-
1
-
-
54249116230
-
-
Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961). A seminal work on the regulation of gene expression; the first to suggest that RNA could have a role.
-
Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961). A seminal work on the regulation of gene expression; the first to suggest that RNA could have a role.
-
-
-
-
2
-
-
12344291073
-
Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
-
Johnson, J. M., Edwards, S., Shoemaker, D. & Schadt, E. E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21, 93-102 (2005).
-
(2005)
Trends Genet
, vol.21
, pp. 93-102
-
-
Johnson, J.M.1
Edwards, S.2
Shoemaker, D.3
Schadt, E.E.4
-
3
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149-1154 (2005).
-
(2005)
Science
, vol.308
, pp. 1149-1154
-
-
Cheng, J.1
-
4
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) project
-
ENCODE Project Consortium
-
ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306, 636-640 (2004).
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
5
-
-
34249069108
-
The ENCODE pilot project: Identification and analysis of functional elements in 1% of the human genome
-
ENCODE Project Consortium, in the press
-
ENCODE Project Consortium. The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome. Nature (in the press).
-
Nature
-
-
-
6
-
-
4344623260
-
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
-
Imanishi, T. et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2, e162 (2004).
-
(2004)
PLoS Biol
, vol.2
-
-
Imanishi, T.1
-
7
-
-
24644519490
-
-
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005). This reference provides an unparalleled insight into the complexity of the mouse transcriptome on the basis of sequencing of full-length cDNAs and cDNA tags.
-
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005). This reference provides an unparalleled insight into the complexity of the mouse transcriptome on the basis of sequencing of full-length cDNAs and cDNA tags.
-
-
-
-
8
-
-
33745286231
-
TUF love for 'junk' DNA
-
Willingham, A. T. & Gingeras, T. R. TUF love for 'junk' DNA. Cell 125, 1215-1220 (2006).
-
(2006)
Cell
, vol.125
, pp. 1215-1220
-
-
Willingham, A.T.1
Gingeras, T.R.2
-
9
-
-
34249105047
-
Genome-wide RNA maps reveal interlaced transcript architecture, new classes of RNAs and possible function for pervasive transcription
-
in the press
-
Kapranov, P. et al. Genome-wide RNA maps reveal interlaced transcript architecture, new classes of RNAs and possible function for pervasive transcription. Science (in the press).
-
Science
-
-
Kapranov, P.1
-
10
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama, S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566 (2005).
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
-
11
-
-
33749870103
-
A large quantity of novel human antisense transcripts detected by LongSAGE
-
Ge, X., Wu, Q., Jung, Y. C., Chen, J. & Wang, S. M. A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics 22, 2475-2479 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2475-2479
-
-
Ge, X.1
Wu, Q.2
Jung, Y.C.3
Chen, J.4
Wang, S.M.5
-
12
-
-
33746785696
-
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species
-
Zhang, Y., Liu, X. S., Liu, Q. R. & Wei, L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 34, 3465-3475 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3465-3475
-
-
Zhang, Y.1
Liu, X.S.2
Liu, Q.R.3
Wei, L.4
-
13
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genet. 38, 626-635 (2006).
-
(2006)
Nature Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
-
14
-
-
34250369629
-
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
-
in the press
-
Denoeud, F. et al. Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. (in the press).
-
Genome Res
-
-
Denoeud, F.1
-
15
-
-
33749153857
-
Biological function of unannotated transcription during the early development of Drosophila melanogaster
-
Manak, J. R. et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genet. 38, 1151-1158 (2006).
-
(2006)
Nature Genet
, vol.38
, pp. 1151-1158
-
-
Manak, J.R.1
-
16
-
-
22244442468
-
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
-
Kapranov, P. et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15, 987-997 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 987-997
-
-
Kapranov, P.1
-
17
-
-
30044445670
-
Tandem chimerism as a means to increase protein complexity in the human genome
-
Parra, G. et al. Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res. 16, 37-44 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 37-44
-
-
Parra, G.1
-
19
-
-
32544451144
-
Alternative trans-splicing: A novel mode of pre-mRNA processing
-
Horiuchi, T. & Aigaki, T. Alternative trans-splicing: a novel mode of pre-mRNA processing. Biol. Cell 98, 135-140 (2006).
-
(2006)
Biol. Cell
, vol.98
, pp. 135-140
-
-
Horiuchi, T.1
Aigaki, T.2
-
20
-
-
0036123757
-
Intergenic mRNAs. Minor gene products or tools of diversity?
-
Finta, C., Warner, S. C. & Zaphiropoulos, P. G. Intergenic mRNAs. Minor gene products or tools of diversity? Histol. Histopathol. 17, 677-682 (2002).
-
(2002)
Histol. Histopathol
, vol.17
, pp. 677-682
-
-
Finta, C.1
Warner, S.C.2
Zaphiropoulos, P.G.3
-
21
-
-
17644392110
-
High frequency trans-splicing in a cell line producing spliced and polyadenylated RNA polymerase I transcripts from an rDNA-myc chimeric gene
-
Chen, C. et al. High frequency trans-splicing in a cell line producing spliced and polyadenylated RNA polymerase I transcripts from an rDNA-myc chimeric gene. Nucleic Acids Res. 33, 2332-2342 (2005).
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2332-2342
-
-
Chen, C.1
-
22
-
-
0037014661
-
Naturally occurring heterologous trans-splicing of adenovirus RNA with host cellular transcripts during infection
-
Kikumori, T., Cote, G. J. & Gagel, R. F. Naturally occurring heterologous trans-splicing of adenovirus RNA with host cellular transcripts during infection. FEBS Lett. 522, 41-46 (2002).
-
(2002)
FEBS Lett
, vol.522
, pp. 41-46
-
-
Kikumori, T.1
Cote, G.J.2
Gagel, R.F.3
-
23
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509 (2004).
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
-
24
-
-
0142027777
-
-
Martone, R. et al. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA 100, 12247-12252 (2003). References 23 and 24 represent the first reports of the unbiased profiling of transcription factor binding sites and provide the first comprehensive evidence for the utilization of promoters in non-canonical genomic locations.
-
Martone, R. et al. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA 100, 12247-12252 (2003). References 23 and 24 represent the first reports of the unbiased profiling of transcription factor binding sites and provide the first comprehensive evidence for the utilization of promoters in non-canonical genomic locations.
-
-
-
-
25
-
-
0347135948
-
An abundance of bidirectional promoters in the human genome
-
Trinklein, N. D. et al. An abundance of bidirectional promoters in the human genome. Genome Res. 14, 62-66 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 62-66
-
-
Trinklein, N.D.1
-
26
-
-
0033926304
-
Stability and evolution of overlapping genes
-
Krakauer, D. C. Stability and evolution of overlapping genes. Evolution 54, 731-739 (2000).
-
(2000)
Evolution
, vol.54
, pp. 731-739
-
-
Krakauer, D.C.1
-
27
-
-
0034221653
-
Overlapping genes in bacterial and bacteriophage genomes
-
Shcherbakov, D. V. & Garber, M. B. Overlapping genes in bacterial and bacteriophage genomes. Mol. Biol. (Mosk) 34, 572-583 (2000).
-
(2000)
Mol. Biol. (Mosk)
, vol.34
, pp. 572-583
-
-
Shcherbakov, D.V.1
Garber, M.B.2
-
28
-
-
19844379515
-
Genome-wide assembly and analysis of alternative transcripts in mouse
-
Sharov, A. A., Dudekula, D. B. & Ko, M. S. Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res. 15, 748-754 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 748-754
-
-
Sharov, A.A.1
Dudekula, D.B.2
Ko, M.S.3
-
29
-
-
0038349624
-
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
-
Zavolan, M. et al. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 13, 1290-1300 (2003).
-
(2003)
Genome Res
, vol.13
, pp. 1290-1300
-
-
Zavolan, M.1
-
30
-
-
0014690698
-
Gene regulation for higher cells: A theory
-
Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349-357 (1969).
-
(1969)
Science
, vol.165
, pp. 349-357
-
-
Britten, R.J.1
Davidson, E.H.2
-
31
-
-
33746018653
-
Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript
-
Gupta, A., Gartner, J. J., Sethupathy, P., Hatzigeorgiou, A. G. & Fraser, N. W. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442, 82-85 (2006).
-
(2006)
Nature
, vol.442
, pp. 82-85
-
-
Gupta, A.1
Gartner, J.J.2
Sethupathy, P.3
Hatzigeorgiou, A.G.4
Fraser, N.W.5
-
32
-
-
24644446398
-
Ribo-gnome: The big world of small RNAs
-
Zamore, P. D. & Haley, B. Ribo-gnome: the big world of small RNAs. Science 309, 1519-1524 (2005).
-
(2005)
Science
, vol.309
, pp. 1519-1524
-
-
Zamore, P.D.1
Haley, B.2
-
35
-
-
20644449571
-
An abundance of RNA regulators
-
Storz, G., Altuvia, S. & Wassarman, K. M. An abundance of RNA regulators. Annu. Rev. Biochem. 74, 199-217 (2005).
-
(2005)
Annu. Rev. Biochem
, vol.74
, pp. 199-217
-
-
Storz, G.1
Altuvia, S.2
Wassarman, K.M.3
-
36
-
-
33748303049
-
Non-coding-RNA regulators of RNA polymerase II transcription
-
Goodrich, J. A. & Kugel, J. F. Non-coding-RNA regulators of RNA polymerase II transcription. Nature Rev. Mol. Cell Biol. 7, 612-616 (2006).
-
(2006)
Nature Rev. Mol. Cell Biol
, vol.7
, pp. 612-616
-
-
Goodrich, J.A.1
Kugel, J.F.2
-
37
-
-
33846169089
-
-
Prasanth, K. V. & Spector, D. L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21, 11-42 (2007). A comprehensive review of ncRNAs.
-
Prasanth, K. V. & Spector, D. L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21, 11-42 (2007). A comprehensive review of ncRNAs.
-
-
-
-
38
-
-
1842584883
-
RNA regulation: A new genetics?
-
Mattick, J. S. RNA regulation: a new genetics? Nature Rev. Genet. 5, 316-323 (2004).
-
(2004)
Nature Rev. Genet
, vol.5
, pp. 316-323
-
-
Mattick, J.S.1
-
39
-
-
0028631058
-
Introns: Evolution and function
-
Mattick, J. S. Introns: evolution and function. Curr. Opin. Genet. Dev. 4, 823-831 (1994).
-
(1994)
Curr. Opin. Genet. Dev
, vol.4
, pp. 823-831
-
-
Mattick, J.S.1
-
40
-
-
0035195942
-
Non-coding RNAs: The architects of eukaryotic complexity
-
986-991
-
Mattick, J. S. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2, 986-991 (2001).
-
(2001)
EMBO Rep
, vol.2
-
-
Mattick, J.S.1
-
41
-
-
0141867857
-
-
Mattick, J. S. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25, 930-939 (2003). References 38-41 review the concept of RNA as a carrier of information in the cell.
-
Mattick, J. S. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25, 930-939 (2003). References 38-41 review the concept of RNA as a carrier of information in the cell.
-
-
-
-
42
-
-
33344477448
-
Genomics of microRNA
-
Kim, V. N. & Nam, J. W. Genomics of microRNA. Trends Genet. 22, 165-173 (2006).
-
(2006)
Trends Genet
, vol.22
, pp. 165-173
-
-
Kim, V.N.1
Nam, J.W.2
-
43
-
-
0037133942
-
Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions
-
Kiss, T. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109, 145-148 (2002).
-
(2002)
Cell
, vol.109
, pp. 145-148
-
-
Kiss, T.1
-
44
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
45
-
-
0036591884
-
Biogenesis of small nucleolar ribonucleoproteins
-
Filipowicz, W. & Pogacic, V. Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol. 14, 319-327 (2002).
-
(2002)
Curr. Opin. Cell Biol
, vol.14
, pp. 319-327
-
-
Filipowicz, W.1
Pogacic, V.2
-
46
-
-
23644457818
-
Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs
-
Huang, Z. P. et al. Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs. RNA 11, 1303-1316 (2005).
-
(2005)
RNA
, vol.11
, pp. 1303-1316
-
-
Huang, Z.P.1
-
47
-
-
6344281172
-
Identification of mammalian microRNA host genes and transcription units
-
Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. & Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902-1910 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 1902-1910
-
-
Rodriguez, A.1
Griffiths-Jones, S.2
Ashurst, J.L.3
Bradley, A.4
-
48
-
-
13944260434
-
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
-
Baskerville, S. & Bartel, D. P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241-247 (2005).
-
(2005)
RNA
, vol.11
, pp. 241-247
-
-
Baskerville, S.1
Bartel, D.P.2
-
49
-
-
33745175558
-
Profiling Caenorhabditis elegans noncoding RNA expression with a combined microarray
-
He, H. et al. Profiling Caenorhabditis elegans noncoding RNA expression with a combined microarray. Nucleic Acids Res. 34, 2976-2983 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2976-2983
-
-
He, H.1
-
50
-
-
20944450160
-
Combinatorial microRNA target predictions
-
Krek, A. et al. Combinatorial microRNA target predictions. Nature Genet. 37, 495-500 (2005).
-
(2005)
Nature Genet
, vol.37
, pp. 495-500
-
-
Krek, A.1
-
51
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
52
-
-
0346094457
-
Prediction of mammalian microRNA targets
-
Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787-798 (2003).
-
(2003)
Cell
, vol.115
, pp. 787-798
-
-
Lewis, B.P.1
Shih, I.H.2
Jones-Rhoades, M.W.3
Bartel, D.P.4
Burge, C.B.5
-
53
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
-
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434, 338-345 (2005).
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
-
54
-
-
13944282215
-
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
-
Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773 (2005).
-
(2005)
Nature
, vol.433
, pp. 769-773
-
-
Lim, L.P.1
-
55
-
-
29144505309
-
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution
-
Farh, K. K. et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310, 1817-1821 (2005).
-
(2005)
Science
, vol.310
, pp. 1817-1821
-
-
Farh, K.K.1
-
56
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
Pollard, K. S. et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443, 167-172 (2006).
-
(2006)
Nature
, vol.443
, pp. 167-172
-
-
Pollard, K.S.1
-
57
-
-
33846950027
-
A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas
-
Lin, R., Maeda, S., Liu, C., Karin, M. & Edgington, T. S. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 26, 851-858 (2006).
-
(2006)
Oncogene
, vol.26
, pp. 851-858
-
-
Lin, R.1
Maeda, S.2
Liu, C.3
Karin, M.4
Edgington, T.S.5
-
58
-
-
33645823589
-
A noncoding RNA is a potential marker of cell fate during mammary gland development
-
Ginger, M. R. et al. A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc. Natl Acad. Sci. USA 103, 5781-5786 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 5781-5786
-
-
Ginger, M.R.1
-
59
-
-
24644481406
-
-
Willingham, A. T. et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309, 1570-1573 (2005). An example of the use of high-throughput technologies to elucidate the function of human ncRNAs.
-
Willingham, A. T. et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309, 1570-1573 (2005). An example of the use of high-throughput technologies to elucidate the function of human ncRNAs.
-
-
-
-
60
-
-
33644514069
-
Noncoding RNAs of trithorax response elements recruit Drosophila ASH1 to Ultrabithorax
-
Sanchez-Elsner, T., Gou, D., Kremmer, E. & Sauer, F. Noncoding RNAs of trithorax response elements recruit Drosophila ASH1 to Ultrabithorax. Science 311, 1118-1123 (2006).
-
(2006)
Science
, vol.311
, pp. 1118-1123
-
-
Sanchez-Elsner, T.1
Gou, D.2
Kremmer, E.3
Sauer, F.4
-
61
-
-
29444448047
-
On a chromosome far, far away: LCRs and gene expression
-
Dean, A. On a chromosome far, far away: LCRs and gene expression. Trends Genet. 22, 38-45 (2006).
-
(2006)
Trends Genet
, vol.22
, pp. 38-45
-
-
Dean, A.1
-
62
-
-
0036839549
-
Locus control regions
-
Li, Q., Peterson, K. R., Fang, X. & Stamatoyannopoulos, G. Locus control regions. Blood 100, 3077-3086 (2002).
-
(2002)
Blood
, vol.100
, pp. 3077-3086
-
-
Li, Q.1
Peterson, K.R.2
Fang, X.3
Stamatoyannopoulos, G.4
-
63
-
-
33645460549
-
How imprinting centres work
-
Lewis, A. & Reik, W. How imprinting centres work. Cytogenet. Genome Res. 113, 81-89 (2006).
-
(2006)
Cytogenet. Genome Res
, vol.113
, pp. 81-89
-
-
Lewis, A.1
Reik, W.2
-
64
-
-
22144442010
-
Globalisation reaches gene regulation: The case for vertebrate limb development
-
Zuniga, A. Globalisation reaches gene regulation: the case for vertebrate limb development. Curr. Opin. Genet. Dev. 15, 403-409 (2005).
-
(2005)
Curr. Opin. Genet. Dev
, vol.15
, pp. 403-409
-
-
Zuniga, A.1
-
65
-
-
21744448354
-
The HS2 enhancer of the β-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter
-
Ling, J., Baibakov, B., Pi, W., Emerson, B. M. & Tuan, D. The HS2 enhancer of the β-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter. J. Mol. Biol. 350, 883-896 (2005).
-
(2005)
J. Mol. Biol
, vol.350
, pp. 883-896
-
-
Ling, J.1
Baibakov, B.2
Pi, W.3
Emerson, B.M.4
Tuan, D.5
-
66
-
-
0037320461
-
Chromatin remodeling and extragenic transcription at the MHC class II locus control region
-
Masternak, K., Peyraud, N., Krawczyk, M., Barras, E. & Reith, W. Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nature Immunol. 4, 132-137 (2003).
-
(2003)
Nature Immunol
, vol.4
, pp. 132-137
-
-
Masternak, K.1
Peyraud, N.2
Krawczyk, M.3
Barras, E.4
Reith, W.5
-
67
-
-
0030826364
-
Intergenic transcription and transinduction of the human β-globin locus
-
Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. & Proudfoot, N. J. Intergenic transcription and transinduction of the human β-globin locus. Genes Dev. 11, 2494-2509 (1997).
-
(1997)
Genes Dev
, vol.11
, pp. 2494-2509
-
-
Ashe, H.L.1
Monks, J.2
Wijgerde, M.3
Fraser, P.4
Proudfoot, N.J.5
-
68
-
-
17444410031
-
The influence of non-coding RNAs on allele-specific gene expression in mammals
-
O'Neill, M. J. The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum. Mol. Genet. 14, R113-R120 (2005).
-
(2005)
Hum. Mol. Genet
, vol.14
-
-
O'Neill, M.J.1
-
69
-
-
0037075032
-
The non-coding Air RNA is required for silencing autosomal imprinted genes
-
Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810-813 (2002).
-
(2002)
Nature
, vol.415
, pp. 810-813
-
-
Sleutels, F.1
Zwart, R.2
Barlow, D.P.3
-
70
-
-
33646598385
-
Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes
-
Mancini-Dinardo, D., Steele, S. J., Levorse, J. M., Ingram, R. S. & Tilghman, S. M. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 20, 1268-1282 (2006).
-
(2006)
Genes Dev
, vol.20
, pp. 1268-1282
-
-
Mancini-Dinardo, D.1
Steele, S.J.2
Levorse, J.M.3
Ingram, R.S.4
Tilghman, S.M.5
-
71
-
-
33746423865
-
Locus control region transcription plays an active role in long-range gene activation
-
Ho, Y., Elefant, F., Liebhaber, S. A. & Cooke, N. E. Locus control region transcription plays an active role in long-range gene activation. Mol. Cell 23, 365-675 (2006).
-
(2006)
Mol. Cell
, vol.23
, pp. 365-675
-
-
Ho, Y.1
Elefant, F.2
Liebhaber, S.A.3
Cooke, N.E.4
-
72
-
-
10944220506
-
-
Ling, J. et al. HS2 enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter. J. Biol. Chem. 279, 51704-51713 (2004). References 69-72 show that long-range transcription is required for gene activation and silencing.
-
Ling, J. et al. HS2 enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter. J. Biol. Chem. 279, 51704-51713 (2004). References 69-72 show that long-range transcription is required for gene activation and silencing.
-
-
-
-
73
-
-
33646589016
-
Imprinting mechanisms - it only takes two
-
Pauler, F. M. & Barlow, D. P. Imprinting mechanisms - it only takes two. Genes Dev. 20, 1203-1206 (2006).
-
(2006)
Genes Dev
, vol.20
, pp. 1203-1206
-
-
Pauler, F.M.1
Barlow, D.P.2
-
74
-
-
8744308029
-
Properties of overlapping genes are conserved across microbial genomes
-
Johnson, Z. I. & Chisholm, S. W. Properties of overlapping genes are conserved across microbial genomes. Genome Res. 14, 2268-2272 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 2268-2272
-
-
Johnson, Z.I.1
Chisholm, S.W.2
-
75
-
-
19444386412
-
Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts
-
Chen, J., Sun, M., Hurst, L. D., Carmichael, G. G. & Rowley, J. D. Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet. 21, 326-329 (2005).
-
(2005)
Trends Genet
, vol.21
, pp. 326-329
-
-
Chen, J.1
Sun, M.2
Hurst, L.D.3
Carmichael, G.G.4
Rowley, J.D.5
-
76
-
-
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
-
77
-
-
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
-
78
-
-
0031816558
-
Antisense WT1 transcription parallels sense mRNA and protein expression in fetal kidney and can elevate protein levels in vitro
-
Moorwood, K. et al. Antisense WT1 transcription parallels sense mRNA and protein expression in fetal kidney and can elevate protein levels in vitro. J. Pathol. 185, 352-359 (1998).
-
(1998)
J. Pathol
, vol.185
, pp. 352-359
-
-
Moorwood, K.1
-
79
-
-
0017798436
-
Evolution of overlapping genes
-
Miyata, T. & Yasunaga, T. Evolution of overlapping genes. Nature 272, 532-535 (1978).
-
(1978)
Nature
, vol.272
, pp. 532-535
-
-
Miyata, T.1
Yasunaga, T.2
-
80
-
-
5444230036
-
-
Shirasawa, S. et al. SNPs in the promoter of a B cellspecific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum. Mol. Genet. 13, 2221-2231 (2004). An example of an intronic SNP that causes predisposition to a disease by influencing the levels of an antisense transcript.
-
Shirasawa, S. et al. SNPs in the promoter of a B cellspecific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum. Mol. Genet. 13, 2221-2231 (2004). An example of an intronic SNP that causes predisposition to a disease by influencing the levels of an antisense transcript.
-
-
-
-
81
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
-
82
-
-
0016283394
-
The metabolism of a poly(A) minus mRNA fraction in HeLa cells
-
Milcarek, C., Price, R. & Penman, S. The metabolism of a poly(A) minus mRNA fraction in HeLa cells. Cell 3, 1-10 (1974).
-
(1974)
Cell
, vol.3
, pp. 1-10
-
-
Milcarek, C.1
Price, R.2
Penman, S.3
-
83
-
-
0016826992
-
Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos
-
Hough, B. R., Smith, M. J., Britten, R. J. & Davidson, E. H. Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos. Cell 5, 291-299 (1975).
-
(1975)
Cell
, vol.5
, pp. 291-299
-
-
Hough, B.R.1
Smith, M.J.2
Britten, R.J.3
Davidson, E.H.4
-
84
-
-
0019332437
-
Sequence complexity of nuclear and messenger RNA in HeLa cells
-
Holland, C. A., Mayrand, S. & Pederson, T. Sequence complexity of nuclear and messenger RNA in HeLa cells. J. Mol. Biol. 138, 755-778 (1980).
-
(1980)
J. Mol. Biol
, vol.138
, pp. 755-778
-
-
Holland, C.A.1
Mayrand, S.2
Pederson, T.3
-
85
-
-
0019323954
-
Satellite DNA is transcribed on lampbrush chromosomes
-
Varley, J. M., Macgregor, H. C. & Erba, H. P. Satellite DNA is transcribed on lampbrush chromosomes. Nature 283, 686-688 (1980).
-
(1980)
Nature
, vol.283
, pp. 686-688
-
-
Varley, J.M.1
Macgregor, H.C.2
Erba, H.P.3
-
86
-
-
0019524412
-
-
Salditt-Georgieff, M., Harpold, M. M., Wilson, M. C. & Darnell, J. E. Jr. Large heterogeneous nuclear ribonucleic acid has three times as many 5′ caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol. Cell. Biol. 1, 179-187 (1981). References 82-86 provide the first indications that a large fraction of the eukaryotic genome is transcribed, and that non-polyadenylated RNA is prevalent.
-
Salditt-Georgieff, M., Harpold, M. M., Wilson, M. C. & Darnell, J. E. Jr. Large heterogeneous nuclear ribonucleic acid has three times as many 5′ caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol. Cell. Biol. 1, 179-187 (1981). References 82-86 provide the first indications that a large fraction of the eukaryotic genome is transcribed, and that non-polyadenylated RNA is prevalent.
-
-
-
-
87
-
-
0033664358
-
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
-
Selinger, D. W. et al. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnol. 18, 1262-1268 (2000).
-
(2000)
Nature Biotechnol
, vol.18
, pp. 1262-1268
-
-
Selinger, D.W.1
-
88
-
-
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
-
89
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655-660 (2004).
-
(2004)
Science
, vol.306
, pp. 655-660
-
-
Stolc, V.1
-
90
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone, P. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242-2246 (2004).
-
(2004)
Science
, vol.306
, pp. 2242-2246
-
-
Bertone, P.1
-
91
-
-
29444438757
-
Genome-wide transcription analyses in rice using tiling microarrays
-
Li, L. et al. Genome-wide transcription analyses in rice using tiling microarrays. Nature Genet. 38, 124-129 (2006).
-
(2006)
Nature Genet
, vol.38
, pp. 124-129
-
-
Li, L.1
-
92
-
-
33751011601
-
The transcriptome of the sea urchin embryo
-
Samanta, M. P. et al. The transcriptome of the sea urchin embryo. Science 314, 960-962 (2006).
-
(2006)
Science
, vol.314
, pp. 960-962
-
-
Samanta, M.P.1
-
93
-
-
33645785104
-
A high-resolution map of transcription in the yeast genome
-
David, L. et al. A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA 103, 5320-5325 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 5320-5325
-
-
David, L.1
-
94
-
-
0037012881
-
-
Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919 (2002). The first unbiased high-resolution microarraybased study of the genomics era, showing that the transcriptional complexity of human cytosolic polyadenylated RNA is up to an order of magnitude more complex that can be explained by exons of known genes.
-
Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919 (2002). The first unbiased high-resolution microarraybased study of the genomics era, showing that the transcriptional complexity of human cytosolic polyadenylated RNA is up to an order of magnitude more complex that can be explained by exons of known genes.
-
-
-
-
95
-
-
0037442493
-
The transcriptional activity of human Chromosome 22
-
Rinn, J. L. et al. The transcriptional activity of human Chromosome 22. Genes Dev. 17, 529-540 (2003).
-
(2003)
Genes Dev
, vol.17
, pp. 529-540
-
-
Rinn, J.L.1
-
96
-
-
9144233601
-
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
-
Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA 100, 15776-15781 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 15776-15781
-
-
Shiraki, T.1
-
97
-
-
20844463584
-
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
-
Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2, 105-111 (2005).
-
(2005)
Nature Methods
, vol.2
, pp. 105-111
-
-
Ng, P.1
-
98
-
-
0037126025
-
Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags
-
Chen, J. et al. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl Acad. Sci. USA 99, 12257-12262 (2002).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 12257-12262
-
-
Chen, J.1
-
99
-
-
0036246030
-
Using the transcriptome to annotate the genome
-
Saha, S. et al. Using the transcriptome to annotate the genome. Nature Biotechnol. 20, 508-512 (2002).
-
(2002)
Nature Biotechnol
, vol.20
, pp. 508-512
-
-
Saha, S.1
-
100
-
-
0037737975
-
-
Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818 (2003).
-
Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807-818 (2003).
-
-
-
-
101
-
-
30044435097
-
Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
-
Deng, W. et al. Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res. 16, 20-29 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 20-29
-
-
Deng, W.1
-
102
-
-
33845436047
-
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
-
Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193-1207 (2006).
-
(2006)
Cell
, vol.127
, pp. 1193-1207
-
-
Ruby, J.G.1
-
103
-
-
24644490196
-
Elucidation of the small RNA component of the transcriptome
-
Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science 309, 1567-1569 (2005).
-
(2005)
Science
, vol.309
, pp. 1567-1569
-
-
Lu, C.1
-
104
-
-
33745402414
-
A novel class of small RNAs bind to MILI protein in mouse testes
-
Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203-207 (2006).
-
(2006)
Nature
, vol.442
, pp. 203-207
-
-
Aravin, A.1
-
105
-
-
33745336617
-
-
Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199-202 (2006).
-
Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199-202 (2006).
-
-
-
-
106
-
-
33745621037
-
A novel class of small RNAs in mouse spermatogenic cells
-
Grivna, S. T., Beyret, E., Wang, Z. & Lin, H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev. 20, 1709-1714 (2006).
-
(2006)
Genes Dev
, vol.20
, pp. 1709-1714
-
-
Grivna, S.T.1
Beyret, E.2
Wang, Z.3
Lin, H.4
-
107
-
-
33746527679
-
Characterization of the piRNA complex from rat testes
-
Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363-367 (2006).
-
(2006)
Science
, vol.313
, pp. 363-367
-
-
Lau, N.C.1
-
108
-
-
33745599586
-
Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
-
Watanabe, T. et al. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 20, 1732-1743 (2006).
-
(2006)
Genes Dev
, vol.20
, pp. 1732-1743
-
-
Watanabe, T.1
-
109
-
-
22244475458
-
An atlas of human gene expression from massively parallel signature sequencing (MPSS)
-
Jongeneel, C. V. et al. An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res. 15, 1007-1014 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1007-1014
-
-
Jongeneel, C.V.1
-
110
-
-
0142104045
-
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
-
Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573 (2002).
-
(2002)
Nature
, vol.420
, pp. 563-573
-
-
Okazaki, Y.1
-
111
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876-880 (2005).
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
-
112
-
-
30344478870
-
A global map of p53 transcriptionfactor binding sites in the human genome
-
Wei, C. L. et al. A global map of p53 transcriptionfactor binding sites in the human genome. Cell 124, 207-219 (2006).
-
(2006)
Cell
, vol.124
, pp. 207-219
-
-
Wei, C.L.1
-
113
-
-
0028789793
-
Serial analysis of gene expression
-
Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene expression. Science 270, 484-487 (1995).
-
(1995)
Science
, vol.270
, pp. 484-487
-
-
Velculescu, V.E.1
Zhang, L.2
Vogelstein, B.3
Kinzler, K.W.4
-
114
-
-
28844463698
-
Emerging technologies in DNA sequencing
-
Metzker, M. L. Emerging technologies in DNA sequencing. Genome Res. 15, 1767-1776 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1767-1776
-
-
Metzker, M.L.1
-
115
-
-
33644875376
-
Microarray expression technology: From start to finish
-
Elvidge, G. Microarray expression technology: from start to finish. Pharmacogenomics 7, 123-134 (2006).
-
(2006)
Pharmacogenomics
, vol.7
, pp. 123-134
-
-
Elvidge, G.1
-
116
-
-
3242766188
-
Beyond expression profiling: Next generation uses of high density oligonucleotide arrays
-
Kapranov, P., Sementchenko, V. I. & Gingeras, T. R. Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Brief. Funct. Genomic. Proteomic. 2, 47-56 (2003).
-
(2003)
Brief. Funct. Genomic. Proteomic
, vol.2
, pp. 47-56
-
-
Kapranov, P.1
Sementchenko, V.I.2
Gingeras, T.R.3
-
117
-
-
10644247621
-
Applications of DNA tiling arrays for whole-genome analysis
-
Mockler, T. C. et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1-15 (2005).
-
(2005)
Genomics
, vol.85
, pp. 1-15
-
-
Mockler, T.C.1
-
118
-
-
0037250168
-
The UCSC Genome Browser Database
-
Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-54 (2003).
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 51-54
-
-
Karolchik, D.1
-
119
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
|