scholarly journals Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

2011 ◽  
Vol 5 (8) ◽  
pp. 1291-1302 ◽  
Author(s):  
Céline Brochier-Armanet ◽  
Philippe Deschamps ◽  
Purificación López-García ◽  
Yvan Zivanovic ◽  
Francisco Rodríguez-Valera ◽  
...  
Keyword(s):  
Fosmid End Sequences ◽  
End Sequences

Construction and characterization of a sugar beet (Beta vulgaris) fosmid library

Genome ◽  
2008 ◽  
Vol 51 (11) ◽  
pp. 948-951 ◽  
Author(s):  
Cornelia Lange ◽  
Daniela Holtgräwe ◽  
Britta Schulz ◽  
Bernd Weisshaar ◽  
Heinz Himmelbauer
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Fosmid Library ◽  
Average Insert Size ◽  
Size Estimation ◽  
Insert Size ◽  
Pcr Screening ◽  
Organellar Dna ◽  
Fosmid End Sequences ◽  
End Sequences

A sugar beet ( Beta vulgaris ) fosmid library from the doubled haploid accession KWS2320 encompassing 115 200 independent clones was constructed and characterized. The average insert size of the fosmid library was determined by pulsed field gel electrophoresis to be 39 kbp on average, thus representing 5.9-fold coverage of the sugar beet genome (758 Mbp). PCR screening of plate pools with primer pairs against nine sugar beet genes supported the insert size estimation. BLAST searches with 2951 fosmid end-sequences originating from 1510 clones (1536 clones attempted) revealed little contamination with organellar DNA (2.1% chloroplast DNA, 0.3% mitochondrial DNA). The sugar beet fosmid library will be integrated in the presently ongoing efforts to determine the sequence of the sugar beet genome. Fosmids will be publicly available in the format of plate pools and individual clones.

scholarly journals A human–horse comparative map based on equine BAC end sequences

Genomics ◽  
2006 ◽  
Vol 87 (6) ◽  
pp. 772-776 ◽  
Author(s):  
Tosso Leeb ◽  
Claus Vogl ◽  
Baoli Zhu ◽  
Pieter J. de Jong ◽  
Matthew M. Binns ◽  
...  
Keyword(s):  
Comparative Map ◽  
End Sequences

scholarly journals Site-Directed Mutagenesis Studies of Tn5 Transposase Residues Involved in Synaptic Complex Formation

2007 ◽  
Vol 189 (20) ◽  
pp. 7436-7441 ◽  
Author(s):  
Soheila Vaezeslami ◽  
Rachel Sterling ◽  
William S. Reznikoff
Keyword(s):  
Complex Formation ◽  
Catalytic Reactions ◽  
Site Directed Mutagenesis ◽  
Dna Interactions ◽  
Synaptic Complex ◽  
Biochemical Assays ◽  
Protein Dna Interactions ◽  
End Sequences ◽  
Tn5 Transposase ◽  
Cocrystal Structure

ABSTRACT Transposition (the movement of discrete segments of DNA, resulting in rearrangement of genomic DNA) initiates when transposase forms a dimeric DNA-protein synaptic complex with transposon DNA end sequences. The synaptic complex is a prerequisite for catalytic reactions that occur during the transposition process. The transposase-DNA interactions involved in the synaptic complex have been of great interest. Here we undertook a study to verify the protein-DNA interactions that lead to synapsis in the Tn5 system. Specifically, we studied (i) Arg342, Glu344, and Asn348 and (ii) Ser438, Lys439, and Ser445, which, based on the previously published cocrystal structure of Tn5 transposase bound to a precleaved transposon end sequence, make cis and trans contacts with transposon end sequence DNA, respectively. By using genetic and biochemical assays, we showed that in all cases except one, each of these residues plays an important role in synaptic complex formation, as predicted by the cocrystal structure.

Compositional Distribution of Binary Living Copolymers and Their End Sequences

2021 ◽  
pp. 2100002
Author(s):  
Olga Trhlíková ◽  
Zuzana Walterová ◽  
Miroslav Janata ◽  
Lívia Kanizsová ◽  
Jiří Horský
Keyword(s):  
Compositional Distribution ◽  
End Sequences

scholarly journals The integration preference of Sleeping Beauty at non-TA site is related to the transposon end sequences

2019 ◽  
Author(s):  
Yiting Zhou ◽  
Guangwei Ma ◽  
Jiawen Yang ◽  
Yabin Guo
Keyword(s):  
Site Selection ◽  
Genomic Dna ◽  
Consensus Sequence ◽  
Mouse Cell ◽  
Sleeping Beauty ◽  
Consensus Sequences ◽  
Target Site Selection ◽  
Target Sites ◽  
End Sequences ◽  
Selection Of

Abstract Background: Sleeping Beauty (SB) transposon had been thought to strictly integrate into TA dinucleotides. Recently, we found that SB also integrates into non-TA sites at a lower frequency. Here we performed further study on the non-TA integration of SB. Results: 1) SB can integrate into non-TA sites in HEK293T cells as well as in mouse cell lines. 2) Both the hyperactive transposase SB100X and the traditional SB11 catalyze integrations at non-TA sites. 3) The consensus sequence of the non-TA target sites only occur at the opposite side of the sequenced junction between transposon end and the genomic sequences, indicating that the integrations at non-TA sites are mainly aberrant integrations. 4) The consensus sequence of the non-TA target sites is corresponding to the transposon end sequence. When the transposon end sequence is mutated, the consensus sequences changed too. Conclusion: The interaction between the SB transposon end and genomic DNA may be involved in the target site selection of the SB integrations at non-TA sites.

scholarly journals Addition of Poly(A) and Heteropolymeric 3′ Ends in Bacillus subtilis Wild-Type and Polynucleotide Phosphorylase-Deficient Strains

2005 ◽  
Vol 187 (14) ◽  
pp. 4698-4706 ◽  
Author(s):  
Juan Campos-Guillén ◽  
Patricia Bralley ◽  
George H. Jones ◽  
David H. Bechhofer ◽  
Gabriela Olmedo-Alvarez
Keyword(s):  
Bacillus Subtilis ◽  
Bacterial Species ◽  
Synthetic Activity ◽  
Polynucleotide Phosphorylase ◽  
Wild Type ◽  
Mutant Strains ◽  
Mean Size ◽  
Identical Nucleotide ◽  
End Sequences ◽  
Polymerase I

ABSTRACT Polyadenylation plays a role in decay of some bacterial mRNAs, as well as in the quality control of stable RNA. In Escherichia coli, poly(A) polymerase I (PAP I) is the main polyadenylating enzyme, but the addition of 3′ tails also occurs in the absence of PAP I via the synthetic activity of polynucleotide phosphorylase (PNPase). The nature of 3′-tail addition in Bacillus subtilis, which lacks an identifiable PAP I homologue, was studied. Sizing of poly(A) sequences revealed a similar pattern in wild-type and PNPase-deficient strains. Sequencing of 152 cloned cDNAs, representing 3′-end sequences of nontranslated and translated RNAs, revealed modified ends mostly on incomplete transcripts, which are likely to be decay intermediates. The 3′-end additions consisted of either short poly(A) sequences or longer heteropolymeric ends with a mean size of about 40 nucleotides. Interestingly, multiple independent clones exhibited complex heteropolymeric ends of very similar but not identical nucleotide sequences. Similar polyadenylated and heteropolymeric ends were observed at 3′ ends of RNA isolated from wild-type and pnpA mutant strains. These data demonstrated that, unlike the case of some other bacterial species and chloroplasts, PNPase of Bacillus subtilis is not the major enzyme responsible for the addition of nucleotides to RNA 3′ ends.

BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea

2004 ◽  
Vol 41 (7) ◽  
pp. 657-666 ◽  
Author(s):  
Michael R. Thon ◽  
Stanton L. Martin ◽  
Stephen Goff ◽  
Rod A. Wing ◽  
Ralph A. Dean
Keyword(s):  
Transposable Element ◽  
Magnaporthe Grisea ◽  
Physical Map ◽  
Element Content ◽  
End Sequences ◽  
Clustering Patterns

Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus

2010 ◽  
Vol 97 (11) ◽  
pp. e124-e129 ◽  
Author(s):  
Frédérique Ollitrault ◽  
Javier Terol ◽  
Jose Antonio Pina ◽  
Luis Navarro ◽  
Manuel Talon ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Citrus Clementina ◽  
End Sequences
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