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Oxford University Press - Online Resource Centres

Elliott & Elliott: Biochemistry and Molecular Biology 4e

Chapter 23

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mRNA editing

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

Gilbert, W. (1987). The exon theory of genes. ColdSpring Harbor Symp. Quant. Biological LII, 901-5.
Describes the ?introns early? theory of assemblage of genes from mini-genes.

Go, M. and Nosaka, M. (1987). Protein architecture and the origin of introns. Cold Spring Harbor Symp. Quant. Biol., LII, 915-24.
Considers the two theories of the origins of introns.

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].

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.

Splicing

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.

Orgel, L. E. (1994). The origin of life on earth. Sci. Am., 271(4), 52-61.
Growing evidence supports the idea that the emergence of catalytic RNA was a crucial early step.

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.

RNA self-cleavage

Fedor, M. J. (1998). Ribozymes. Curr. Biol., 8, R441-3 [DOI: 10.1016/S0960-9822(98)70287-8].
Concise summary

Chromatin remodelling

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].

Ogbourne, S. and Antalis, T. M. (1998). Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes. Biochem. J., 331, 1-14.
A review article

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

Berger, S. L. (2007). The complex language of chromatin regulation during transcription. Nature, 447, 407-11 [DOI: 10.1038/nature05915] [PubMed: 17522673].
An Insight review

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].

Richardson, J. P. (2003). Loading Rho to terminate transcription. Cell 114, 157-9 [DOI: 10.1016/S0092-8674(03)00554-3] [PubMed: 12887917].
Minireview on the Rho mechanism

RNA polymerase machinery

Landick, R. (2001). RNA polymerase clamps down. Cell 105, 567-70 [DOI: 10.1016/S0092-8674(01)00381-6] [PubMed: 11389826].
Discusses mechanism of RNA polymerase holding on to DNA being transcribed.

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].

DNA-binding proteins

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

Klevit, R. E. (1991). Recognition of DNA by Cys2, His2 zinc fingers. Science, 253, 1367 [DOI: 10.1126/science.1896847] [PubMed: 1896847], 1393.
Concise summary

Rhodes, D. and Klug, A. (1993). Zinc fingers. Sci. Am., 263(2), 56-65.
Discusses structures, functions, and distribution of these transcription factors.

Klug, A. and Schwabe, J. W. R. (1995). Zinc fingers. FASEB J., 9, 597-604.
A complete account of the structure of this protein motif and its role in DNA binding.

DNA-binding proteins - leucine zippers

McKnight, S. L. (1991). Molecular zippers. Sci. Am., 264(4), 32-9.

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].