Searching journal content for articles similar to Shibata et al. 5 (4): 400.

Displaying results 1-10 of 10

For checked items

view abstracts
download to citation manager

Select this article
Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
..., and blocking splicing leads to significant reduction of GAG protein translation (Oberlin et al. 2017).After VLP formation in the cytoplasm, LTR retrotransposons proliferate through tRNA-primed reverse transcription of gRNA, followed by nuclear import of double-stranded cDNA and integration into new loci...
Select this article
Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
- Christelle Cayrou,
- Philippe Coulombe,
- Alice Vigneron,
- Slavica Stanojcic,
- Olivier Ganier,
- Isabelle Peiffer,
- Eric Rivals,
- Aurore Puy,
- Sabine Laurent-Chabalier,
- Romain Desprat,
- and Marcel Méchali
Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
...replication origins: General features Ori mapping by purification of RNA-primedNS is a well-established procedure. NS purification is achieved through (1) size selection of RNA-primed NS at Oris and (2) specific enrichment using lambda exonuclease (Fig. 1A) as RNA-primedNS are resistant to this enzyme, while...
Select this article
Resource: A quantitative atlas of polyadenylation in five mammals
- Adnan Derti,
- Philip Garrett-Engele,
- Kenzie D. MacIsaac,
- Richard C. Stevens,
- Shreedharan Sriram,
- Ronghua Chen,
- Carol A. Rohl,
- Jason M. Johnson,
- and Tomas Babak
Genome Res. June 2012 22: 1173-1183; Published in Advance March 27, 2012, doi:10.1101/gr.132563.111
...polyA sites would not reveal the original RNA priming site, since the primer used in firststrand synthesis is incorporated into the sequencing library (not the RNA priming site) (Fig. 1A). Finally, we note that including a parameter that represents the read counts for each site to aid in discriminating...
OPEN ACCESS ARTICLE
Select this article
Method: Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
- Saiful Islam,
- Una Kjällquist,
- Annalena Moliner,
- Pawel Zajac,
- Jian-Bing Fan,
- Peter Lönnerberg,
- and Sten Linnarsson
Genome Res. July 2011 21: 1160-1167; Published in Advance May 4, 2011, doi:10.1101/gr.110882.110
...DNA polymerase: RNA detection and analysis in vitro and in situ by target RNA-primed RCA. RNA 15: 765–771. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human . Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25. Moliner A...
Select this article
Research: Genome-wide depletion of replication initiation events in highly transcribed regions
- Melvenia M. Martin,
- Michael Ryan,
- RyangGuk Kim,
- Anna L. Zakas,
- Haiqing Fu,
- Chii Mei Lin,
- William C. Reinhold,
- Sean R. Davis,
- Sven Bilke,
- Hongfang Liu,
- James H. Doroshow,
- Mark A. Reimers,
- Manuel S. Valenzuela,
- Yves Pommier,
- Paul S. Meltzer,
- and Mirit I. Aladjem
Genome Res. November 2011 21: 1822-1832; Published in Advance August 3, 2011, doi:10.1101/gr.124644.111
...regions. Arrows on RefSeq genes indicate the direction of transcription. Initiation at select sites was verified using real-time PCR, with primers listed in Table 2. Examples of control and nascent strand tracks are shown in Supplemental Figure 1A. (A–C ) Mapping replication initiation events...
Select this article
Research: Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription
- Larry D. Mesner,
- Veena Valsakumar,
- Neerja Karnani,
- Anindya Dutta,
- Joyce L. Hamlin,
- and Stefan Bekiranov
Genome Res. March 2011 21: 377-389; Published in Advance December 20, 2010, doi:10.1101/gr.111328.110
...in a log-phase population. A subsequent modification utilizes lambda-exonuclease to attempt to rid the preparations of the huge background of non-RNA-primed small broken DNA fragments (Bielinsky and Gerbi 1998). In two different studies, nascent strand preparations isolated from human HeLa cells were...
Select this article
LETTER: Human–Ovine Comparative Sequencing of a 250-kb Imprinted Domain Encompassing the Callipyge (clpg) Locus and Identification of Six Imprinted Transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8
- Carole Charlier,
- Karin Segers,
- Danny Wagenaar,
- Latifa Karim,
- Stéphane Berghmans,
- Olivier Jaillon,
- Tracy Shay,
- Jean Weissenbach,
- Noelle Cockett,
- Gabor Gyapay,
- and Michel Georges
Genome Res. May 1, 2001 11: 850-862; doi:10.1101/gr.172701
...-Pure (Eurogentech) according to the manufacturer's instructions. First strand cDNA was synthesized by use of the GeneAmp RNA PCR Kit (Perkin Elmer) starting from 1 μg of total RNA primed either with an oligo(dT) primer ( DLK1, GTL2, DAT, MEG8 ) or the transcript-specific primers reported in Table 2 ( PEG11 and anti...
Select this article
Methods: Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
- Eugene Berezikov,
- Geert van Tetering,
- Mark Verheul,
- Jose van de Belt,
- Linda van Laake,
- Joost Vos,
- Robert Verloop,
- Marc van de Wetering,
- Victor Guryev,
- Shuji Takada,
- Anton Jan van Zonneveld,
- Hiroyuki Mano,
- Ronald Plasterk,
- and Edwin Cuppen
Genome Res. October 2006 16: 1289-1298; Published in Advance September 5, 2006, doi:10.1101/gr.5159906
...profiles and RNA folding criteria ( Berezikov et al. 2005 ). To verify these predicted miRNA candidate genes experimentally, we now employed a modified RNA-primed Array-based Klenow Extension (RAKE) approach ( Nelson et al. 2004 ). This assay is based on the ability of an RNA molecule to function...
Select this article
LETTER: Evolutionary History of Cer Elements and Their Impact on the C. elegans Genome
- Eric W. Ganko,
- Kevin T. Fielman,
- and John F. McDonald
Genome Res. December 1, 2001 11: 2066-2074; doi:10.1101/gr.196201
...nucleotide sequences were added to establish subfamily structure (red). tRNA primer binding sites (PBSs) are highlighted to show conservation of tRNA priming across families. Alignments were produced via MacVector ( http://www.gcg.com ) and ClustalX 1.8 ( Thompson et al. 1997 ). * PBS reported by Frame et al...
Select this article
LETTER: A Novel Class of Mammalian-Specific Tailless Retropseudogenes
- Jürgen Schmitz,
- Gennady Churakov,
- Hans Zischler,
- and Jürgen Brosius
Genome Res. October 2004 14: 1911-1915; Published in Advance September 13, 2004, doi:10.1101/gr.2720104
.... ( B ) The genomic integration site with the consensus sequence TT/WX 1-17 (in this particular case, TT/WX 6 ) is shown above the bracket. The RNA priming site is boxed, the direction of reverse transcription is indicated by an arrow. The presumed single-stranded, staggered end is shown by a double...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Shibata et al. 5 (4): 400.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: