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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...various combinations of alternative splicing, transcription initiation, and polyadenylation. The enormous complexity of the mammalian transcriptome was first exposed by large-scale sequencing of full-length cDNA transcripts frommouse (Okazaki et al. 2002;Maeda et al. 2006) and chromosome tiling array...
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LETTER: Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
- Yijun Ruan,
- Hong Sain Ooi,
- Siew Woh Choo,
- Kuo Ping Chiu,
- Xiao Dong Zhao,
- K.G. Srinivasan,
- Fei Yao,
- Chiou Yu Choo,
- Jun Liu,
- Pramila Ariyaratne,
- Wilson G.W. Bin,
- Vladimir A. Kuznetsov,
- Atif Shahab,
- Wing-Kin Sung,
- Guillaume Bourque,
- Nallasivam Palanisamy,
- and Chia-Lin Wei
Genome Res. June 2007 17: 828-838; doi:10.1101/gr.6018607
...promise for highly comprehensive transcriptome analysis. However, the exon data provided by tiling array have no inherent structural information for each characterized transcript; i.e., it is not straightforward to define the start and termination positions or the connectivity of individual transcript...
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ARTICLE: Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
- France Denoeud,
- Philipp Kapranov,
- Catherine Ucla,
- Adam Frankish,
- Robert Castelo,
- Jorg Drenkow,
- Julien Lagarde,
- Tyler Alioto,
- Caroline Manzano,
- Jacqueline Chrast,
- Sujit Dike,
- Carine Wyss,
- Charlotte N. Henrichsen,
- Nancy Holroyd,
- Mark C. Dickson,
- Ruth Taylor,
- Zahra Hance,
- Sylvain Foissac,
- Richard M. Myers,
- Jane Rogers,
- Tim Hubbard,
- Jennifer Harrow,
- Roderic Guigó,
- Thomas R. Gingeras,
- Stylianos E. Antonarakis,
- and Alexandre Reymond
Genome Res. June 2007 17: 746-759; doi:10.1101/gr.5660607
...of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5′ distal to the annotated 5′ terminus and internal to the annotated gene bounds for the vast majority (81...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
...the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one...
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LETTER: A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
- Zheng Lian,
- Alexander Karpikov,
- Jin Lian,
- Milind C. Mahajan,
- Stephen Hartman,
- Mark Gerstein,
- Michael Snyder,
- and Sherman M. Weissman
Genome Res. August 2008 18: 1224-1237; Published in Advance May 16, 2008, doi:10.1101/gr.075804.107
...of the method, we selected 19 of the 3′ end HeLa signals that did not lie within 2.5 kb of any 3′ end annotated in RefSeq. For each such signal, we designed a pair of PCR primers with one upstream and the other downstream from the estimated position of the poly(A) site and performed 3′ RACE on HeLa cell c...
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LETTER: Structured RNAs in the ENCODE selected regions of the human genome
- Stefan Washietl,
- Jakob S. Pedersen,
- Jan O. Korbel,
- Claudia Stocsits,
- Andreas R. Gruber,
- Jörg Hackermüller,
- Jana Hertel,
- Manja Lindemeyer,
- Kristin Reiche,
- Andrea Tanzer,
- Catherine Ucla,
- Carine Wyss,
- Stylianos E. Antonarakis,
- France Denoeud,
- Julien Lagarde,
- Jorg Drenkow,
- Philipp Kapranov,
- Thomas R. Gingeras,
- Roderic Guigó,
- Michael Snyder,
- Mark B. Gerstein,
- Alexandre Reymond,
- Ivo L. Hofacker,
- and Peter F. Stadler
Genome Res. June 2007 17: 852-864; doi:10.1101/gr.5650707
...score for a given alignment. The transcription of these RNAs was confirmed by 5′-RACE/array analysis. Examples D and E (in Fig. 7D,E ) show two sequence-constrained “islands” in introns of well-known protein-coding genes. They do not overlap with any predicted coding exons, but show clear signs...
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Methods: Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
- Ghia M. Euskirchen,
- Joel S. Rozowsky,
- Chia-Lin Wei,
- Wah Heng Lee,
- Zhengdong D. Zhang,
- Stephen Hartman,
- Olof Emanuelsson,
- Viktor Stolc,
- Sherman Weissman,
- Mark B. Gerstein,
- Yijun Ruan,
- and Michael Snyder
Genome Res. June 2007 17: 898-909; doi:10.1101/gr.5583007
...format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When...
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ARTICLE: Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
- Nathan D. Trinklein,
- Ulaş Karaöz,
- Jiaqian Wu,
- Anason Halees,
- Shelley Force Aldred,
- Patrick J. Collins,
- Deyou Zheng,
- Zhengdong D. Zhang,
- Mark B. Gerstein,
- Michael Snyder,
- Richard M. Myers,
- and Zhiping Weng
Genome Res. June 2007 17: 720-731; doi:10.1101/gr.5716607
...-sense), others provide an alternative TSS (and hence a new variant), and the remaining are anti-sense to an exon (typically the 5′-UTR or 3′-UTR and less frequently an internal exon) of the associated gene. Figure 4 and Supplemental Figure 4 show three examples of anti-sense transcripts represented by our RACE...
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ARTICLE: The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
- Joel S. Rozowsky,
- Daniel Newburger,
- Fred Sayward,
- Jiaqian Wu,
- Greg Jordan,
- Jan O. Korbel,
- Ugrappa Nagalakshmi,
- Jin Yang,
- Deyou Zheng,
- Roderic Guigó,
- Thomas R. Gingeras,
- Sherman Weissman,
- Perry Miller,
- Michael Snyder,
- and Mark B. Gerstein
Genome Res. June 2007 17: 732-745; doi:10.1101/gr.5696007
...obtained from these experiments was the discovery of tissue-specific alternative transcription start sites (TSSs), found by conducting 5′ RACE extensions from exons of known transcripts. Many of the TSSs were found to be &gt;100 kb upstream of the annotated start site. Although these alternate long...
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LETTER: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
- Marcel E. Dinger,
- Paulo P. Amaral,
- Tim R. Mercer,
- Ken C. Pang,
- Stephen J. Bruce,
- Brooke B. Gardiner,
- Marjan E. Askarian-Amiri,
- Kelin Ru,
- Giulia Soldà,
- Cas Simons,
- Susan M. Sunkin,
- Mark L. Crowe,
- Sean M. Grimmond,
- Andrew C. Perkins,
- and John S. Mattick
Genome Res. September 2008 18: 1433-1445; Published in Advance June 18, 2008, doi:10.1101/gr.078378.108
...equally to this work. Abstract The transcriptional networks that regulate embryonic stem (ES) cell pluripotency and lineage specification are the subject of considerable attention. To date such studies have focused almost exclusively on protein-coding transcripts. However, recent transcriptome...

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