DNA palindromes: The role of repair functions
Notice bibliographique
Résumé
2624 DNA palindromes consist of pairs of inversely repeated sequences having central symmetry that, along with forming typical B-form double helices, are able to form intra-strand hairpin and cruciform structures. However, the ability of palindromes to form hairpins and cruciforms poses a special threat to the genome as these secondary structures can block replication and lead to genetic rearrangements. In human and rodent systems, a unique mechanism for dealing with palindromes has been demonstrated, termed the Center-Break Model. In this mechanism, each of the hairpin tips are nicked, creating a double strand break at the center of symmetry. This break is then repaired by the NHEJ pathway, a process which often results in deletion of sequence creating a central asymmetry. While sequence analysis of breakpoints demonstrates the Center-Break mechanism, it is unknown which pathway(s) of detection and repair functions are involved. Investigations are being undertaken using both chromosomally and extra-chromosomally located palindromes combined with genetic knock-out and knock-down techniques in order to implicate both proteins and a potential pathway. For the chromosomal palindrome investigation, a mouse model carrying a 15.6kb perfect palindrome on chromosome 17, termed the Line 78 mouse is being used. The role of several proteins in palindrome processing are being tested, the first being the Werner’s syndrome protein because it is required for genome stability and affects the stability of the Tg.AC palindrome. Also, the potential roles for DNA-Pk, Ku70 because of their roles in NHEJ, and Artemis, as the hairpin-nicking nuclease in V(D)J recombination are being explored. Abelson cell lines generated from crosses of these mice are then monitored for palindrome rearrangement using subcloning, inverse-PCR and Southern blot techniques. Previous work in the lab had shown that the rate of rearrangement of the Line 78 palindrome in different wild-type backgrounds is 0.5% per generation. By determining the rate of rearrangement, as well as the quality (i.e. larger versus small deletions), in a variety of genetic backgrounds, I will be able to implicate various proteins and pathways in the process of palindrome rearrangement. The second approach to investigate the role of DNA repair functions in palindrome instability is an extra-chromosomal transfection assay. This approach examines rearrangement of a palindromic circular dimer, which can be transfected into cell cultures of interest. This palindrome is reproducibly and site-specifically resolved into monomer circles. This assay is being carried out in cell lines of the genetic backgrounds mentioned above, and is also being combined with RNAi techniques in oreder to expand the number of genetic influences that can be examined. This extra-chromosomal transfections assay will allow for rapid and varied investigation of the role of certain proteins in palindrome processing.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,000 |
| Bibliométrie | 0,001 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,001 |
| Communication savante | 0,002 | 0,001 |
| Science ouverte | 0,001 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,003 | 0,002 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».