The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl.html) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. While automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO), the preferred submission tool for individual submitters is Webin (WWW). Through all stages, dataflow is monitored by EBI biologists communicating with the sequencing groups. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI). Database releases are produced quarterly and are distributed on CD-ROM. Network services allow access to the most up-to-date data collection via Internet and World Wide Web interface. EBI's Sequence Retrieval System (SRS) is a Network Browser for Databanks in Molecular Biology, integrating and linking the main nucleotide and protein databases, plus many specialised databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, Blast etc) are available for external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

/pdf/the-embl-nucleotide-sequence-database-4jalicikpk.pdf

The EMBL Nucleotide Sequence Database

Here, we describe a fast, simple method for constructing fulllength cDNA libraries using SMART™ technology. This novel procedure uses the template-switching activity of Moloney murine leukemia viru...

https://www.future-science.com/doi/pdf/10.2144/01304pf02

Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction.

Interspecific or intergeneric hybridization, followed by chromosome doubling, can lead to the formation of new allopolyploid species. Recent studies indicate that allopolyploid formation is associated with genetic and epigenetic changes, although little is known about the type of changes that occur, how rapidly they occur, and the type of sequences involved. To address these matters, we have surveyed F1 hybrids between diploid species from the wheat (Aegilops and Triticum) group and their derived allotetraploids by screening a large number of loci using amplified fragment length polymorphism and DNA gel blot analysis and by assaying the extent of cytosine methylation. We found that sequence elimination is one of the major and immediate responses of the wheat genome to wide hybridization or allopolyploidy, that it affects a large fraction of the genome, and that it is reproducible. In one cross between Ae. sharonensis × Ae. umbellulata, 14% of the loci from Ae. sharonensis were eliminated compared with only 0.5% from Ae. umbellulata, with most changes occurring in the F1 hybrid. In contrast, crosses between Ae. longissima × T. urartu showed that sequence elimination was more frequent after chromosome doubling. Alterations in cytosine methylation occurred in ∼13% of the loci, either in the F1 hybrid or in the allopolyploid. For eight of nine bands that were isolated, the sequences that underwent elimination corresponded to low-copy DNA, whereas alterations in methylation patterns affected both repetitive DNA sequences, such as retrotransposons, and low-copy DNA in approximately equal proportions.

Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat

Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.

Biology of DNA restriction.

Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes.

/pdf/effect-of-site-specific-modification-on-restriction-2my7dk9v8t.pdf

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

We present in Table I an updated list of the sensitivities of 298 restriction endonucleases and 20 DNA methyltransferases to sitespecific modification at 4-methylcytosine (\"HT), 5-methylcytosine C^C), 5-hydroxymethylcytosine OTM^), and 6-methyladenine (^A) (McC14), four modifications that are common in the DNA of prokaryotes, eukaryotes, and their viruses (Mc2,Mc5,Mc8,Mcll,Ne3,Ne4). In addition, new information is included on restriction endonuclease cleavage at sites modified with 5-hydroxymethyluracil ( ^ U ) . Knowledge of the sensitivity of restriction endonucleases to site-specific modification can be used to study cellular DNA methylation. Several restriction-modification enzymes share the same recognition sequence specificity, but have different sensitivities to site-specific methylation. Table II lists 32 known isoschizomer pairs and one isomethylator pair, along with the modified recognition sites at which they differ. The data presented here and an additional three other tables are available in printed form or as a text file on a 3.5\" Macintosh diskette. The extra tables include Table HI which is a list of over 205 characterized DNA methyltransferases. A detailed list of cloned restriction-modification genes has been made by Wilson (Wi4). Table IV lists the sensitivities of over 20 Type II DNA methyltransferases to \"^C, C, C, and \"^A modification. Most DNA methyltransferases are sensitive to non-canonical modifications within their recognition sequences (Bu9,MclO, Ne3,Po4), and this sensitivity often differs from that of their restriction endonuclease partners. Table V gives a list of restriction systems in this review alphabetized by recognition sequence. The data can be supplied as a Microsoft Word, Macwrite or MS-DOS file. Please contact Michael McClelland at CTBR, phone 619 535 5486, FAX 619 535 5472.

/pdf/effect-of-site-specific-methylation-on-restriction-2kyrge1olw.pdf

Eberhard Raschke

Papers

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases.