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Methods: The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis
- Blake C. Meyers,
- Shivakundan Singh Tej,
- Tam H. Vu,
- Christian D. Haudenschild,
- Vikas Agrawal,
- Steve B. Edberg,
- Hassan Ghazal,
- and Shannon Decola
Genome Res. August 2004 14: 1641-1653; doi:10.1101/gr.2275604
...the quantitative levels of gene expression have made significant advances. Large-scale quantitative expression technologies involve the generation of short sequence tags from a given RNA sample, and use the abundance of these sequence tags to determine the relative abundance of each transcript. These methods...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...was tested by cDNA sequencing with inverse PCR. Surprisingly, 44% of the validated predictions in “intronic” regions revealed a transcript independent of the surrounding gene, and 40% of the validated predictions in “intergenic” regions were part of existing genes. See Fig. 3 for examples. Results...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
..., including RNA editing of mitochondrial transcripts (Shapiro and Englund 1995), polycistronic transcription of nuclear genes (Borst 1986; Tschudi and Ullu 1988), and segregation of chromosomes via an unconventional kinetochore apparatus comprising components distinct from other eukaryotic groups (Akiyoshi...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...-seq and ATAC-seq profiles around the heat shock protein GrpE2 gene. (G) KAS-seq and ATAC-seq profiles around the LuxR2 transcriptional activator gene. (H) KAS-seq and ATAC-seq profiles near the origin of replication of the Bacteriovorax chromosome.Examination of local browser tracks (Fig. 3B,C) revealed...
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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
...of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...rectangle) with an untemplated guanine (underlined G), and was followed by a long, pure 3′ poly(A) tract. The transduction indicated a putative donor L1 intronic to the PRDM4 gene on Chromosome 11 (L1RSPRDM4).Using the TEBreak computational pipeline (Carreira et al. 2016), we identified 194 L1, 3348 Alu...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...out by complete sequencing analysis. Alternatively, the large size of DNA fragments can be analyzed by single-end sequencing or paired-end sequencing. EST was the first tag-based approach, generating one tag per sequencing read, to represent full-length transcripts of expressed genes. The original...
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ARTICLE: Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
- Piero Carninci,
- Kazunori Waki,
- Toshiyuki Shiraki,
- Hideaki Konno,
- Kazuhiro Shibata,
- Masayoshi Itoh,
- Katsunori Aizawa,
- Takahiro Arakawa,
- Yoshiyuki Ishii,
- Daisuke Sasaki,
- Hidemasa Bono,
- Shinji Kondo,
- Yuichi Sugahara,
- Rintaro Saito,
- Naoki Osato,
- Shiro Fukuda,
- Kenjiro Sato,
- Akira Watahiki,
- Tomoko Hirozane-Kishikawa,
- Mari Nakamura,
- Yuko Shibata,
- Ayako Yasunishi,
- Noriko Kikuchi,
- Atsushi Yoshiki,
- Moriaki Kusakabe,
- Stefano Gustincich,
- Kirk Beisel,
- William Pavan,
- Vassilis Aidinis,
- Akira Nakagawara,
- William A. Held,
- Hiroo Iwata,
- Tomohiro Kono,
- Hiromitsu Nakauchi,
- Paul Lyons,
- Christine Wells,
- David A. Hume,
- Michela Fagiolini,
- Takao K. Hensch,
- Michelle Brinkmeier,
- Sally Camper,
- Junji Hirota,
- Peter Mombaerts,
- Masami Muramatsu,
- Yasushi Okazaki,
- Jun Kawai,
- and Yoshihide Hayashizaki
Genome Res. June 2003 13: 1273-1289; doi:10.1101/gr.1119703
...into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5′ end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best...
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Research: Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events
- Jinfeng Liu,
- William Lee,
- Zhaoshi Jiang,
- Zhongqiang Chen,
- Suchit Jhunjhunwala,
- Peter M. Haverty,
- Florian Gnad,
- Yinghui Guan,
- Houston N. Gilbert,
- Jeremy Stinson,
- Christiaan Klijn,
- Joseph Guillory,
- Deepali Bhatt,
- Steffan Vartanian,
- Kimberly Walter,
- Jocelyn Chan,
- Thomas Holcomb,
- Peter Dijkgraaf,
- Stephanie Johnson,
- Julie Koeman,
- John D. Minna,
- Adi F. Gazdar,
- Howard M. Stern,
- Klaus P. Hoeflich,
- Thomas D. Wu,
- Jeff Settleman,
- Frederic J. de Sauvage,
- Robert C. Gentleman,
- Richard M. Neve,
- David Stokoe,
- Zora Modrusan,
- Somasekar Seshagiri,
- David S. Shames,
- and Zemin Zhang
Genome Res. December 2012 22: 2315-2327; Published in Advance October 2, 2012, doi:10.1101/gr.140988.112
...the fusion junction. Among these predicted chimeras, 44% have more than one genomic sequencing read supporting the same gene pair (Supplemental Fig. 6), suggesting that they may result from genomic-level SVs, rather than read-through at the transcript level. Among the SVs supported by both genomic...
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LETTER: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes
- Mohammed Sebaihia,
- Michael W. Peck,
- Nigel P. Minton,
- Nicholas R. Thomson,
- Matthew T.G. Holden,
- Wilfrid J. Mitchell,
- Andrew T. Carter,
- Stephen D. Bentley,
- David R. Mason,
- Lisa Crossman,
- Catherine J. Paul,
- Alasdair Ivens,
- Marjon H.J. Wells-Bennik,
- Ian J. Davis,
- Ana M. Cerdeño-Tárraga,
- Carol Churcher,
- Michael A. Quail,
- Tracey Chillingworth,
- Theresa Feltwell,
- Audrey Fraser,
- Ian Goodhead,
- Zahra Hance,
- Kay Jagels,
- Natasha Larke,
- Mark Maddison,
- Sharon Moule,
- Karen Mungall,
- Halina Norbertczak,
- Ester Rabbinowitsch,
- Mandy Sanders,
- Mark Simmonds,
- Brian White,
- Sally Whithead,
- and Julian Parkhill
Genome Res. July 2007 17: 1082-1092; Published in Advance May 22, 2007, doi:10.1101/gr.6282807
...and Group II C. botulinum ), a prophage (Group III C. botulinum ), or a plasmid (Group IV C. botulinum ). In Group I (proteolytic) C. botulinum strain Hall A (ATCC 3502), they are organized in two divergent transcriptional units on the chromosome, cntAB and cntCDE , which bracket the regulatory gene, cnt...
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