![Transcription factories in a Hela cell [from Cook PR (1999) Science 284, 1790]](../images/pombo.png)
Updated on 6 September, 2016
Principles
Box 4-1. Mapping transcription units
Tracking versus immobile RNA polymerases
Box 4-2. The RNA polymerase of E. coli
The untwining and supercoiling problems
Attached polymerases can work in vitro
Transcribing chromatin
The three kinds of eukaryotic RNA polymerase
RNA polymerase I
Box 4-3. Ribosome synthesis
RNA polymerase II and its transcription factors
Promoters (polymerase II)
Number and activity of RNA polymerases
Box 4-4. Transcription of heat-shock loci
Box 4-5. Message/protein profiles - 'microarrays', 'SAGE', 'deep' sequencing, 'two-hybrid', mass spectrometry
Transcription factories
Nucleolar factories containing polymerase I
Extra-nucleolar factories containing polymerases II and III
Dynamics
Processing and transport of polymerase II transcripts
Capping the 5' end
Box 4-6. Analyzing caps
Polyadenylating the 3' end
Splicing the middle
Box 4-7. Autoimmune antibodies
Packaging transcripts into ribonucleoprotein particles
Fidelity and quality control
Nuclear translation
The organization of processing
Transport to the cytoplasm
Principles
Figure: 4-1, 4-2, 4-3.
Additional reference:
Fuda, N.J., Ardehali, M.B., and Lis, JT. (2009). Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461, 186-192. [PubMed]
Hurwitz, J. (2005). The discovery of RNA polymerase. J. Biol. Chem. 280, 42477-42485. [PubMed]
Nudler, E. (2009). RNA polymerase active center: the molecular engine of transcription. Annu. Rev. Biochem. 78, 335-361. [PubMed]
Web link:
http://www.accessexcellence.com/AB/GG/ The basics from the National Health Museum, USA.
Box 4-1. Mapping transcription units
Reference:
Marzluff, W.F. and Huang, R.C.C. (1984). Transcription of RNA in isolated nuclei. In 'Transcription and translation: a practical approach'. Eds B.D. Hames and S.J. Higgins. IRL Press, Oxford.
Additional reference:
Fuda, N.J., Ardehali, M.B., and Lis, JT. (2009). Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461, 186-192. [PubMed]
Djebali S., et al. (2012). Landscape of transcription in human cells. Nature 489, 101-108. [PubMed]
Tracking versus immobile RNA polymerases
Figure: 4-4, 4-5, 4-6.
Reference:
Jackson, D.A. and Cook, P.R. (1985). Transcription occurs at a nucleoskeleton. EMBO J. 4, 919-925. [PubMed]
Jackson, D.A., Hassan, A.B., Errington, R.J. and Cook, P.R. (1993). Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065. [PubMed]
von Hippel, P.H. (1998). An integrated model of the transcription complex in elongation, termination, and editing. Science 281, 660-665. [PubMed]
Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]
Additional reference:
Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1–10. [PubMed]
Reference:
Chamberlin, M. (1982). Bacterial DNA-dependent RNA polymerases. In 'The Enzymes', 3rd ed (P. Boyer, ed), Vol 15B, pp61-108. Academic Press, New York.
Additional reference:
Borukhov, S., and Lee, J. (2005). RNA polymerase structure and function at lac operon. C. R. Biol. 328, 576-587. [PubMed]
Hurwitz, J. (2005). The discovery of RNA polymerase. J. Biol. Chem. 280, 42477-42485. [PubMed]
Mooney, R.A., Darst, S.A., and Landick, R. (2005). Sigma and RNA polymerase: an on-again, off-again relationship? Mol. Cell 20, 335-345. [PubMed]
Nudler, E. (2009). RNA polymerase active center: the molecular engine of transcription. Annu. Rev. Biochem. 78, 335-361. [PubMed]
The untwining and supercoiling problems
Figure: 4-7, 4-8, 4-9, 4-10.
Reference:
Liu, L.F. and Wang, J.C. (1987). Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. U.S.A. 84, 7024-7027. [PubMed]
Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]
Additional reference:
Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1–10. [PubMed]
Koster, D.A., Crut, A., Shuman, S., Bjornsti, M.A., and Dekker, N.H. (2010). Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell 142, 519-530. [PubMed]
Pommier, Y., Sun, Y., Huang, S.N., Nitiss, J.L. (2016). Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat. Rev. Mol. Cell Biol. 17, 703-721. [PubMed]
Attached polymerases can work in vitro
Figure: 4-11.
Reference:
Schafer, D.A., Gelles, J., Sheetz, M.P. and Landick, R. (1991). Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352, 444-448. [PubMed]
Cook, P.R. and Gove, F. (1992). Transcription by an immobilized RNA polymerase from bacteriophage T7 and the topology of transcription. Nucl. Acids Res. 20, 3591-3598. [PubMed]
Gelles, J. and Landick, R. (1998). RNA polymerase as a molecular motor. Cell 93, 13-16.
Additional reference:
Harada, Y., Ohara, O., Takatsuki, A., Itoh, H., Shimamoto, N. and Kinosita, K. (2001). Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409, 113-115. [PubMed]
Herbert, K.M., Greenleaf, W.J., and Block, S.M. (2008). Single-molecule studies of RNA polymerase: motoring along. Annu. Rev. Biochem. 77, 149-176.[PubMed]
Transcribing chromatin
Reference:
Bednar, J., Studitsky, V.M., Grigoryev, S.A., Felsenfeld, G. and Woodcock, C.L. (1999). The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy. Mol. Cell 4, 377-386. [PubMed]
Additional reference:
Kimura, H. and Cook, P.R. (2001). Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153, 1341-1353. [PubMed] [Full text]
Li, B., Carey, M., and Workman, J.L. (2007). The role of chromatin during transcription. Cell 128, 707-719. [PubMed]
The three kinds of eukaryotic RNA polymerase
Figure: 4-12.
Reference:
Roeder, R.G. (1996). Nuclear RNA polymerases: role of general initiation factors and cofactors in eukaryotic transcription. Methods Enzymol. 272, 165-171.
Paule, M.R. and White, R.J. (2000). Transcription by RNA polymerases I and III. Nucleic Acids Res. 28, 1283-1298. [PubMed] [Full text]
Additional reference:
Trinh, V., Langelier, M.F., Archambault, J., and Coulombe, B. (2006). Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol. Mol. Biol. Rev. 70, 12-36. [PubMed]
Vannini, A., and Cramer, P. (2012). Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol. Cell 45, 439-446. [PubMed]
White, R.J. (2011). Transcription by RNA polymerase III: more complex than we thought. Nat. Rev. Genet. 12, 459-463. [PubMed]
RNA polymerase I
Figure: 4-13, 4-14.
Reference:
Miller, O.L. (1981). The nucleolus, chromosomes, and visualization of genetic activity. J. Cell Biol. 91, 15s-27s.
Scheer, U. and D. Weisenberger (1994). The nucleolus. Curr. Opin. Cell Biol. 6, 354-359.
Additional reference:
Denissov, S., Lessard, F., Mayer, C., Stefanovsky, V., van Driel, M., Grummt, I., Moss, T., and Stunnenberg, H.G. (2011). A model for the topology of active ribosomal RNA genes. EMBO Rep. 12, 231-237. [PubMed]
Dinman, J.D. (2009). The eukaryotic ribosome: current status and challenges. J. Biol. Chem 284, 11761-11765. [PubMed]
Dundr, M., Hoffmann-Rohrer, U., Hu, Q., Grummt, I., Rothblum, L.I., Phair, R.D. and Misteli, T. (2002). A kinetic framework for a mammalian RNA polymerase in vivo. Science 298, 1623-1626. [PubMed]
McStay, B., and Grummt, I. (2008). The epigenetics of rRNA genes: from molecular to chromosome biology. Annu. Rev. Cell Biol. 24, 131-157. [PubMed]
Box 4-3. Ribosome synthesis
Reference:
Venema, J. and Tollervey, D. (1999). Ribosome synthesis in Saccharomyces cerevisiae. Annu. Rev. Genet. 33, 261-311. [PubMed]
Additional reference:
Connolly, K., and Culver, G. (2009). Deconstructing ribosome construction. Trends Biochem. 34, 256-263. [PubMed]
Web link:
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html snoRNA database.
RNA polymerase II and its transcription factors
Table: 4-1.
Figure: 4-15.
Reference:
Pabo, C.O. and Sauer, R.T. (1992). Transcription factors: structural families and principles of DNA recognition. Annu Rev. Biochem. 61, 1053-1095.
Orphanides, G., Lagrange, T. and Reinberg, D. (1996). The general transcription factors of RNA polymerase II. Genes Dev. 10, 2657-2683.
Cosma, M.P., Tanaka, T. and Nasmyth, K. (1999). Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally-regulated promoter. Cell 97, 299-311. [PubMed]
Kimura, H., Tao, Y., Roeder, R.G. and Cook, P.R. (1999). Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol. Cell. Biol. 19, 5383-5392. [PubMed] [Full text]
Buratowski, S. (2000). Snapshots of RNA polymerase II transcription initiation. Current Opinion Cell Biol. 12, 320-325. [PubMed]
Cramer, P., Bushnell, D.A., Fu, J., Gnatt, A.L., Maier-Davis, B., Thompson, N.E., Burgess, R.R., Edwards, A.M., David, P.R. and Kornberg, R.D. (2000). Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640-649. [PubMed]
Additional reference:
Bentley DL. (2014). Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163-175. [PubMed]
Biggin, M.D. (2011). Animal transcription networks as highly connected, quantitative continua. Dev. Cell 21, 611-626. [PubMed]
Cheung, A.C., and Cramer, P. (2012). A movie of RNA polymerase II transcription. Cell 149, 1431-1437. [PubMed]
de Lanerolle, P. (2012). Nuclear actin and myosins at a glance. J. Cell Sci 125, 4945-4949. [PubMed]
Fromm, G., Gilchrist, D.A., and Adelman, K. (2013). SnapShot: Transcription Regulation: Pausing. Cell 153, 930-930. [PubMed]
Guo, J., and Price, D.H. (2013). RNA polymerase II transcription elongation control. Chem. Rev. 113, 8583-8603. [PubMed]
Kornberg, R.D. (2007). The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. USA 104, 12955-12961. [PubMed]
Lenhard, B., Sandelin, A., and Carninci, P. (2012). Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat. Rev. Genet. 13, 233-245.
[PubMed]
McKenna, N.J., and O'Malley, B.W. (2010). SnapShot: Nuclear receptors I. Cell 142, 822-822.e1. [PubMed]
McKenna, N.J., and O'Malley, B.W. (2010). SnapShot: Nuclear Receptors II. Cell 142, 986-986.e2. [PubMed]
Ohlsson, R., Bartkuhn, M., and Renkawitz, R. (2010). CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin. Chromosoma 119, 351-360. [PubMed]
Sainsbury, S., Bernecky, C., and Cramer, P. (2015). Structural basis of transcription initiation by RNA polymerase II. Nat. Rev. Mol. Cell. Biol. 16, 129-143. [PubMed]
Zaborowska, J., Egloff, S., and Murphy, S. (2016). The pol II CTD: new twists in the tail. Nat. Struct. Mol. Biol. 23, 771-777.
Web link:
http://www.ergito.com Access to the 'Great Experiments' pages is free, so sign in and go to Mark Ptashne, Grace Gill, and Roger Brent on the 'Modularity of eukaryotic transcription activators'.
http://jcs.biologists.org/cgi/content/full/116/4/585 The nuclear receptor superfamily from J. Cell Science.
Promoters (polymerase II)
Additional eference:
Seila, A.C, Core, L.J, Lis, J.T, and Sharp, P.A. (2009). Divergent transcription: a new feature of active promoters. Cell Cycle 8, 2557-2564. [PubMed]
Venters, B.J., and Pugh, B.F. (2013). Genomic organization of human transcription initiation complexes. Nature 502, 53-58. [PubMed]
Number and activity of RNA polymerases
Reference:
Shermoen, A.W. and O'Farrell, P.H. (1991). Progression of the cell cycle through mitosis leads to abortion of nascent transcripts. Cell 67, 303-310. [PubMed]
Iyer, V. and Struhl, K. (1996). Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 93, 5208-5212. [PubMed] [Full text]
Jackson, D.A., Iborra, F.J., Manders, E.M.M. and Cook, P.R. (1998). Numbers and organization of RNA polymerases, nascent transcripts and transcription units in HeLa nuclei. Mol. Biol. Cell 9, 1523-1536. [PubMed] [Full text]
Additional reference:
Bon, M., McGowan, S., and Cook, P.R. (2006). Many expressed genes in bacteria and yeast are transcribed only once per cell cycle. FASEB J. 20 , 1721-1723. [ PubMed ]
Swinburne, I.A., and Silver, P.A. (2008). Intron delays and transcriptional timing during development. Dev. Cell. 14, 324-330. [PubMed]
Box 4-4. Transcription of heat-shock loci
Reference:
Lis, J. and Wu, C. (1993). Protein traffic on the heat shock promoter: parking, stalling and trucking along. Cell 74, 1-4.
Additional reference:
Core, L.J., and Lis, J.T. (2008). Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791-1792. [PubMed]
Mariner, P.D., Walters, R.D., Espinoza, C.A., Drullinger, L.F., Wagner, S.D., Kugel, J.F., Goodrich, J.A. (2008). Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 29, 499-509. [PubMed]
Richter, K., Haslbeck, M., and Buchner, J. (2010). The heat shock response: life on the verge of death. Mol. Cell 40, 253-266. [PubMed]
Box 4-5. Message/protein profiles - 'microarrays', 'SAGE', 'deep' sequencing, 'two-hybrid', mass spectrometry
Reference:
Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995). Serial analysis of gene expression. Science 270, 484-487. [PubMed]
Hibi, K., Liu, Q., Beaudry, G.A., Madden, S.L., Westra, W.H., Wehage, S.L., Yang, S.C., Heitmiller, R.F., Bertelsen, A.H., Sidransky, D. and Jen, J. (1998). Serial analysis of gene expression in non-small cell lung cancer. Cancer Res. 58, 5690-5694. [PubMed]
Holstege, F.C.P., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S. and Young, R.A. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728. [PubMed]
Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C.F., Trent, J.M., Staudt, L.M., Hudson, J., Boguski, M.S., Shalon, D., Botstein, D. and Brown, P.O. (1999). The transcriptional program in the response of human fibroblasts to serum. Science 283, 83-87. [PubMed]
Lockhart, D.J., and Winzeler, E.A. (2000). Genomics, gene expression and DNA arrays. Nature 405, 827-836. [PubMed]
Pandey, A. and Mann, M. (2000). Proteomics to study genes and genomes. Science 405, 837-846. [PubMed]
Young, R.A. (2000). Biomedical discovery with DNA arrays. Cell 102, 9-15.
Additional reference:
Ansorge, W.J. (2009). Next-generation DNA sequencing techniques. Nature Biotechnol. 25, 195-203. [PubMed]
Cox, J., and Mann M. (2007). Is proteomics the new genomics? Cell 130, 395-398. [PubMed]
Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63. [PubMed]
Web link:
http://gcat.davidson.edu/Pirelli/index.htm Primer on microarrays.
http://www.bio.davidson.edu/courses/movies.html Go to the microarray and yeast two-hybrid movies.
http://learn.genetics.utah.edu/content/labs/microarray/ Primer from the University of Utah.
Transcription factories
Reference:
Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]
Additional reference:
Chakalova, L., and Fraser, P. (2010). Organization of transcription. Cold Spring Harb. Perspect. Biol. 2, a000729 [PubMed].
Cook, P.R. (2010). A model for all genomes; the role of transcription factories. J. Mol. Biol. 395, 1–10. [PubMed]
Göndör, A., and Ohlsson, R. (2009). Chromosome crosstalk in three dimensions. Nature 461, 212-217. [Pubmed]
Sutherland, H., and Bickmore, W.A. (2009). Transcription factories: gene expression in unions? Nat. Rev. Genet. 10, 457-466. [PubMed]
Ghamari, A., van de Corput, M.P., Thongjuea, S., van Cappellen, W.A., van Ijcken, W., van Haren, J., Soler, E., Eick, D., Lenhard, B., and Grosveld, F.G. (2013). In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev. 27, 767-777. [PubMed]
Nucleolar factories containing polymerase I
Figure: 4-16.
Reference:
Hozák, P., Cook, P.R., Schöfer, C., Mosgöller, W. and Wachtler, F. (1994). Site of transcription of ribosomal RNA and intra-nucleolar structure in HeLa cells. J. Cell Sci. 107, 639-648. [PubMed] [Full text]
Additional reference:
Boisvert, F.M., van Koningsbruggen, S., Navascués, J., and Lamond, A.I. (2007). The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574-585. [PubMed]
McKeown, P.C., and Shaw, P.J. (2009). Chromatin: linking structure and function in the nucleolus. Chromosoma 118, 11-23. [PubMed]
Extra-nucleolar factories containing polymerases II and III
Figure: 4-17.
Reference:
Jackson, D.A., Hassan, A.B., Errington, R.J. and Cook, P.R. (1993). Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065. [PubMed]
Iborra, F.J., Pombo, A., Jackson, D.A. and Cook, P.R. (1996). Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. J. Cell Sci. 109, 1427-1436. [PubMed] [Full text]
Pombo, A., Jackson, D.A., Hollinshead, M., Wang, Z., Roeder, R.G. and Cook, P.R. (1999). Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241-2253. [PubMed] [Full text]
Additional reference:
Eskiw, C.H., Rapp, A., Carter, D.R.F., and Cook, P.R. (2008). RNA polymerase II activity is located on the surface of ~87 nm protein-rich transcription factories. J. Cell Sci. 121 , 1999-2007. [ PubMed ]
Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., Chew, E.G., et al. (2009). An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58-64. [PubMed]
Hopper, A.K., Pai, D.A., and Engelke, D.R. (2010). Cellular dynamics of tRNAs and their genes. FEBS Lett. 584, 310-317. [PubMed]
Osborne, C.S., Chakalova, C., Brown, K.E., Carter, D., Horton, A., Debrand, E., Goyenechea, B., Mitchell, J.A., Lopes, S., Reik, W. and Fraser, P. (2004). Active genes dynamically co-localize to shared sites of ongoing transcription. Nat. Genet. 36, 1065-1071. [PubMed]
Dynamics
Reference:
Emerman, M. and Temin, H.M. (1984). Genes with promoters in retrovirus vectors can be independently suppressed by an epigenetic mechanism. Cell 39, 459-500.
Pombo, A., Cuello, P., Schul, W., Yoon, J.-B., Roeder, R.G., Cook, P.R. and Murphy, S. (1998). Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle. EMBO J. 17, 1768-1778. [PubMed] [Full text]
Cook, P.R. (1999). The organization of replication and transcription. Science 284, 1790-1795. [PubMed]
Additional reference:
Chubb, J.R. and Bickmore, W.A. (2003). Considering nuclear compartmentalization in the light of nuclear dynamics. Cell 112, 403-406. [PubMed]
Core, L.J., and Lis, J.T. (2008). Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791-1792. [PubMed]
Price, D.H. (2008). Poised polymerases: on your mark...get set...go! Mol. Cell 30, 7-10. [PubMed]
Processing and transport of polymerase II transcripts
Reference:
Nevins, J.R. (1983). The pathway of eukaryotic mRNA formation. Annu Rev. Biochem. 52, 441-466.
Additional reference:
Bentley DL. (2014). Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163-175. [PubMed]
Capping the 5' end
Reference:
Hirose, Y. and Manley, J.L. (2000). RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415-1429.
Additional reference:
Gu, M., and Lima, C.D. (2005). Processing the message: structural insights into capping and decapping mRNA. Curr. Opin. Struct. Biol. 15, 99-106. [PubMed]
Schoenberg, D.R., and Maquat, L.E. (2009). Re-capping the message. Trends Biochem. Sci. 34, 435-342. [PubMed]
Box 4-6. Analyzing caps
Reference:
Banerjee, A.K. (1980). Cap structure in mRNA. Microbiol. Revs 44, 175-205.
Polyadenylating the 3' end
Reference:
Zhao, J., Hyman, L. and Moore, C. (1999). Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Molec. Biol. Rev. 63, 405-445. [PubMed] [Full text]
Additional reference:
Proudfoot, N.J. (2011). Ending the message: poly(A) signals then and now. Genes Dev. 25, 1770-1782. [PubMed]
Shi, Y., Di Giammartino, D.C., Taylor, D., Sarkeshik, A., Rice, W.J., Yates, J.R., Frank, J., and Manley, J.L. (2009). Molecular architecture of the human pre-mRNA 3' processing complex. Mol. Cell 33, 365-376. [PubMed]
Splicing the middle
Figure: 4-18, 4-19, 4-20.
Reference:
Chow, L.T., Gelinas, R.E., Broker, T.R. and Roberts, R.J. (1977). An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA. Cell 35, 1-8. [PubMed]
Jeffreys, A.J. and Flavell, R.A. (1977). The rabbit β-globin gene contains a large insert in the coding sequence. Cell 12, 1097-1108.
Sharp, P.A. (1994). Split genes and RNA splicing. Cell 77, 805-815.
Zhang, G., Taneja, K.L., Singer, R.H. and Green, M.R. (1994). Localization of pre-mRNA splicing in mammalian nuclei. Nature 372, 809-812. [PubMed]
Additional reference:
Chen, W., and Moore, M.J. (2015). Spliceosomes. Curr. Biol. 25, R181-183. [PubMed]
Fica, S.M., Tuttle, N., Novak, T., Li, N.S., Lu, J., Koodathingal, P., Dai, Q., Staley, J.P., and Piccirilli, J.A. (2013). RNA catalyses nuclear pre-mRNA splicing. Nature 503, 229-234. [PubMed]
Keren, H., Lev-Maor, G., and Ast, G. (2010). Alternative splicing and evolution: diversification, exon definition and function. Nat. Rev. Genet.11, 345-355. [PubMed]
Tilgner, H., Knowles, D.G., Johnson, R., Davis, C.A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T.R., and Guigó, R. (2012). Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 22, 1616-1625. [PubMed]
Swinburne, I.A., and Silver, P.A. (2008). Intron delays and transcriptional timing during development. Dev. Cell. 14, 324-330. [PubMed]
Wang, G.S., and Cooper, T.A. (2007). Splicing in disease: disruption of the splicing code and the decoding machinery. Nat. Rev. Genet. 8, 749-761. [PubMed]
Web link:
http://jcs.biologists.org/cgi/content/full/117/26/6261 Cell Science at a Glance gives an overview of splicing.
http://www.ergito.com/ Access to the 'Great Experiments' pages is free, so sign in and go to Phillip Sharp on 'The discovery of RNA splicing', Richard Roberts on 'The discovery of split genes and RNA splicing', and Joan Steitz on 'The discovery of snRNPs and their role in splicing.'
Box 4-7. Autoimmune antibodies
Reference:
Damjanov, I. and Linder, M.D. (1996). 'Anderson's pathology'. Mosby-Year Book, Inc. St Louis.
Packaging transcripts into ribonucleoprotein particles
Reference:
Dreyfuss, G. (1986). Stucture and function of nuclear and cytoplasmic ribonucleoprotein particles. Annu Rev. Cell Biol. 2, 459-498.
Additional reference:
Carmody, S.R., and Wente, S.R. (2009). mRNA nuclear export at a glance. J Cell Sci 122, 1933-1937. [PubMed]
He, Y., and Smith, R. (2009). Nuclear functions of heterogeneous nuclear ribonucleoproteins A/B. Cell Mol. Life Sci. 66, 1239-1256. [PubMed]
Visa, N., and Percipalle, P. (2010). Nuclear functions of actin. Cold Spring Harb. Perspect. Biol. 2, a000620. [PubMed]
Fidelity and quality control
Figure: 4-21.
Reference:
Thomas, M.J., Platas, A.A. and Hawley, D.K. (1998). Transcriptional fidelity and proofreading by RNA polymerase II. Cell 93, 627-637. [PubMed]
Hilleren, P. and Parker, R. (1999). Mechanisms of mRNA surveillance in eukaryotes. Annu. Rev. Genet. 33, 229-260. [PubMed]
Jackson, D.A., Pombo, A., Iborra, F.J. (2000). The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells. FASEB J. 14, 242-254. [PubMed] [Full text]
Additional reference:
Durand, S., and Lykke-Andersen, J. (2011). SnapShot: Nonsense-mediated mRNA decay. Cell 145, 324-324. [PubMed]
Kervestin, S., and Jacobson, A. (2012). NMD: a multifaceted response to premature translational termination. Nat. Rev. Mol. Cell Biol. 13, 700-712. [PubMed]
Iborra, F.J., Jackson, D.A. and Cook, P.R. (2004). The case for nuclear translation. J. Cell Sci. 117, 5713-5720. [PubMed] [PDF file, with permission of J. Cell Sci (http://jcs.biologists.org).]
Parker, R. (2012). RNA degradation in Saccharomyces cerevisae. Genetics 191, 671-702. [PubMed]
Nuclear translation (new section)
Reference:
Iborra, F.J., Jackson, D.A. and Cook, P.R. (2001). Coupled transcription and translation within nuclei of mammalian cells. Science 293, 1139-1142. [PubMed]
Iborra, F.J., Jackson, D.A. and Cook, P.R. (2004). The case for nuclear translation. J. Cell Sci. 117, 5713-5720. [PubMed] [PDF file, with permission of J. Cell Sci (http://jcs.biologists.org).]
The organization of processing
Figure: 4-22.
Reference:
Hirose, Y. and Manley, J.L. (2000). RNA polymerase II and the integration of nuclear events. Genes Dev. 14 1415-1429.
Lewis, J.D. and Tollervey, D. (2000). Like attracts like: getting RNA processing together in the nucleus. Science 288, 1385-1389. [PubMed]
Additional reference:
Moore, M.J., and Proudfoot, N.J. (2009). Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688-700. [PubMed]
Sheth, U. and Parker, R. (2003). Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300, 805-808. [PubMed]
Wetterberg, I., Zhao, J., Masich, S., Wieslander, L. and Skoglund, U. (2001). In situ transcription and splicing in the Balbiani ring 3 gene. EMBO J. 20, 2564-2574. [PubMed] [Full text]
Transport to the cytoplasm
Reference:
Iborra, F.J., Jackson, D.A. and Cook, P.R. (1998). The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins. J. Cell Sci. 111, 2269-2282. [PubMed] [Full text]
Stutz, F. and Rosbash, M. (1998). Nuclear RNA export. Genes Dev. 12, 3303-3319. [Full text]
Additional reference:
Carmody, S.R., and Wente, S.R. (2009). mRNA nuclear export at a glance. J Cell Sci 122, 1933-1937. [PubMed]
Grünwald, D., Singer, R.H., and Rout, M. (2011). Nuclear export dynamics of RNA-protein complexes. Nature 475, 333-341. [PubMed]
Niño, C.A., Hérissant, L., Babour, A., and Dargemont, C. (2013). mRNA nuclear export in yeast. Chem. Rev. 113, 8523-8545. [PubMed]
Visa, N., and Percipalle, P. (2010). Nuclear functions of actin. Cold Spring Harb. Perspect. Biol. 2, a000620. [PubMed]