Reassignment of the murine 3'TRDD1 recombination signal sequence.

T cell receptor genes are assembled in developing T lymphocytes from discrete V, D, and J genes by a site-specific somatic rearrangement mechanism. A flanking recombination signal, composed of a conserved heptamer and a semiconserved nonamer separated by 12 or 23 variable nucleotides, targets the activity of the rearrangement machinery to the adjoining V, D, and J genes. Following the rearrangement of V, D, or J genes, their respective recombination signals are ligated together. Although these signal joints are allegedly invariant, created by the head-to-head abuttal of the heptamers, some do exhibit junctional diversity. Recombination signals were initially identified by comparison and alignment of germ-line sequences with the sequence of rearranged genes. However, their overall low level of sequence conservation makes their characterization solely from sequence data difficult. Recently, computational analysis unraveled correlations between nucleotides at several positions scattered within the spacer and recombination activity, so that it is now possible to identify putative recombination signals and determine and predict their recombination efficiency. In this paper, we analyzed the variability introduced in signal joints generated after rearrangement of the TRDD1 and TRDD2 genes in murine thymocytes. The recurrent presence of identical nucleotides inserted in these signal joints led us to reconsider the location and sequence of the TRDD1 recombination signal. By combining molecular characterization and computational analysis, we show that the functional TRDD1 recombination signal is shifted inside the putative coding sequence of the TRDD1 gene and, consequently, that this gene is shorter than indicated in the databases

Shape-Based Tracking Allows Functional Discrimination of Two Immune Cell Subsets Expressing the Same Fluorescent Tag in Mouse Lung Explant

Dendritic Cells (DC) represent a key lung immune cell population, which play a critical role in the antigen presenting process and initiation of the adaptive immune response. The study of DCs has largely benefited from the joint development of fluorescence microscopy and knock-in technology, leading to several mouse strains with constitutively labeled DC subsets. However, in the lung most transgenic mice do express fluorescent protein not only in DCs, but also in closely related cell lineages such as monocytes and macrophages. As an example, in the lungs of CX3CR1+/gfp mice the green fluorescent protein is expressed mostly by both CD11b conventional DCs and resident monocytes. Despite this non-specific staining, we show that a shape criterion can discriminate these two particular subsets. Implemented in a cell tracking code, this quantified criterion allows us to analyze the specific behavior of DCs under inflammatory conditions mediated by lipopolysaccharide on lung explants. Compared to monocytes, we show that DCs move slower and are more confined, while both populations do not have any chemotactism-associated movement. We could generalize from these results that DCs can be automatically discriminated from other round-shaped cells expressing the same fluorescent protein in various lung inflammation models

Analyse de la recombinaison des gènes TCRAD : réarrangements radio-induits et structure des jonctions signal.

We have shown that irradiation of pre-TCR-deficient CD3ε-/- mice restores thymocyte differentiation, by a p53-dependent and by a p53-independent pathway. Events normally associated during normal thymocyte development are dissociated in response to radiation exposure. Both of these pathways require LAT expression. Therefore, radiation exposure activates pre-TCR-like signals. TCRA gene rearrangement is induced following radiation exposure. The signal joints resulting from TCRA gene rearrangement have the same structure than those found in wild type mice. All signal joint analyzed in un-manipulated wild type mice do exhibit junctionnal diversity. This diversity results mainly from TdT activity. We present evidences that proteins involved in DNA repair and genomic stability participated in SJ formation. We propose that signal joint diversity is not an aberrant process but is a key feature of V(D)J recombination. All our work increases our understanding of molecular events associated with V(D)J recombination.La différenciation des lymphocytes T dans le thymus est strictement contrôlée par le réarrangement des gènes codants pour les chaînes du TCR et leur expression en surface dans le cadre du pré-TCR ou du TCR. Les souris incapables d'assembler un pré-TCR présentent un blocage précoce du développement des thymocytes. Nous avons montré que l'irradiation de souris CD3ε-/-, qui sont déficientes en pré-TCR, restaure la différenciation des thymocytes par des voies différentes selon que p53 soit présente ou non. En réponse à l'irradiation, il existe une dissociation temporelle de l'activation des voies de signalisations contrôlant plusieurs événements co-régulés durant le développement des thymocytes. Ces voies sont cependant toutes deux centralisées au niveau de LAT. L'irradiation induit donc des voies de signalisations mimant les effets de l'activation du pré-TCR.La différenciation radio-induite des thymocytes immatures s'accompagne du réarrangement de novo des gènes TCRA. L'étude des jonctions signal (JS) formées lors du réarrangement des gènes TCRA ne montre pas de différences de structure entre les JS de souris sauvages ou les JS formées suite à l'irradiation. Le réarrangement TCRA radio-induit est donc probablement l'œuvre de la machinerie de recombinaison traditionnelle. Contrairement au modèles actuels de recombinaison V(D)J les JS de souris sauvages analysées présentent des modifications, quels que soient les gènes réarrangés. Nous avons pu montrer une influence de plusieurs protéines impliquées dans la réparation de l'ADN et le maintient de la stabilité du génome sur la structure des JS. Nous proposons que ces modifications ne sont pas le résultat d'un processus de recombinaison aberrant mais constituent une propriété intrinsèque de la recombinaison. Nos travaux permettent donc une meilleure compréhension des mécanismes moléculaires de la recombinaison V(D)J

Analyse de la recombinaison des gènes TCRAD (Réarrangements radio-induits et structure des jonctions signal)

La différenciation des thymocytes est strictement contrôlée par le réarrangement des gènes codants pour les chaînes du TCR et leur expression dans le cadre du pré-TCR ou du TCR. Les souris incapables d'assembler un pré-TCR présentent un blocage du développement des thymocytes. Nous avons montré que l'irradiation de souris CD3e-/- restaure la différenciation des thymocytes en empruntant une voie P53 dépendante et une voie P53 indépendante. En réponse à l'irradiation, il existe une dissociation temporelle de l'activation des voies de signalisations contrôlant l'expression de CD2 et la reprise de la différenciation. Ces voies sont cependant toutes deux centralisées par LAT. L'irradiation active donc les voies de signalisations préTCR like. La différenciation radio-induite s'accompagne de plus du réarrangement de novo des gènes TCRA. L'étude des jonctions signal (JS) formées lors du réarrangement des gènes TCRA ne montre pas de différences de structure entre les JS de souris sauvages ou les JS formées suite à l'irradiation. Le réarrangement TCRA radio-induit est donc probablement l'œuvre de la machinerie de recombinaison traditionnelle. Quelques soient les gènes qui réarrangent, les JS de souris wt analysées, présentent des modifications résultant majoritairement de l'action de la TdT. Il semble donc que ces modifications sont une propriété intrinsèque de la recombinaison et non le résultat d'un processus infidèle. Pour finir nous avons pu montrer une influence des protéines de réparation et de maintient de la stabilité du génôme sur la structure des JS. Nos travaux permettent donc une meilleure compréhension des mécanismes moléculaires de la recombinaison V(D)J.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Gene-specific signal joint modifications during V(D)J recombination of TCRAD locus genes in murine and human thymocytes.

V(D)J recombination assembles functional T-cell receptor (TCR) genes from V, D and J components in developing thymocytes. Extensive processing of V, D and J extremities before they are ligated creates a high degree of junctional diversity which results in the generation of a large repertoire of different TCR chains. In contrast, the extremities of the intervening DNA segment, which bear the recombination signal sequences, are generally held to be monomorphic, so that signal joints (SJs) consist of the perfect head-to-head juxtaposition of recombination signal extremities. We analyzed the structure of SJs generated during the recombination of TCRAD locus genes in murine and human thymocytes. Junctional diversity resulting from N nucleotide additions or from N nucleotide additions and base loss was found for each type of SJ examined. Different patterns of processing/modification were found, suggesting that different enzymatic activities operate during recombination of TCRA and TCRD genes, although they are located within the same genetic locus. Recombination of the deltaRec-1 element generates a diverse repertoire of SJs exhibiting both combinatorial and junctional diversity in murine and human thymocytes. Therefore, SJ diversity appears to be an intrinsic feature of V(D)J recombination in unmanipulated thymocytes

Gene-specific signal joint modifications during V(D)J recombination of TCRAD locus genes in murine and human thymocytes

International audienceV(D)J recombination assembles functional T-cell receptor (TCR) genes from V, D and J components in developing thymocytes. Extensive processing of V, D and J extremities before they are ligated creates a high degree of junctional diversity which results in the generation of a large repertoire of different TCR chains. In contrast, the extremities of the intervening DNA segment, which bear the recombination signal sequences, are generally held to be monomorphic, so that signal joints (SJs) consist of the perfect head-to-head juxtaposition of recombination signal extremities. We analyzed the structure of SJs generated during the recombination of TCRAD locus genes in murine and human thymocytes. Junctional diversity resulting from N nucleotide additions or from N nucleotide additions and base loss was found for each type of SJ examined. Different patterns of processing/modification were found, suggesting that different enzymatic activities operate during recombination of TCRA and TCRD genes, although they are located within the same genetic locus. Recombination of the deltaRec-1 element generates a diverse repertoire of SJs exhibiting both combinatorial and junctional diversity in murine and human thymocytes. Therefore, SJ diversity appears to be an intrinsic feature of V(D)J recombination in unmanipulated thymocytes

Parameters used for individual cell analysis.

<p>A: Edge detection of two CX₃CR1+ pulmonary cells and their roundness coefficient. Scale bar  = 10 µm. B: The relevant parameters used in this work are: i) the Mean Roundness Coefficient (MRC), calculated for each cell by meaning Instantaneous Roundness Coefficient (IRC) at each consecutive observable time; ii) the Maximal Distance (MD) of a cell (red arrow) is the longest distance covered from the first position; iii) the Meandering Index (MI) is the final distance from the first position <i>D_n</i> divided by the total length covered.</p

Velocity of CX₃CR1-GFP positive pulmonary Dendritic-shaped and Round-shaped cells.

<p>A: Dendritic-shaped cells and B: Round-shaped cells at an early stage (average values from 1h30 to 2h30 post injection, closed symbols) and a late stage (average values from 5h to 6h post injection, open symbols) after injection of PBS (rounds) or LPS (squares). Three mice in each group, one symbol by cell. * for p<0.05; ** for p<0.01; *** for p<0.0001; ns for not significant.</p

Phenotype of CX₃CR1-GFP cell subsets in the lung.

<p>A: Total lung cells of CX₃CR1^+/gfp mice were gated on CX₃CR1 and analyzed for NK1.1, CD3e, CD11c, and CD11b expressions. B: Autofluorescence, CD80 and MHCII expressions on gate G1, G2 and G3 of panel A. Black histogram, isotype control; grey histogram, positive staining. C: Total lung cells were pre-gated on CD11c+ low autofluorecent cells and analyzed for the expression of CD11b and CD103. The expression of CX₃CR1 is shown on the left panel for gate G4 (CD11b⁻CD103⁺ DCs, grey histogram) and for gate G5 (CD11b⁺CD103⁻ DCs, black line). D: Total cells were pre-gated on CD45 cells and analyzed for the expression of F4/80 and CD11c. Expression of CX₃CR1 and CD11b is shown on the left panels for gate G6 (CD11c^lowF4/80^high), G7 (CD11c^highF4/80^high) and G8 (CD11c^highF4/80^low).Data from flow cytometry, performed on one CX₃CR1^+/gfp mouse lung harvested 30 minutes after intratracheal PBS injection. Data are representative of two distinct experiments.</p