BITS Meetings' Virtual Library:
Abstracts from Italian Bioinformatics Meetings from 1999 to 2013

766 abstracts overall from 11 distinct proceedings

1. Fabbri M, Guffanti A, Cocito A, Furia L, Fallini R, McBlane F
RSSDB: A database of cryptic recombination signal sequences involved in V(D)J recombination.
Meeting: BITS 2005 - Year: 2005
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Topic: Unspecified

Abstract: The antigen receptor repertoire is generated through rearrangements of Immunoglobulin (Ig) and T-cell receptor (TCR) gene segments into functional genes by a mechanism named V(D)J recombination. This is a two-step process: a cleavage step in which double-strand DNA cuts are made at specific sequences, followed by a joining step to repair the breaks. The coding segments of Ig and TCR genes are flanked by short recombination signal sequences (RSS). The RSS are recognized by a complex of the lymphocyte specific recombination proteins RAG1 and RAG2, which cleave the DNA between the coding sequence and the RSS. The broken coding strands are then rejoined to produce a rearranged gene. Mistakes in this process can generate chromosomal translocations that are involved in acute lymphoid leukemias and non-Hodgkin lymphomas. These errors include cleavage of DNA sequences, termed cryptic RSS, similar to functional RSS but located outside the Ig or TCR loci. We have screened the human and mouse genomes for the presence of putative cryptic RSS. To provide an initial list enriched in cryptic RSS, we used an original search algorithm. This primary set was then further filtered for biologically functional sequences using a published method. We have created a web-accessible database containing these putative recombination signals in the genome context. This is the first repository containing a genome-wide collection of RSS sequences. These sequence tags can be retrieved from a number of starting points including RSS type (with 12- or 23 bp spacer), chromosomal region, cytoband and gene identity. For visualization of our RSS search results, we have chosen to rely on an existing genome annotation knowledgebase and correlate our results with the gene structure, analysis, annotation and browsing features of the UCSC Genome Browser. Sequences of interest may also be searched for the occurrence of RSS and the corresponding tracks searched from within the genome database.

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