-
1
-
-
80052979140
-
Mechanisms and consequences of alternative polyadenylation
-
Di Giammartino, D.C., Nishida, K. & Manley, J.L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866 (2011).
-
(2011)
Mol. Cell
, vol.43
, pp. 853-866
-
-
Di Giammartino, D.C.1
Nishida, K.2
Manley, J.L.3
-
2
-
-
80052447253
-
Ending the message: Poly(A) signals then and now
-
Proudfoot, N.J. Ending the message: poly(A) signals then and now. Genes Dev. 25, 1770-1782 (2011).
-
(2011)
Genes Dev
, vol.25
, pp. 1770-1782
-
-
Proudfoot, N.J.1
-
3
-
-
76249122261
-
The spen family protein FPA controls alternative cleavage and polyadenylation of RNA
-
Hornyik, C., Terzi, L.C. & Simpson, G.G. The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev. Cell 18, 203-213 (2010).
-
(2010)
Dev. Cell
, vol.18
, pp. 203-213
-
-
Hornyik, C.1
Terzi, L.C.2
Simpson, G.G.3
-
4
-
-
0032541403
-
Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae
-
Greger, I.H. & Proudfoot, N.J. Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae. EMBO J. 17, 4771-4779 (1998).
-
(1998)
EMBO J
, vol.17
, pp. 4771-4779
-
-
Greger, I.H.1
Proudfoot, N.J.2
-
5
-
-
79952592361
-
Autoregulation of convergent RNAi genes in fssion yeast
-
Gullerova, M., Moazed, D. & Proudfoot, N.J. Autoregulation of convergent RNAi genes in fssion yeast. Genes Dev. 25, 556-568 (2011).
-
(2011)
Genes Dev
, vol.25
, pp. 556-568
-
-
Gullerova, M.1
Moazed, D.2
Proudfoot, N.J.3
-
6
-
-
79955475464
-
Unravelling the means to an end: RNA polymerase II transcription termination
-
Kuehner, J.N., Pearson, E.L. & Moore, C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat. Rev. Mol. Cell Biol. 12, 283-294 (2011).
-
(2011)
Nat. Rev. Mol. Cell Biol.
, vol.12
, pp. 283-294
-
-
Kuehner, J.N.1
Pearson, E.L.2
Moore, C.3
-
7
-
-
3543007130
-
Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing
-
Meyers, B.C. et al. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat. Biotechnol. 22, 1006-1011 (2004).
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1006-1011
-
-
Meyers, B.C.1
-
8
-
-
0242300620
-
Empirical analysis of transcriptional activity in the Arabidopsis genome
-
Yamada, K. et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842-846 (2003).
-
(2003)
Science
, vol.302
, pp. 842-846
-
-
Yamada, K.1
-
9
-
-
20144386497
-
Identifcation of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
-
Stolc, V. et al. Identifcation of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl. Acad. Sci. USA 102, 4453-4458 (2005).
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 4453-4458
-
-
Stolc, V.1
-
10
-
-
79961084431
-
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation
-
Wu, X. et al. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Natl. Acad. Sci. USA 108, 12533-12538 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 12533-12538
-
-
Wu, X.1
-
11
-
-
0018716671
-
A detailed model of reverse transcription and tests of crucial aspects
-
Gilboa, E., Mitra, S.W., Goff, S. & Baltimore, D. A detailed model of reverse transcription and tests of crucial aspects. Cell 18, 93-100 (1979).
-
(1979)
Cell
, vol.18
, pp. 93-100
-
-
Gilboa, E.1
Mitra, S.W.2
Goff, S.3
Baltimore, D.4
-
12
-
-
0014933641
-
DNA-directed DNA polymerase activity in oncogenic RNA viruses
-
Spiegelman, S. et al. DNA-directed DNA polymerase activity in oncogenic RNA viruses. Nature 227, 1029-1031 (1970).
-
(1970)
Nature
, vol.227
, pp. 1029-1031
-
-
Spiegelman, S.1
-
13
-
-
0037197827
-
Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
-
Nam, D.K. et al. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc. Natl. Acad. Sci. USA 99, 6152-6156 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6152-6156
-
-
Nam, D.K.1
-
14
-
-
77957893329
-
Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
-
Houseley, J. & Tollervey, D. Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS ONE 5, e12271 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Houseley, J.1
Tollervey, D.2
-
15
-
-
36148972085
-
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
-
Perocchi, F., Xu, Z., Clauder-Munster, S. & Steinmetz, L.M. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res. 35, e128 (2007).
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Perocchi, F.1
Xu, Z.2
Clauder-Munster, S.3
Steinmetz, L.M.4
-
16
-
-
78650972252
-
Formation regulation and evolution of Caenorhabditis elegans 3′UTRs
-
Jan, C.H., Friedman, R.C., Ruby, J.G. & Bartel, D.P. Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature 469, 97-101 (2011).
-
(2011)
Nature
, vol.469
, pp. 97-101
-
-
Jan, C.H.1
Friedman, R.C.2
Ruby, J.G.3
Bartel, D.P.4
-
17
-
-
77956340995
-
Comprehensive comparative analysis of strand-specifc RNA sequencing methods
-
Levin, J.Z. et al. Comprehensive comparative analysis of strand-specifc RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
-
18
-
-
78649910014
-
Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
-
Ozsolak, F. et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143, 1018-1029 (2010).
-
(2010)
Cell
, vol.143
, pp. 1018-1029
-
-
Ozsolak, F.1
-
19
-
-
7044269115
-
Nontemplated nucleotide addition prior to polyadenylation: A comparison of Arabidopsis cDNA and genomic sequences
-
Jin, Y. & Bian, T. Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA 10, 1695-1697 (2004).
-
(2004)
RNA
, vol.10
, pp. 1695-1697
-
-
Jin, Y.1
Bian, T.2
-
20
-
-
27244444905
-
Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures
-
Loke, J.C. et al. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 138, 1457-1468 (2005).
-
(2005)
Plant Physiol
, vol.138
, pp. 1457-1468
-
-
Loke, J.C.1
-
21
-
-
77954847055
-
The landscape of C. elegans 3′UTRs
-
Mangone, M. et al. The landscape of C. elegans 3′UTRs. Science 329, 432-435 (2010).
-
(2010)
Science
, vol.329
, pp. 432-435
-
-
Mangone, M.1
-
22
-
-
81755172088
-
Autoregulation of the nonsense-mediated mRNA decay pathway in human cells
-
Yepiskoposyan, H., Aeschimann, F., Nilsson, D., Okoniewski, M. & Muhlemann, O. Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA 17, 2108-2118 (2011).
-
(2011)
RNA
, vol.17
, pp. 2108-2118
-
-
Yepiskoposyan, H.1
Aeschimann, F.2
Nilsson, D.3
Okoniewski, M.4
Muhlemann, O.5
-
23
-
-
60149090021
-
The many pathways of RNA degradation
-
Houseley, J. & Tollervey, D. The many pathways of RNA degradation. Cell 136, 763-776 (2009).
-
(2009)
Cell
, vol.136
, pp. 763-776
-
-
Houseley, J.1
Tollervey, D.2
-
24
-
-
37349038984
-
Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome
-
Chekanova, J.A. et al. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131, 1340-1353 (2007).
-
(2007)
Cell
, vol.131
, pp. 1340-1353
-
-
Chekanova, J.A.1
-
25
-
-
0037264089
-
Plant snoRNAs: Functional evolution and new modes of gene expression
-
Brown, J.W., Echeverria, M. & Qu, L.H. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 8, 42-49 (2003).
-
(2003)
Trends Plant Sci
, vol.8
, pp. 42-49
-
-
Brown, J.W.1
Echeverria, M.2
Qu, L.H.3
-
26
-
-
45849150615
-
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome
-
Wu, J.Q. et al. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 9, R3 (2008).
-
(2008)
Genome Biol
, vol.9
-
-
Wu, J.Q.1
-
27
-
-
77952905505
-
Most "dark matter" transcripts are associated with known genes
-
van Bakel, H., Nislow, C., Blencowe, B.J. & Hughes, T.R. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 8, e1000371 (2010).
-
(2010)
PLoS Biol.
, vol.8
-
-
Van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
Hughes, T.R.4
-
28
-
-
44349101881
-
Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster
-
Okamura, K., Balla, S., Martin, R., Liu, N. & Lai, E.C. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat. Struct. Mol. Biol. 15, 581-590 (2008).
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 581-590
-
-
Okamura, K.1
Balla, S.2
Martin, R.3
Liu, N.4
Lai, E.C.5
-
29
-
-
29244490062
-
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
-
Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R. & Zhu, J.K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279-1291 (2005).
-
(2005)
Cell
, vol.123
, pp. 1279-1291
-
-
Borsani, O.1
Zhu, J.2
Verslues, P.E.3
Sunkar, R.4
Zhu, J.K.5
-
30
-
-
33845202133
-
A pathogen-inducible endogenous siRNA in plant immunity
-
Katiyar-Agarwal, S. et al. A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl. Acad. Sci. USA 103, 18002-18007 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 18002-18007
-
-
Katiyar-Agarwal, S.1
-
31
-
-
1442313922
-
Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase
-
Kaufmann, I., Martin, G., Friedlein, A., Langen, H. & Keller, W. Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase. EMBO J. 23, 616-626 (2004).
-
(2004)
EMBO J
, vol.23
, pp. 616-626
-
-
Kaufmann, I.1
Martin, G.2
Friedlein, A.3
Langen, H.4
Keller, W.5
-
32
-
-
0028351948
-
The contribution of AAUAAA and the upstream element UUUGUA to the effciency of mRNA 3′-end formation in plants
-
Rothnie, H.M., Reid, J. & Hohn, T. The contribution of AAUAAA and the upstream element UUUGUA to the effciency of mRNA 3′-end formation in plants. EMBO J. 13, 2200-2210 (1994).
-
(1994)
EMBO J
, vol.13
, pp. 2200-2210
-
-
Rothnie, H.M.1
Reid, J.2
Hohn, T.3
-
33
-
-
0026078053
-
A dissection of the caulifower mosaic virus polyadenylation signal
-
Sanfaçon, H., Brodmann, P. & Hohn, T. A dissection of the caulifower mosaic virus polyadenylation signal. Genes Dev. 5, 141-149 (1991).
-
(1991)
Genes Dev.
, vol.5
, pp. 141-149
-
-
Sanfaçon, H.1
Brodmann, P.2
Hohn, T.3
-
34
-
-
68749113985
-
Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
-
Mayr, C. & Bartel, D.P. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684 (2009).
-
(2009)
Cell
, vol.138
, pp. 673-684
-
-
Mayr, C.1
Bartel, D.P.2
-
35
-
-
78751477191
-
Gene silencing by microRNAs: Contributions of translational repression and mRNA decay
-
Huntzinger, E. & Izaurralde, E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet. 12, 99-110 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 99-110
-
-
Huntzinger, E.1
Izaurralde, E.2
-
36
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
Bartel, D.P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233 (2009).
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
37
-
-
0037173089
-
Transcriptional collision between convergent genes in budding yeast
-
Prescott, E.M. & Proudfoot, N.J. Transcriptional collision between convergent genes in budding yeast. Proc. Natl. Acad. Sci. USA 99, 8796-8801 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8796-8801
-
-
Prescott, E.M.1
Proudfoot, N.J.2
-
38
-
-
34447132252
-
Distinct expression patterns of natural antisense transcripts in Arabidopsis
-
Henz, S.R. et al. Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol. 144, 1247-1255 (2007).
-
(2007)
Plant Physiol
, vol.144
, pp. 1247-1255
-
-
Henz, S.R.1
-
39
-
-
24644488895
-
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation
-
Jen, C.H., Michalopoulos, I., Westhead, D.R. & Meyer, P. Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol. 6, R51 (2005).
-
(2005)
Genome Biol.
, vol.6
-
-
Jen, C.H.1
Michalopoulos, I.2
Westhead, D.R.3
Meyer, P.4
-
40
-
-
78149425378
-
Crosstalk between mRNA 3′ end processing and transcription initiation
-
Mapendano, C.K., Lykke-Andersen, S., Kjems, J., Bertrand, E. & Jensen, T.H. Crosstalk between mRNA 3′ end processing and transcription initiation. Mol. Cell 40, 410-422 (2010).
-
(2010)
Mol. Cell
, vol.40
, pp. 410-422
-
-
Mapendano, C.K.1
Lykke-Andersen, S.2
Kjems, J.3
Bertrand, E.4
Jensen, T.H.5
-
41
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
-
42
-
-
70349956497
-
Direct RNA sequencing
-
Ozsolak, F. et al. Direct RNA sequencing. Nature 461, 814-818 (2009).
-
(2009)
Nature
, vol.461
, pp. 814-818
-
-
Ozsolak, F.1
-
43
-
-
70349739736
-
The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets
-
Nicol, J.W., Helt, G.A., Blanchard, S.G. Jr., Raja, A. & Loraine, A.E. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730-2731 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2730-2731
-
-
Nicol, J.W.1
Helt, G.A.2
Blanchard Jr., S.G.3
Raja, A.4
Loraine, A.E.5
-
44
-
-
33751009398
-
SnoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome
-
Yang, J.H. et al. snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res. 34, 5112-5123 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5112-5123
-
-
Yang, J.H.1
-
45
-
-
66249110326
-
Mining small RNA sequencing data: A new approach to identify small nucleolar RNAs in Arabidopsis
-
Chen, H.M. & Wu, S.H. Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis. Nucleic Acids Res. 37, e69 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Chen, H.M.1
Wu, S.H.2
-
46
-
-
77953234404
-
Plant U13 orthologues and orphan snoRNAs identifed by RNomics of RNA from Arabidopsis nucleoli
-
Kim, S.H. et al. Plant U13 orthologues and orphan snoRNAs identifed by RNomics of RNA from Arabidopsis nucleoli. Nucleic Acids Res. 38, 3054-3067 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 3054-3067
-
-
Kim, S.H.1
-
47
-
-
67650100790
-
Processing of a dicistronic tRNA-snoRNA precursor: Combined analysis in vitro and in vivo reveals alternate pathways and coupling to assembly of snoRNP
-
Barbezier, N. et al. Processing of a dicistronic tRNA-snoRNA precursor: combined analysis in vitro and in vivo reveals alternate pathways and coupling to assembly of snoRNP. Plant Physiol. 150, 1598-1610 (2009).
-
(2009)
Plant Physiol
, vol.150
, pp. 1598-1610
-
-
Barbezier, N.1
|