Marqueur de séquence exprimée

Résumé

Un marqueur de séquence exprimée, ou expressed sequence tag (EST), est une courte portion séquencée d'un ADN complémentaire (ADNc), utilisée comme marqueur pour différencier les gènes entre eux dans une séquence ADN et identifier les gènes homologues dans d'autres espèces. Parce qu'il est généralement assez facile de récupérer des brins d'ARNm des cellules, les biologistes récupèrent ces séquences et les convertissent en ADNc, qui est bien plus stable. Un ARNm étant forcément l'expression d'un gène du génome, cet ADNc n'est pas une copie exacte de la séquence ADN qui a généré l'ARN car, à la suite de l'épissage, l'ARN ne garde pas les régions non codantes de l'ADN (introns). Si le génome est correctement identifié, les gènes le composant ne le sont pas encore tous. Et certains gènes identifiés ont une fonction encore inconnue. En utilisant les EST, on cherche à identifier un gène par le chemin inverse, c'est-à-dire que l'on prend la séquence d'ARN pour trouver la séquence d'ADN qui

Source officielle

https://fr.wikipedia.org/wiki/Marqueur_de_s%C3%A9quence_exprim%C3%A9e

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In systems biology, proteomics represents an essential pillar. The understanding of protein function and regulation provides key information to decipher the complexity of living systems. Proteomic technology now enables deep quantitative proteome mapping via mass spectrometry.

Chemical biology is a key discipline in biomedical research for drug discovery, synthetic biology and protein functional annotation. We will give a broad perspective of the field ranging from seminal classical experiments to state-of-the-art approaches to dissect and perturb biological systems.

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Nineteen additional unpredicted transcripts from human chromosome 21

Philipp Bucher

The identification of all human chromosome 21 (HC21) genes is a necessary step in understanding the molecular pathogenesis of trisomy 21 (Down syndrome). The first analysis of the sequence of 21q included 127 previously characterized genes and predicted an additional 98 novel anonymous genes. Recently we evaluated the quality of this annotation by characterizing a set of HC21 open reading frames (C21orfs) identified by mapping spliced expressed sequence tags (ESTs) and predicted genes (PREDs), identified only in silico. This study underscored the limitations of in silico-only gene prediction, as many PREDs were incorrectly predicted. To refine the HC21 annotation, we have developed a reliable algorithm to extract and stringently map sequences that contain bona fide 3' transcript ends to the genome. We then created a specific 21q graphical display allowing an integrated view of the data that incorporates new ESTs as well as features such as CpG islands, repeats, and gene predictions. Using these tools we identified 27 new putative genes. To validate these, we sequenced previously cloned cDNAs and carried out RT-PCR, 5'- and 3'-RACE procedures, and comparative mapping. These approaches substantiated 19 new transcripts, thus increasing the HC21 gene count by 9.5%. These transcripts were likely not previously identified because they are small and encode small proteins. We also identified four transcriptional units that are spliced but contain no obvious open reading frame. The HC21 data presented here further emphasize that current gene prediction algorithms miss a substantial number of transcripts that nevertheless can be identified using a combination of experimental approaches and multiple refined algorithms.

2002

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trEST, trGEN and Hits: access to databases of predicted protein sequences

Philipp Bucher

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits. isb-sib.ch).

2001

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The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In the work presented here, we have focused on mapping mRNA 3' ends onto the genome by use of the raw data generated by the expressed sequence tag (EST) sequencing projects. We find that at least half of the human genes encode multiple transcripts whose polyadenylation is driven by multiple signals. The corresponding transcript 3' ends are spread over distances in the kilobase range. This finding has profound implications for our understanding of gene expression regulation and of the diversity of human transcripts, for the design of cDNA microarray probes, and for the interpretation of gene expression profiling experiments.

2002

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