An extensive network of coupling among gene expression machines

Nature

Volumn 416, Issue 6880, 2002, Pages 499-506

  Maniatis, Tom ^a   Reed, Robin ^b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; RNA;

GENE EXPRESSION;

GENETIC ENGINEERING;

GENETICS;

ARTICLE; COUPLING FACTOR; ENZYME SPECIFICITY; EUKARYOTE EVOLUTION; GENE EXPRESSION REGULATION; MACHINE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DEGRADATION; RNA PROCESSING; RNA TRANSLATION; TRANSCRIPTION REGULATION;

GENE EXPRESSION; MODELS, GENETIC; POLY A; RNA CAPS; RNA POLYMERASE II; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 0037041395     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/416499a     Document Type: Article

References (100)

1. Coupling RNA polymerase II transcription with pre-mRNA processing
2. RNA polymerase II and the integration of nuclear events
3. Connecting transcription to messenger RNA processing
4. The ends of the affair: Capping and polyadenylation
5. Coordination between transcription and pre-mRNA processing
6. Reversible phosphorylation of the C-terminal domain of RNA polymerase II
7. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription
8. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain
9. Characterization of the residues phosphorylated in vitro by different C-terminal domain kinases
10. P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II
11. 5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II
12. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the of the RNA polymerase II carboxy-terminal domain
13. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription
14. Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: Different functions for different segments of the CTD
15. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
16. Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme
17. Dynamic association of capping enzymes with transcribing RNA polymerase II
18. Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain
19. Interaction between P-TEFb and the C-terminal domain of RNA polymerase II activates transcriptional elongation from sites upstream or downstream of target genes
20. Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro
21. Positive transcription elongation factor B phosphorylates hSPT5 and RNA polymerase II carboxyl-terminal domain independently of cyclin-dependent kinase-activating kinase
22. Transcription elongation factor hSPT 5 stimulates mRNA capping
23. Stimulatory effect of splicing factors on transcriptional elongation
24. NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II
25. Tat-SF1 protein associates with RAP30 and human SPT5 proteins
26. CUS2, a yeast homolog of human Tat-SF1, rescues function of misfolded U2 through an unusual RNA recognition motif
27. A handful of intron -containing genes produces the lion's share of yeast mRNA
28. A human RNA polymerase II-containing complex associated with factors necessary for spliceosome assembly
29. A CTD function linking transcription to splicing
30. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II
31. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals
32. Exon recognition in vertebrate splicing
33. Co-transcriptional splicing of pre-messenger RNAs: C-Considerations for the mechanism of alternative splicing
34. A human papillomavirus E2 transcriptional activator. The interactions with cellular splicing factors and potential function in pre-mRNA processing
35. A novel transcriptional coactivator, p52, functionally interacts with the essential splicing factor ASF/SF2
36. Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1
37. Human staga complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo
38. Sorting out the complexity of SR protein functions
39. SR proteins are 'locators' of the RNA splicing machinery
40. A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis
41. Functional association between promoter structure and transcript alternative splicing
42. Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer
43. Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing
44. Effects of RNA secondary structure on alternative splicing of pre-mRNA: Is folding limited to a region behind the transcribing RNA polymerase?
45. Co-transcriptional commitment to alternative splice site selection
46. A nuclear cap-binding complex facilitates association of UI snRNP with the cap-proximal 5′ splice site
47. The yeast splicing factor Mud 13p is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex
48. The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3′-end processing and splicing
49. SRm 160 splicing coactivator promotes transcript 3′-end cleavage
50. Mechanisms of fidelity in pre-mRNA splicing
51. How RNA polymerase II terminates transcription in higher eukaryotes
52. Coupling termination of transcription to messenger RNA maturation in yeast
53. Role of RNA polymerase II carboxy-terminal domain in coordinating transcription with RNA processing
54. Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II
55. EM visualization of transcription by RNA polymerase II: Downstream termination requires a poly(A) signal but not transcript cleavage
56. Mechanism of poly(A) signal transduction to RNA polymerase II in vitro
57. Transcriptional termination factors for RNA polymerase II in yeast
58. Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination
59. Inefficient processing impairs release of RNA from the site of transcription
60. A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription
61. A role for Cajal bodies in assembly of the nuclear transcription machinery
62. Functional architecture in the cell nucleus
63. Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway
64. The dynamics of a pre-mRNA splicing factor in living cells
65. Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo
66. RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo
67. High mobility of proteins in the mammalian cell nucleus
68. Active RNA polymerases are localized within discrete transcription "factories" in human nuclei
69. The organization of replication and transcription
70. In situ transcription and splicing in the Balbiani ring 3 gene
71. Splicing is required for rapid and efficient mRNA export in metazoans
72. Pre-mRNA splicing alters mRNP composition: Evidence for stable association of proteins at exon-exon junctions
73. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans
74. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions
75. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly
76. Splicing factor Sub 2p is required for nuclear mRNA export through its interaction with Yra1p
77. The DExH/D box protein HEL/UAP 56 is essential for mRNA nuclear export in Drosophila
78. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay
79. Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm
80. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1
81. The Y14 protein communicates to the cytoplasm the position of exon-exon junctions
82. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex
83. The C-terminal domain of TAP interacts with the nuclear pore complex and promotes export of specific CTE-bearing RNA substrates
84. Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores
85. The DECD box putative ATPase Sub2p is an early mRNA export factor
86. A new view of mRNA export: Separating the wheat from the chaff
87. Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA
88. Quality control of mRNA 3′ -end processing is linked to the nuclear exosome
89. Messenger RNAs are recruited for nuclear export during transcription
90. Rna15 interaction with the a-rich yeast polyadenylation signal is an essential step in mRNA 3′-end formation
91. Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3′ -end formation in yeast
92. The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for nonsense-mediated mRNA decay
93. Quality control of mRNA function
94. Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)
95. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon
96. A perfect message: RNA surveillance and nonsense-mediated decay
97. Precursor RNAs harboring nonsense codons accumulate near the site of transcription
98. Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20
99. Should we kill the messenger? The role of the surveillance complex in translation termination and mRNA turnover