. Sci., 29, 80-7 [DOI: 10.1016/j.tibs.2003.12.002].
Natural antisense transcripts have been implicated in many aspects of eukaryotic gene expression.

Hannon, G. J. (2002). RNA interference. Nature, 418, 244-51 [DOI: 10.1038/418244a] [PubMed: 12110901].
An Insight review article

Nelson, P., Kiriakodou, M., Sharma, A., Maniataki, E., and Mourelatos, Z. (2003). The microRNA world: small is mighty. Trends Biochem. Sci., 28, 534-40 [DOI: 10.1016/j.tibs.2003.08.005].

Ambros, V. (2004). The functions of animal microRNAs. Nature, 431, 350-5 [DOI: 10.1038/nature02871] [PubMed: 15372042].
Useful introduction to the subject of microRNAs.

Bartel, D. P. (2004). MicroRNAs. Genomics, biogenesis mechanism and function. Cell 116, 281-97 [DOI: 10.1016/S0092-8674(04)00045-5] [PubMed: 14744438].
Very comprehensive, more suitable for instructors

Meister, G. and Tuschl, T. (2004). Mechanisms of gene silencing by double-stranded RNA. Nature, 431, 343-9 [DOI: 10.1038/nature02873] [PubMed: 15372041].
A general review

Mello, C. C. and Conte, D. (2004). Revealing the world of RNA interference. Nature, 431, 338-42 [DOI: 10.1038/nature02872] [PubMed: 15372040].

Eckstein, F. (2005). Small non-coding RNAs as magic bullets. Trends Biochem. Sci., 30, 445-52 [DOI: 10.1016/j.tibs.2005.06.008].
Very good summary of all aspects

Lu, J. et al. (2005). MicroRNA expression profiles classify human cancers. Nature, 435, 834-8 [DOI: 10.1038/nature03702] [PubMed: 15944708].

Storz, G., Alluvia, S., and Wassarman, K. M. (2005). An abundance of RNA regulators. Annu. Rev. Biochem., 74, 199-217 [DOI: 10.1146/annurev.biochem.74.082803.133136].

Mattick, J. S. and Makunin, I. V. (2006). Noncoding RNA. Human Molecular Genetics, R17-R29.

Kloosterman, W. P. and Plasterk, R. H. A. (2006). The diverse functions of microRNAs in animal development and disease. Devel. Cell, 11, 441-50 [DOI: 10.1016/j.devcel.2006.09.009].

Parker, S. and Barford, D. (2006). Argonaute: a scaffold for the function of short regulatory RNAs. Trends Biochem. Sci., 31, 622-30 [DOI: 10.1016/j.tibs.2006.09.010].

Plasterk, R. H. A. (2006). MicroRNAs in animal development. Cell 124, 877-81 [DOI: 10.1016/j.cell.2006.02.030] [PubMed: 16530032].

Hernando, E. (2007). MicroRNAs and cancer: role in tumorigenesis, patient classification and therapy. Clinical and Translational Oncology, 9, 155-60 [DOI: 10.1007/s12094-007-0029-0] [PubMed: 17403626].
This review examines the role of miRNAs in the pathogenesis of cancer as well as miRNA-profiling studies performed in human malignancies.

Ma, L., Teruya-Feldstein, J., and Weinberg, R. A. (2007). Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature, 449, 682-8 [DOI: 10.1038/nature06174] [PubMed: 17898713].

Mattick, J. (2007). A new paradigm for developmental biology. J. Exptl. Biol., 210, 1526-47 [DOI: 10.1242/jeb.005017].

Proposes a model for RNA regulatory networks, Zhao, Y. and Srivastava, D.. (2007). Trends Biochem. Sci., 32.

Zhongxing. (2007). Blockade of invasion and metastasis of breast cancer cells via targeting CXCR4 with an artificial microRNA. Biochem. Biophys. Res. Commun., 363, 542-6 [DOI: 10.1016/j.bbrc.2007.09.007].
CXCR4 is a chemokine receptor

Amaral, P. P. et al. (2008). The eukaryotic genome as an RNA machine. Science, 319, 1787-9 [DOI: 10.1126/science.1155472] [PubMed: 18369136].
A Science perspective article

Nowacki, M., Vijayan, V., Zhou, Y., Schotanus. K., Doak, T. G., and Landweber, L. F. (2008). RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature, 451, 153-60 [DOI: 10.1038/nature06452] [PubMed: 18046331].