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Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
- A. Sorana Morrissy,
- Malachi Griffith,
- and Marco A. Marra
Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
...lymphoblastoid cell lines revealed that the majority of expressed sense–antisense genes exhibited alternative splicing events that were correlated to the expression of the antisense gene. Most of these events occurred in areas of sense–antisense (SAS) gene overlap, which were significantly enriched in both exons...
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LETTER: Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
- Kouichi Kimura,
- Ai Wakamatsu,
- Yutaka Suzuki,
- Toshio Ota,
- Tetsuo Nishikawa,
- Riu Yamashita,
- Jun-ichi Yamamoto,
- Mitsuo Sekine,
- Katsuki Tsuritani,
- Hiroyuki Wakaguri,
- Shizuko Ishii,
- Tomoyasu Sugiyama,
- Kaoru Saito,
- Yuko Isono,
- Ryotaro Irie,
- Norihiro Kushida,
- Takahiro Yoneyama,
- Rie Otsuka,
- Katsuhiro Kanda,
- Takahide Yokoi,
- Hiroshi Kondo,
- Masako Wagatsuma,
- Katsuji Murakawa,
- Shinichi Ishida,
- Tadashi Ishibashi,
- Asako Takahashi-Fujii,
- Tomoo Tanase,
- Keiichi Nagai,
- Hisashi Kikuchi,
- Kenta Nakai,
- Takao Isogai,
- and Sumio Sugano
Genome Res. January 2006 16: 55-65; Published in Advance December 12, 2005, doi:10.1101/gr.4039406
...( Kapranov et al. 2005 ), including transcripts generated from many so-called overlapping genes and anti-sense genes ( Kiyosawa et al. 2003 ; Imanishi et al. 2004 ; Dahary et al. 2005 ). Newly identified additional PAPs (and thus first exons) have expanded the transcript regions (from TSSs to transcript...
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Methods: Next-generation tag sequencing for cancer gene expression profiling
- A. Sorana Morrissy,
- Ryan D. Morin,
- Allen Delaney,
- Thomas Zeng,
- Helen McDonald,
- Steven Jones,
- Yongjun Zhao,
- Martin Hirst,
- and Marco A. Marra
Genome Res. October 2009 19: 1825-1835; Published in Advance June 18, 2009, doi:10.1101/gr.094482.109
...compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors, antisense transcripts, and intronic sequences, the latter possibly representing novel exons or genes. We observed increases in the diversity, abundance...
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PERSPECTIVE: Origin of phenotypes: Genes and transcripts
- Thomas R. Gingeras
Genome Res. June 2007 17: 682-690; doi:10.1101/gr.6525007
...transcript through what appears to be a mechanism of transcription interference. Diploid cells with IME4 antisense transcription have reduced sense transcripts and do not enter meiosis. Furthermore, human diseases ranging from breast cancer and lymphoma to thalassemia have been linked to naturally occurring...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...overlap in their 3′ UTRs ( Shendure and Church 2002 ; Yelin et al. 2003 ) and in light of accumulating evidence for the importance of antisense transcription in various kinds of transcriptional and post-transcriptional regulation ( Lavorgna et al. 2004 ; Dahary et al. 2005 ). However, we have not observed...
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LETTER: Transcription-mediated gene fusion in the human genome
- Pinchas Akiva,
- Amir Toporik,
- Sarit Edelheit,
- Yifat Peretz,
- Alex Diber,
- Ronen Shemesh,
- Amit Novik,
- and Rotem Sorek
Genome Res. January 2006 16: 30-36; Published in Advance December 12, 2005, doi:10.1101/gr.4137606
...aligned to the , containing at least one RNA sequence. We next searched for clusters reporting on fusion between two genes. To avoid cases in which such clusters are caused by natural antisense overlaps, we used the “Antisensor” algorithm ( Yelin et al. 2003 ) to identify and separate such clusters...
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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...conserved phylogenetically, while others are recurrently involved in chromosomal rearrangement, resulting in breakpoint reuse. Both gene order conservation and breakpoint reuse can result from the existence of functional constraints on where chromosomal breakpoints occur or from the existence of regions...
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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
...in testes may have biological implications, and this observation is in accordance with previous reports ( Kleene et al. 1998 ; Reymond et al. 2002 ; Marques et al. 2005 ) and especially a recent finding that transcription of human retrocopies mainly (and/or initially) occurs in testes ( Vinckenbosch et al...
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METHODS: Selecting Open Reading Frames From DNA
- Paola Zacchi,
- Daniele Sblattero,
- Fiorella Florian,
- Roberto Marzari,
- and Andrew R.M. Bradbury
Genome Res. May 1, 2003 13: 980-990; doi:10.1101/gr.861503
...investment required, suffers from the problem that not all proteins can be easily expressed and purified. An alternative method would be to randomly fragment DNA enriched in coding sequences, and to rely on the variable expression of different polypeptides to provide overlapping fragmented representation...

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