| References |
|
|
Ara T,
Lopez F,
Ritchie W,
Benech P and
Gautheret D
(2006)
Conservation of alternative polyadenylation patterns in mammalian genes.
BMC Genomics
7:
189.
|
|
|
Barbosa-Morais NL,
Carmo-Fonseca M and
Aparicio S
(2006)
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion.
Genome Research
16:
66–77.
|
|
|
Beaudoing E,
Freier S,
Wyatt JR,
Claverie JM and
Gautheret D
(2000)
Patterns of variant polyadenylation signal usage in human genes.
Genome Research
10:
1001–1010.
|
|
|
Chen JM,
Ferec C and
Cooper DN
(2006)
A systematic analysis of disease-associated variants in the 3¢ regulatory regions of human protein-coding genes I: general principles and overview.
Human Genetics
120:
1–21.
|
|
|
Cheng J,
Kapranov P,
Drenkow J et al.
(2005)
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
Science
308:
1149–1154.
|
|
|
Colgan DF and
Manley JL
(1997)
Mechanism and regulation of mRNA polyadenylation.
Genes & Development
11:
2755–2766.
|
|
|
Edwalds-Gilbert G,
Veraldi KL and
Milcarek C
(1997)
Alternative poly(A) site selection in complex transcription units: means to an end?
Nucleic Acids Research
25:
2547–2561.
|
|
|
Houseley J,
LaCava J and
Tollervey D
(2006)
RNA-quality control by the exosome.
Nature Reviews. Molecular Cell Biology
7:
529–539.
|
|
|
Hu J,
Lutz CS,
Wilusz J and
Tian B
(2005)
Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation.
RNA
11:
1485–1493.
|
|
|
Lee JY,
Yeh I,
Park JY and
Tian B
(2007)
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.
Nucleic Acids Research
35:
D165–D168.
|
|
|
Paule MR and
White RJ
(2000)
SURVEY AND SUMMARY Transcription by RNA polymerases I and III.
Nucl Acids Research
28:
1283–1298.
|
|
|
Proudfoot NJ,
Furger A and
Dye MJ
(2002)
Integrating mRNA processing with transcription.
Cell
108:
501–512.
|
|
|
Richter JD
(1999)
Cytoplasmic polyadenylation in development and beyond.
Microbiology and Molecular Biology Reviews
63:
446–456.
|
|
|
Rosonina E,
Kaneko S and
Manley JL
(2006)
Terminating the transcript: breaking up is hard to do.
Genes & Development
20:
1050–1056.
|
|
|
Salisbury J,
Hutchison KW and
Graber JH
(2006)
A multispecies comparison of the metazoan 3¢-processing downstream elements and the CstF-64 RNA recognition motif.
BMC Genomics
7:
55.
|
|
|
Tian B,
Hu J,
Zhang H and
Lutz CS
(2005)
A large-scale analysis of mRNA polyadenylation of human and mouse genes.
Nucleic Acids Research
33:
201–212.
|
|
|
Weiner AM
(2005)
E Pluribus Unum: 3¢ end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs.
Molecular Cell
20:
168–170.
|
|
|
Wickens M,
Anderson P and
Jackson RJ
(1997)
Life and death in the cytoplasm: messages from the 3¢ end.
Current Opinion in Genetics & Development
7:
220–232.
|
|
|
Yan J and
Marr TG
(2005)
Computational analysis of 3¢-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat.
Genome Research
15:
369–375.
|
|
|
Zhang H,
Lee JY and
Tian B
(2005)
Biased alternative polyadenylation in human tissues.
Genome Biology
6:
R100.
|
|
|
Zhang XH and
Chasin LA
(2006)
Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons.
Proceedings of the National Academy of Sciences of the USA
103:
13427–13432.
|
|
|
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.
Microbiology and Molecular Biology Reviews
63:
405–445.
|
| Further Reading |
|
|
Bucheli ME,
He X,
Kaplan CD,
Moore CL and
Buratowski S
(2007)
Polyadenylation site choice in yeast is affected by competition between Npl3 and polyadenylation factor CFI.
RNA
13:
1756–1764.
|
|
|
Danckwardt S,
Kaufmann I,
Gentzel M et al.
(2007)
Splicing factors stimulate polyadenylation via USEs at non-canonical 3¢ end formation signals.
EMBO Journal
26:
2658–2669.
|
|
|
Graham RR,
Kyogoku C,
Sigurdsson S et al.
(2007)
Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus.
Proceedings of the National Academy of Sciences of the USA
104:
6758–6763.
|
|
|
Hall-Pogar T,
Liang S,
Hague LK and
Lutz CS
(2007)
Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3¢-UTR.
RNA
13:
1103–1115.
|
|
|
Kaneko S and
Manley JL
(2005)
The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3¢ end formation.
Molecular Cell
20:
91–103.
|
|
|
Kim Guisbert KS,
Li H and
Guthrie C
(2007)
Alternative 3¢ pre-mRNA processing in Saccharomyces cerevisiae is modulated by Nab4/Hrp1 in vivo.
PLoS Biology
5:
e6.
|
|
|
Kubo T,
Wada T,
Yamaguchi Y,
Shimizu A and
Handa H
(2006)
Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3¢-UTRs.
Nucleic Acids Research
34:
6264–6271.
|
|
|
Kyburz A,
Friedlein A,
Langen H and
Keller W
(2006)
Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3¢ end processing and splicing.
Molecular Cell
23:
195–205.
|
|
|
Millevoi S,
Loulergue C,
Dettwiler S et al.
(2006)
An interaction between U2AF 65 and CF I(m) links the splicing and 3¢ end processing machineries.
EMBO Journal
25:
4854–4864.
|
|
|
Peterson ML,
Bingham GL and
Cowan C
(2006)
Multiple features contribute to the use of the immunoglobulin M secretion-specific poly(A) signal but are not required for developmental regulation.
Molecular and Cellular Biology
26:
6762–6771.
|
|
|
Sheets MD,
Ogg SC and
Wickens MP
(1990)
Point mutations in AAUAAA and the poly (A) addition site: effects on the accuracy and efficiency of cleavage and polyadenylation in vitro.
Nucleic Acids Research
18:
5799–5805.
|
|
|
Venkataraman K,
Brown KM and
Gilmartin GM
(2005)
Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition.
Genes & Development
19:
1315–1327.
|
|
|
Zhu H,
Zhou HL,
Hasman RA and
Lou H
(2007)
Hu proteins regulate polyadenylation by blocking sites containing U-rich sequences.
The Journal of Biological Chemistry
282:
2203–2210.
|
