Articles on ethical issues in genetics are preceded by an asterisk.

Bartel, D. P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297.

An excellent summary of small interfering RNAs and microRNAs, their similarities, and their differences.

R9

Baumann, P., S. A. Qreshi, and S. P. Jackson. 1995. Transcription: new insights from studies on archaea. Trends in Genetics 11:279–283.

A discussion of how transcription in archaea is similar to that in eukaryotes.

Bjork, G. R., J. U. Erikson, C. E. D. Gustafsson, et al. 1987. Transfer RNA modification. Annual Review of Biochemistry 56:263–288.

A review of how transfer RNA is processed.

Blencowe, B. J. 2006. Alternative splicing: new insights from global analyses. Cell 126:37–47.

Reports the extent of alternative splicing in the human genome.

Broker, T. R., L. T. Chow, A. R. Dunn, et al. 1978. Adenovirus-2 messengers: an example of baroque molecular architecture. Cold Spring Harbor Symposium on Quantitative Biology 42:531–534.

One of the first reports on introns in eukaryotic genes.

Cesana, M., D. Cacchiarelli, I. Legnini, et al. 2011. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147:358–369.

Research showing that a lncRNA controls gene regulation by acting as a decoy for miRNAs.

Churchman, L. S., and J. S. Weissman. 2011. Nascent transcript sequencing visualizes transcription at nucleoside resolution. Nature 469:368–373.

An analysis of transcription at the level of individual nucleotides reveals pervasive pausing and backtracking during transcription.

Cramer, P., D. A. Bushnell, J. Fu, et al. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288:640–649.

A report on the detailed structure of RNA polymerase II.

de la Sierra-Galley, I. L., O. Pellegrini, and C. Condon. 2005. Structural basis for substrate binding, cleavage, and allostery in the tRNA maturase RNase Z. Nature 433:657–661.

A report on the structure of RNase P, which is responsible for transfer RNA processing.

Deltcheva, E., K. Chylinski, C. M. Sharma, et al. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNaseIII. Nature 471:602–607.

A research report on CRISPR RNA processing.

Dutta, D., K. Shatalin, V. Epshtein, et al. 2011. Linking RNA polymerase backtracking to genome instability in E. coli. Cell 146:533–543.

Research on RNA backtracking in bacterial cells and how it is related to double-strand breaks in the DNA.

Geiduschek, E. P., and M. Ouhammouch. 2005. Archaeal transcription and its regulators. Molecular Microbiology 56:1397–1407.

A short review of transcription in archaea.

Gesteland, R. F., and J. F. Atkins. 1993. The RNA World. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.

Contains several chapters on ribozymes and their possible role in the early evolution of life.

Gottesman, S. 2011. Dicing defence in bacteria. Nature 471:588–589.

A short review of CRISPR RNAs in prokaryotes.

Hahn, H. 2004. Structure and mechanism of the RNA polymerase II transcription machinery. Nature Structural and Molecular Biology 11:394–403.

An excellent detailed review of RNA polymerase II structure and function.

Hallen, H. E., H. Luo, J. S. Scott-Craig, et al. 2007. Gene family encoding the major toxins of lethal Amanita mushrooms. Proceedings of the National Academy of Sciences of the United States of America 104:19097–19101.

A research report on the genes that produce lethal toxins in Amanita mushrooms.

Hirata, A., B. J. Klein, and K. S. Murakami. 2008. The X-ray crystal structure of RNA polymerase from Archaea. Nature 451:851–854.

Contains information about the structure and function of RNA polymerase in archaea.

Hoskins, A. A., L. J. Friedman, S. S. Gallagher, et al. 2011. Ordered and dynamic assembly of single spliceosomes. Science 331:1289–1295.

Information on the assembly of spliceosomes.

Huarte, M., M. Guttman, D. Feldser, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142:409–419.

Research report that lncRNA regulates genes by repressing p53.

Keller, W. 1995. No end yet to messenger RNA 3′ processing. Cell 81:829–832.

An excellent review of processing at the 3′ end of eukaryotic pre-mRNA.

Korzheva, N., A. Mustaev, M. Kozlov, et al. 2000. A structural model of transcription elongation. Science 289:619–625.

Presentation of a model of the transcription apparatus.

Kuhn, C. D., S. R. Geiger, S. Baumli, et al. 2007. Functional architecture of RNA polymerase I. Cell 131:1260–1272.

Presents structural information about RNA polymerase I.

Landick, R. 2006. A long time in the making: the Nobel Prize for RNA polymerase. Cell 127:1087–1090.

A short discussion of Roger Kornberg’s research on RNA polymerase, for which he was awarded the Nobel Prize in 2006.

Landweber, L. F., P. J. Simon, and T. A. Wagner. 1998. Ribozyme engineering and early evolution. BioScience 48:94–103.

A nice review of the idea that early life may have consisted of an RNA world.

Larson, M. H., W. J. Greenleaf, R. Landick, et al. 2008. Applied force reveals mechanistic and energetic details of transcription termination. Cell 132:971–982.

A research report on the mechanism of rho-independent termination.

Lau, N. C., and D. P. Bartel. 2003. Censors of the genome. Scientific American 289(2): 34–41.

A well-written summary of RNA interference, how it takes place, and possible applications.

Lau, N. C., A. G. Seto, J. Kim, et al. 2006. Characterization of the piRNA complex from rat testis. Science 313:363–367.

A report on the characteristics of Piwi-interacting RNAs.

Lee. J. T. 2012. Epigenetic regulation by long noncoding RNAs. Science 338:1435–1439.

A review of the role of long noncoding RNAs in epigenetics.

Lee, T. I., and R. A. Young. 2000. Transcription of eukaryotic protein-encoding genes. Annual Review of Genetics 34:77–138.

A good review of how eukaryotic genes are transcribed by RNA polymerase II.

R10

Liu, X., D. A. Bushnell, D. Silva, et al. 2011. Initiation complex structure and promoter proofreading. Science 333:633–637.

Research on the initiation complex in eukaryotes and abortive transcription.

Mangone, M., A. P. Manoharan, D. Thierry-Mieg, et al. 2010. The landscape of C. elegans 3′ UTRs. Science 329:432–435.

Report of the distribution of 3′ UTR in worms.

Matzke, M., and A. J. M. Matzke. 2003. RNAi extends its reach. Science 301:1060–1061.

A commentary on an article in this issue of Science by V. Schramke and R. Allshire showing the effects of small interfering RNAs on heterochromatin structure.

McKeown, M. 1992. Alternative mRNA splicing. Annual Review of Cell Biology 8:133–155.

An extensive review that discusses the different types of alternative splicing with specific examples of each type.

Misteli, T., J. F. Caceres, and D. L. Spector. 1997. The dynamics of a pre-mRNA splicing factor in living cells. Nature 387:523–527.

Reports that pre-mRNA splicing and transcription take place at the same sites in the nucleus.

Murakami, K. S., S. Masuda, and S. A. Darst. 2002. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296:1280–1284.

A detailed view of the structure of bacterial RNA polymerase.

Nagano, T., and P. Fraser. 2011. No-nonsense functions for long noncoding RNAs. Cell 145:178–181.

A short review of lncRNAs.

Nature. 2009. Volume 457, issue 7228.

This supplement contains a series of review articles on RNA silencing.

Nature Reviews Genetics. 2007. Volume 8, issue 10.

A collection of five articles on microRNAs.

Noller, H. F. 1984. Structure of ribosomal RNA. Annual Review of Biochemistry 53:119–162.

A review of ribosomal RNA.

Nudler, E. 2012. RNA polymerase backtracking in gene regulation and genome instability. Cell 149:1438–1445.

A review on backtracking by the RNA polymerase during transcription.

O’Donnell, K. A., and J. D. Boeke. 2007. Mighty Piwis defend the germline against genome intruders. Cell 129:37–44.

A good review article on Piwi-RNAs.

Onodera, Y., J. R. Haag, T. Ream, et al. 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120:613–622.

Reports a fourth RNA polymerase in plants.

Plasterk, R. H. A. 2006. Micro RNAs in animal development. Cell 124:877–881.

A discussion of the role of microRNAs in development.

Pomeranz Krummel, D. A., C. Oubridge, A. K. Leung, et al. 2009. Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution. Nature 458:475–480.

A report on the structure of the human spliceosome.

Ptashne, M., and A. Gann. 1997. Transcriptional activation by recruitment. Nature 386:569–577.

An excellent summary of how prokaryotic and eukaryotic proteins that bind to promoters affect transcription.

Reeve, J. N., K. Sandman, and C. J. Daniels. 1997. Archaeal histones, nucleosomes, and transcription initiation. Cell 89:999–1002.

A mini review of archaeal transcription.

Rich, A., and S. H. Kim. 1978. The three-dimensional structure of transfer RNA. Scientific American 238(1): 52–62.

A discussion of the structure of transfer RNA.

Richardson, J. P. 2002. Rho-dependent termination and ATPases in transcript termination. Biochimica et Biophysica Acta 1577:251–260.

A review of rho-dependent termination.

Smith, C. M., and J. A. Steitz. 1997. Sno storm in the nucleolus: new roles for myriad small RNPs. Cell 89:669–672.

A good review of the role of small nucleolar RNAs in ribosomal RNA processing.

Spitali, P., and A. Aartsma-Rus. 2012. Splice modulating therapies for human diseases. Cell 148:1085–1088.

A review of how modification of splicing may be used to treat human diseases.

Storz, G. 2002. An expanding universe of noncoding RNAs. Science 296:1260–1262.

A good review of the structure and function of numerous types of RNA that do not encode proteins. This issue of Science includes several other review articles about RNA.

Tijsterman, M., R. F. Ketting, and R. H. A. Plasterk. 2002. The genetics of RNA silencing. Annual Review of Genetics 36:489–520.

A detailed review of different types of interfering RNAs and how they function.

Vagin, V. V., A. Sigova, C. Li, et al. 2006. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313:320–324.

Another report on Piwi-interacting RNAs.

Vargas, D. Y., K. Shah, and M. Batish, et al. 2011. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147:1054–1065.

Research showing that transcription and splicing are coupled except during alternative splicing.

Vasudevan, S., Y. Tong, and J. A. Steitz. 2007. Switching from repression to activation: microRNAs can up-regulate translation. Science 318:1931–1934.

Reports that miRNAs can both repress and stimulate translation.

von Hippel, P. H. 1998. An integrated model of the transcription complex in elongation, termination, and editing. Science 281:660–665.

A review of how the transcription apparatus elongates, terminates, and edits in the course of transcription.

von Hippel, P. H. 2006. Transcriptional pausing caught in the act. Cell 125:1027–1029.

A short review of transcriptional pausing.

Wang, E. T., R. Sandberg, S. Luo, et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476.

Reports that more than 90% of human genes undergo alternative splicing.

R11

Wierzbicki, A. T., T. S. Ream, J. R. Haag, and C. S. Pikaard. 2009. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nature Genetics 41:630–634.

A research report on the function of RNA polymerase V in plants.

Xiong, Y., and T. A. Steitz. 2004. Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430:640–645.

A report on how the CCA sequence is added to the 3′ end of a transfer RNA.

Young, R. A. 1991. RNA polymerase II. Annual Review of Biochemistry 60:689–716.

A review of RNA polymerase II.

Zamore, P. D. 2006. RNA interference: big applause for silencing in Stockholm. 2006. Cell 127:1083–1086.

An article outlining the work of Craig Mello and Andrew Fire that led to the Nobel Prize in physiology and medicine in 2006.

Zenkin, N., Y. Yuzenkova, and K. Severinov. 2006. Transcript-assisted transcriptional proofreading. Science 313:518–520.

Report on proofreading by RNA polymerase.

Zhang, Y., Y. Feng, S. Chatterjee, et al. 2012. Structural basis of transcription initiation. Science 338:1076–1080.

Study of the structure of the transcription bubble.