Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development.
journal of experimental medicine
2016; 213 (9): 1921-1936
Yin Yang 1 Promotes Thymocyte Survival by Downregulating p53
JOURNAL OF IMMUNOLOGY
2016; 196 (6): 2572-2582
T cell antigen receptor ? (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination events in developing ?? thymocytes. Here, we use linear amplification-mediated high-throughput genome-wide translocation sequencing (LAM-HTGTS) to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in CD4(-)CD8(-) double-negative thymocyte progenitors differentiated in vitro from bone marrow-derived hematopoietic stem cells. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, whereas Trdd1 joining is ordered with joining to Trdd2, a prerequisite for further rearrangement. We also find frequent, previously unappreciated, Trdd1 and Trdd2 rearrangements that inactivate Tcrd, including sequential rearrangements from V(D)J recombination signal sequence fusions. Moreover, we find dozens of RAG off-target sequences that are generated via RAG tracking both upstream and downstream from the Trdd2 recombination center across the Tcrd loop domain that is bounded by the upstream INT1-2 and downstream TEA elements. Disruption of the upstream INT1-2 boundary of this loop domain allows spreading of RAG on- and off-target activity to the proximal Trdv domain and, correspondingly, shifts the Tcrd V(D)J recombination landscape by leading to predominant V(D)J joining to a proximal Trdv3 pseudogene that lies just upstream of the normal boundary.
View details for DOI 10.1084/jem.20160670
View details for PubMedID 27526713
View details for PubMedCentralID PMC4995090
Molecular Analysis of Mouse T Cell Receptor a and ß Gene Rearrangements.
Methods in molecular biology (Clifton, N.J.)
2016; 1323: 179-202
Yin Yang 1 (YY1) is a zinc finger protein that functions as a transcriptional activator or repressor and participates in multiple biological processes, including development and tumorigenesis. To investigate the role of YY1 in developing T cells, we used mouse models that depleted YY1 at two distinct stages of thymocyte development. When YY1 was depleted in CD4(-)CD8(-) double-negative thymocytes, development to the CD4(+)CD8(+) double-positive stage was impaired, due to increased apoptosis that prevented expansion of post-?-selection thymocytes. When YY1 was depleted in double-positive thymocytes, they underwent increased cell-autonomous apoptosis in vitro and displayed a shorter lifespan in vivo, as judged by their ability to undergo secondary V?-to-J? recombination. Mechanistically, we found that the increased apoptosis in YY1-deficient thymocytes was attributed to overexpression of p53, because concurrent loss of p53 completely rescued the developmental defects of YY1-deficient thymocytes. These results indicated that YY1 functions as a critical regulator of thymocyte survival and that it does so by suppressing the expression of p53.
View details for DOI 10.4049/jimmunol.1501916
View details for Web of Science ID 000372338100015
View details for PubMedID 26843327
View details for PubMedCentralID PMC4779672
An Ectopic CTCF Binding Element Inhibits Tcrd Rearrangement by Limiting Contact between V? and D? Gene Segments.
Journal of immunology (Baltimore, Md. : 1950)
2016; 197 (8): 3188?97
PCR on genomic DNA isolated from lymphocyte populations is an invaluable technique to analyze T cell receptor (TCR) ? and ? gene rearrangements. Although this approach is powerful, it also has limitations that must be accounted for in experimental design and data interpretation. Here, we provide background required for understanding these limitations, and then outline standard PCR methods that can be used for analysis of TCR? and ? gene rearrangements in mice.
View details for DOI 10.1007/978-1-4939-2809-5_16
View details for PubMedID 26294409
Inactivation of nuclear GSK3 beta by Ser(389) phosphorylation promotes lymphocyte fitness during DNA double-strand break response
Chromatin looping mediated by the CCCTC binding factor (CTCF) regulates V(D)J recombination at Ag receptor loci. CTCF-mediated looping can influence recombination signal sequence (RSS) accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate long-distance interactions between RSSs, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG tracking, and RAG-independent long-distance interactions. In this study, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of E? in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. The ectopic CBE also limited directional RAG tracking from the Tcrd recombination center, demonstrating that a single CBE can impact the distribution of RAG proteins along chromatin. However, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent contacts between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility, and RAG tracking.
View details for PubMedID 27613698
A discrete chromatin loop in the mouse Tcra-Tcrd locus shapes the TCR delta and TCR alpha repertoires
2015; 16 (10): 1085-?
Variable, diversity and joining (V(D)J) recombination and immunoglobulin class switch recombination (CSR) are key processes in adaptive immune responses that naturally generate DNA double-strand breaks (DSBs) and trigger a DNA repair response. It is unclear whether this response is associated with distinct survival signals that protect T and B cells. Glycogen synthase kinase 3? (GSK3?) is a constitutively active kinase known to promote cell death. Here we show that phosphorylation of GSK3? on Ser(389) by p38 MAPK (mitogen-activated protein kinase) is induced selectively by DSBs through ATM (ataxia telangiectasia mutated) as a unique mechanism to attenuate the activity of nuclear GSK3? and promote survival of cells undergoing DSBs. Inability to inactivate GSK3? through Ser(389) phosphorylation in Ser(389)Ala knockin mice causes a decrease in the fitness of cells undergoing V(D)J recombination and CSR. Preselection-Tcr? repertoire is impaired and antigen-specific IgG antibody responses following immunization are blunted in Ser(389)GSK3? knockin mice. Thus, GSK3? emerges as an important modulator of the adaptive immune response.
View details for DOI 10.1038/ncomms10553
View details for Web of Science ID 000369032900001
View details for PubMedID 26822034
View details for PubMedCentralID PMC4740185
An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development
JOURNAL OF EXPERIMENTAL MEDICINE
2015; 212 (5): 809-824
The locus encoding the T cell antigen receptor (TCR) ?-chain and ?-chain (Tcra-Tcrd) undergoes recombination of its variable-diversity-joining (V(D)J) segments in CD4(-)CD8(-) double-negative thymocytes and CD4(+)CD8(+) double-positive thymocytes to generate diverse TCR? repertoires and TCR? repertoires, respectively. Here we identified a chromatin-interaction network in the Tcra-Tcrd locus in double-negative thymocytes that was formed by interactions between binding elements for the transcription factor CTCF. Disruption of a discrete chromatin loop encompassing the D, J and constant (C) segments of Tcrd allowed a single V segment to frequently contact and rearrange to D and J segments and dominate the adult TCR? repertoire. Disruption of this loop also narrowed the TCR? repertoire, which, we believe, followed as a consequence of the restricted TCR? repertoire. Hence, a single CTCF-mediated chromatin loop directly regulated TCR? diversity and indirectly regulated TCR? diversity.
View details for DOI 10.1038/ni.3232
View details for Web of Science ID 000361686500014
View details for PubMedID 26258942
View details for PubMedCentralID PMC4575630
Rag1 and Rag2 gene expression in CD4(+)CD8(+) double-positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here, we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes.
View details for DOI 10.1084/jem.20142207
View details for Web of Science ID 000353898100019
View details for PubMedID 25847946
View details for PubMedCentralID PMC4419350