Articles on ethical issues in genetics are preceded by an asterisk.
Amit, R., H. G. Garcia, R. Phillips, et al. 2011. Building enhancers from the ground up: a synthetic biology approach. Cell 146:105–118.
Report on bacterial enhancers.
Arteaga-
Research showing that paramutation in corn is caused by siRNAs.
Becker, P. B. 2006. A finger on the mark. Nature 442:31–32.
A short review of the histone code.
Beelman, C. A., and R. Parker. 1995. Degradation of mRNA in eukaryotes. Cell 81:179–183.
An excellent review of the importance of messenger RNA stability in eukaryotic gene regulation and of some of the ways in which messenger RNA is degraded.
Bell, A. C., A. G. West, and G. Felsenfeld. 2001. Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science 291:447–498.
A good introduction to research on insulators.
Bernstein, B. E., A. Meissner, and E. S. Lander. 2007. The mammalian epigenome. Cell 128:669–681.
A review of genome-
Bestor, T. H. 1998. Methylation meets acetylation. Nature 393:311–312.
A short review of research demonstrating a connection between DNA methylation and histone acetylation.
Bird, A. 2007. Perceptions of epigenetics. Nature 447:396–398.
A discussion of the definition of epigenetics.
Bird, A. P., and A. P. Wolffe. 1999. Methylation-
A discussion of the role of methylation in gene regulation and development.
Blackwood, E. M., and J. T. Kadonaga. 1998. Going the distance: a current view of enhancer action. Science 281:60–63.
A review and discussion of models of enhancer action.
Chandler, V. L. 2007. Paramutation: from maize to mice. Cell 128:641–645.
A great review of paramutation and what we know about its molecular mechanisms.
Chandler, V., and M. Alleman. 2008. Paramutation: epigenetic instructions passed across generations. Genetics 178:1839–1844.
A great review of paramutation at the b1 and r1 loci in corn.
Feinberg, A. P. 2007. Phenotypic plasticity and the epigenetics of human disease. Nature 447: 433–440.
A review of the role of epigenetics in human disease.
Fraga, M. F., E. Ballestar, M. F. Paz, et al. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proceedings of the National Academy of Sciences of the United States of America 102:10604–10609.
A research report on epigenetic differences in identical twins.
Gerasimova, T. I., and V. G. Corces. 2001. Chromatin insulators and boundaries: effects on transcription and nuclear organization. Annual Review of Genetics 35:193–208.
Reviews the effects of insulators and chromatin boundaries on the transcription of eukaryotic genes.
Gilchrist, D. A. et al. 2010. Pausing of RNA polymerase II disrupts DNA-
Research on stalling of RNA polymerase.
Goldberg, A. D., C. D. Allis, and E. Bernstein. 2007. Epigenetics: a landscape takes shape. Cell 128:635–638.
A brief discussion of what is meant by the term epigenetics and how epigenetics takes place.
Hartley, P. D., and H. D. Madhani. 2009. Mechanisms that specify promoter nucleosome location and identity. Cell 137:445–458.
A research report on the role of nucleosome positioning in gene regulation.
He, Y., S. D. Michaels, and R. M. Amasino. 2003. Regulation of flowering time by histone acetylation in Arabidopsis. Science 302:1751–1754.
A report on how acetylation helps control flowering time in plants.
Hodgkin, J. 1989. Drosophila sex determination: a cascade of regulated splicing. Cell 56:905–906.
A good short review of alternative splicing and how it regulates sex differentiation in Drosophila.
Jacob, F. 2011. The birth of the operon. Science 332:767.
A short reflection on research that led to the discovery of the lac operon by François Jacob on the 50-
Jacob, F., and J. Monod. 1961. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3:318–356.
A classic paper describing Jacob and Monod’s work on the lac operon, as well as a review of gene control in several other systems.
Jing, Q., S. Huang, S. Guth, et al. 2005. Involvement of microRNA in AU-
A research report showing that AU-
King, M., and A. C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107–116.
Early report suggesting that phenotypic differences between humans and chimpanzees are produced by differences in gene regulation.
Kucharksi, R., J. Maleszka, S. Foret, et al. 2008. Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827–1830.
Research demonstrating that the epigenetic changes brought about by a diet of royal jelly produce differences between queens and workers in honeybees.
Lee, J., E. Smith, and A. Shilatifard. 2010. The language of histone crosstalk. Cell 142:682–685.
R13
A review of research showing that some types of histone modifications facilitate other histone modifications, creating a complex interaction between different types of chromatin regulators.
Lee, J. T., and M. S. Bartolomei. 2013. X-
A good review of X inactivation and genomic imprinting.
Levine, M. 2011. Paused RNA polymerase II as a developmental checkpoint. Cell 145:502–511.
A review of the role of stalled RNA polymerases in control of transcription.
Lister, R., M. Pelizzola, R. H. Dowen, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322.
A research report on the epigenome.
Matzke, M., A. J. M. Matzke, and J. M. Kooter. 2001. RNA: guiding gene silencing. Science 293:1080–1083.
A review of RNA silencing.
Miller, G. 2010. The seductive allure of behavioral epigenetics. Science 329:24–27.
A journalistic article that discusses the excitement and caution surrounding the effects of epigenetic changes on behavior.
Morey, C., and P. Avner. 2011. The demoiselle of X-
A great history of research on X inactivation.
Narlikar, G. J., H. H. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487.
An excellent review of how chromatin structure represses transcription and how proteins modify it.
Ng, H. H., and A. Bird. 2000. Histone deacetylases: silencers for hire. Trends in Biochemical Science 25:121–126.
A review of how deacetylation can affect transcription in eukaryotic cells.
Notoli, G., and J. Andrau. 2012. Noncoding transcription at enhancers: general principles and functional models. Annual Review of Genetics 46:1–20.
A review of enhancers and the evidence that many enhancers are transcribed.
Nowick, K, T., T. Gernat, E. Almaas, et al. 2009. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proceedings of the National Academy of Sciences of the United States of America 106:22358–22363.
Research report on the finding that expression of transcription factors differs between humans and chimpanzees.
Pabo, C. O., and R. T. Sauer. 1992. Transcription factors: structural families and principles. Annual Review of Biochemistry 61:1053–1095.
A review of different DNA-
Petronis, A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 465:721–727.
A review of how epigenetics plays a role in disease and complex traits in humans.
Ray, J. C. J., and O. A. Igoshin. 2012. Interplay of gene expression noise and ultrasensitive dynamics affects bacterial operon organization. PLoS Computational Biology 8:e1002672. doi:10.1371/journal.pcbi.1002672.
Research showing that operons tend to reduce biochemical noise in the cell.
Ross, J. 1989. The turnover of messenger RNA. Scientific American 260(4): 48–55.
A review of factors that control messenger RNA stability in eukaryotes.
Soloway, P. D. 2006. Paramutable possibilities. Nature 441:413–414.
A short review of paramutation and how it might occur.
Stranger, B. E., A. C. Nica, M. S. Forrest, et al. 2007. Population genomics of human gene expression. Nature Genetics 39:1217–1224.
Reports on genetic variation in gene-
Tamkun, J. W. 2007. Stalled polymerases and transcriptional regulation. Nature Genetics 39:1421–1422.
A short report on the stalling of RNA polymerase.
Tian, D., S. Sun, and J. T. Lee. 2010. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143:390–403.
Research reporting that Jpx lncRNA plays an important role in X inactivation.
Tuite, M. F. 1996. Death by decapitation for mRNA. Nature 382:577–579.
A discussion of the interaction of the 3′ poly(A) tail and the 5′ cap in messenger RNA degradation.
Tyler, J. K., and J. T. Kadonaga. 1999. The “dark side” of chromatin remodeling: repressive effects on transcription. Cell 99:443–446.
A discussion of the role of chromatin-
Valencia-
An excellent review of how microRNAs and small interfering RNAs control gene expression.
Varki, A., and T. K. Altheide. 2005. Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Research 15:1746–1758.
Analysis of similarities and differences between human and chimpanzee genomes.
Weaver, I. C., N. Cervoni, F. A. Champagne, et al. 2004. Epigenetic programming by maternal behavior. Nature Neuroscience 7:847–854.
A research report of epigenetic changes produced in rats by maternal grooming and licking.
Wolffe, A. P. 1994. Transcription: in tune with histones. Cell 77:13–16.
A review of the role of histone proteins in eukaryotic gene regulation.
Wolffe, A. P. 1997. Sinful repression. Nature 387:16–17.
A short review of the role of histone acetylation in eukaryotic gene regulation.
Youngson, N. A., and E. Whitelaw. 2008. Transgenerational epigenetic effects. Annual Review of Genomics and Human Genetics 9:233–257.
A good review of epigenetic effects that are passed from one generation to the next.
Zaslaver, A., L. R. Baugh, and P. W. Sternberg. 2011. Metazoan operons accelerate recovery from growth-
Research suggesting why some eukaryotes have evolved operons.