Elliott & Elliott: Biochemistry and Molecular Biology 4e
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Hodges, R. and Scott, J. (1992). Apolipoprotein B mRNA editing; a new tier for the control of gene expression. Trends Biochem. Sci., 17, 77-81 [DOI: 10.1016/0968-0004(92)90506-5].
How mRNA editing leads to the production of two forms of apolipoprotein B from one mRNA transcript.
Proudfoot, N. J., Furger, A. and Dye, M. J. (2002). Integrating mRNA processing with transcription. Cell 108, 501-12 [DOI: 10.1016/S0092-8674(02)00617-7] [PubMed: 11909521].
Reviews eukaryotic transcription and subsequent modification of transcripts
Introns and exons
Protein modules or domains
Doolittle, R. F. (1995). The multiplicity of domains in proteins. Annu. Rev. Biochem., 64, 287-314 [DOI: 10.1146/annurev.bi.64.070195.001443].
A fascinating discussion of domains, domain shuffling, exons, and introns.
Breitbart, R. E., Andreadis, A., and Nadal-Ginard, B. (1987). Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes. Annu. Rev. Biochem., 56, 467-95 [DOI: 10.1146/annurev.bi.56.070187.002343].
Fairly detailed but gives an overview of the biological role.
Nilsen, T. W. (2003). The spliceosome: the most complex macromolecuar machine in the cell? BioEssays, 25, 1147-9 [DOI: 10.1002/bies.10394] [PubMed: 14635248].
A short informative review on how introns are excised rom transcripts.
Fedor, M. J. (1998). Ribozymes. Curr. Biol., 8, R441-3 [DOI: 10.1016/S0960-9822(98)70287-8].
Pollard, K. J. and Peterson C. L. (1998). Chromatin remodelling: a marriage between two families. BioEssays, 20, 771-80 [DOI: 10.1002/(SICI)1521-1878(199809)20:9<771::AID-BIES10>3.0.CO;2-V] [PubMed: 9819566].
Extensive review of two families of remodelling enzymes.
Gregory, P. D. and Horz, W. (1998). Life with nucleosomes: chromatin remodelling in gene regulation. Curr. Opin. Cell Biol., 10, 339-42 [DOI: 10.1016/S0955-0674(98)80009-4].
Kornberg, R. D. (1999). Eukaryote transcriptional control. Trends Cell Biol., Trends Biochem. Sci. and Trends Genet. (joint issue), 24, M46-8.
Millennium review including chromatin remodelling. A short overview of the subject including an account of what still needs to be done.
Sudarsanam, P. and Winston, F. (2000). The Swi/Snf family: nucleosome-remodeling complexes and transcriptional control. Trends Genet., 16, 345-50 [DOI: 10.1016/S0168-9525(00)02060-6].
Lusser, A. and Kadonaga, J. T. (2003) Chromatin remodeling by ATP-dependent molecular machines. BioEssays, 25, 1192-200 [DOI: 10.1002/bies.10359] [PubMed: 14635254].
How nucleosome structure may be re-organized during chromatin remodelling.
Svejstrup, J. Q. (2003). Histones face the FACT. Science, 301, 1053-4 [DOI: 10.1126/science.1088901] [PubMed: 12933997].
This Perspectives article summarizes new evidence on how histones cope with transcription.
Control of eukaryotic transcription
Kiermaier, A. and Eilers, M. (1997). Transcriptional control: calling in histone deacetylase. Curr. Biol., 7, R505-7 [DOI: 10.1016/S0960-9822(06)00249-1].
Siegfried, Z. and Cedar, H. (1997). DNA methylation: a molecular lock. Curr. Biol., 7, R305-7 [DOI: 10.1016/S0960-9822(06)00144-8].
Modulation of gene expression by DNA methylation.
Kuo, M.-H. and Allis, C. D. (1998). Roles of histone acetyltransferases and deacetylases in gene regulation. BioEssays, 20, 615-26 [DOI: 10.1002/(SICI)1521-1878(199808)20:8<615::AID-BIES4>3.0.CO;2-H] [PubMed: 9780836].
Struhl, K. (1999). Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98, 1-4 [DOI: 10.1016/S0092-8674(00)80599-1] [PubMed: 10412974].
Minireview giving a good overview
Fiering, S., Whitelaw, E., and Martin, D. I. K. (2000). To be or not to be active: the stochastic nature of enhancer action. BioEssays, 22, 381-7 [DOI: 10.1002/(SICI)1521-1878(200004)22:4<381::AID-BIES8>3.0.CO;2-E] [PubMed: 10723035].
Ahringer, J. (2000). NuRD and SIN3 histone deacetylase complexes in development. Trends Genet., 16, 351-6 [DOI: 10.1016/S0168-9525(00)02066-7].
Brown, C. E., Lechner, T., Howe, L., and Workman, J. L. (2000) The many HATs of transcription coactivators. Trends Biochem. Sci., 25, 15-18 [DOI: 10.1016/S0968-0004(99)01516-9].
A discussion of the multiple histone acetyltransferases
Malik, S. and Roeder, R. G. (2000). Transcriptional regulation through mediator-like coactivators in yeast and metazoan cells. Trends Biochem. Sci., 25, 277-83 [DOI: 10.1016/S0968-0004(00)01596-6].
Myers, L. C. and Kornberg, R. D. (2000). Mediator of transcriptional regulation. Annu. Rev. Biochem., 69, 729-49 [DOI: 10.1146/annurev.biochem.69.1.729].
More suitable for instructors
Orphanides, G. and Reinberg, D. (2002). A unified theory of gene expression. Cell 108, 439-51 [DOI: 10.1016/S0092-8674(02)00655-4] [PubMed: 11909516].
Wide-ranging review including concept that DNA transcription in eukaryotes is one continuous smooth process up to transport of mRNA from the nucleus.
Freiman, R. N. and Tjlan, R. (2003). Regulating the regulators: lysine modifications make their mark. Cell 112, 11-17 [DOI: 10.1016/S0092-8674(02)01278-3].
Reviews the concept that covalent modifications fine-tune transcription in different organisms. Also discusses the relevance to lack of the correlation between complexity and gene numbers.
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.
Bjorklund, S. and Gustafsson, C. M. (2005). The yeast mediator complex and its regulation. Trends Biochem. Sci., 30, 240-4 [DOI: 10.1016/j.tibs.2005.03.008].
Kornberg, R. (2005). Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci., 30, 235 [DOI: 10.1016/j.tibs.2005.03.011].
Introduces a special edition on mediators
Ferguson-Smith, A. C. and Greally, J. M. (2007). Perceptive enzymes. Nature, 449, 148-9 [DOI: 10.1038/449148a] [PubMed: 17851501].
Adding methyl groups to DNA is a way of regulating some genes and genomic sequences - a window on epigenetic printing. A News and Views article.
Paik, W. K., Paik, D. C., and Kim, S. (2007). Historical review: the field of protein methylation. Trends Biochem. Sci., 32, 101-52 [DOI: 10.1016/j.tibs.2007.01.006].
Reik, W. (2007). Stability and flexibility of epigenetic gene regulation in mammalian development. Nature, 447, 425-32 [DOI: 10.1038/nature05918] [PubMed: 17522676].
An Insight review. An advanced review comparing the concepts of gene regulation by transcription factors and by methylation. Probably more suitable for instructors.
Merger, S. L. (2007). The complex language of chromatin regulation during transcription. Nature, 447, 407-12 [DOI: 10.1038/nature05915].
An advanced Insight review dealing with broad concepts. Probably more suitable for instructors.
Termination of transcription
Reeder, R. H. and Lang, W. H. (1997). Terminating transcription in eukaryotes: lessons learned from RNA polymerase I. Trends Biochem. Sci., 22, 473-7 [DOI: 10.1016/S0968-0004(97)01133-X].
RNA polymerase machinery
Woychik, N. A. and Hampsey, M. (2002). The RNA polymerase II machinery: structure illuminates function. Cell 108, 453-63 [DOI: 10.1016/S0092-8674(02)00646-3] [PubMed: 11909517].
Comprehensive review of eukaryotic transcriptional machinery
Transcription in mitochondria
Clayton, D. A. (1984). Transcription of the mammalian mitochondrial genome. Annu. Rev. Biochem., 53, 573-94 [DOI: 10.1146/annurev.bi.53.070184.003041].
If differs from nuclear transcription. General review of the topic.
Asin-Cayuela, J. and Gustafsson, C. M. (2007). Mitochondrial transcription and its regulation in mammalian cells. Trends Biochem. Sci., 32, 111-7 [DOI: 10.1016/j.tibs.2007.01.003].
Brennan, R. G. and Matthews, B. W. (1989). Structural basis of DNA-protein recognition. Trends Biochem. Sci., 14, 287-90 [DOI: 10.1016/0968-0004(89)90066-2].
Reviews the structures of proteins involved in the control of gene transcription and the way they interact with DNA.
DNA-binding proteins - zinc fingers
DNA-binding proteins - leucine zippers
Ellenberger, T. E., Brandl, C. J., Struhl, K., and Harrison, S. C. (1992). The GCN4 basic region of leucine zipper binds DNA as a dimer of uninterrupted α helices: crystal structure of the protein-DNA complex. Cell 71, 1223-37 [DOI: 10.1016/S0092-8674(05)80070-4] [PubMed: 1473154].
A research paper, with molecular illustrations
Gamsjaeger, R. et al. (2007). Sticky fingers as protein-recognition motifs. Trends Biochem. Sci., 32, 63-70 [DOI: 10.1016/j.tibs.2006.12.007].