Characterization of immature thymocyte lines derived from T-cell receptor or recombination activating gene 1 and p53 double mutant mice.

Mombaerts, Peter; Terhorst, Cox; Jacks, Tyler; Tonegawa, Susumu; Sancho, Jaime

doi:10.1073/pnas.92.16.7420

Cited by 44 publications

(38 citation statements)

References 31 publications

(42 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The P5424 cell line is originated from early developing T cells and resembles DP thymocytes at phenotypic and transcriptomic levels (ref. 8 and Supplementary Fig. 1a,b).…”

Section: Resultsmentioning

confidence: 99%

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

et al. 2015

View full text Add to dashboard Cite

Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starrseq technique. Extensive assessment of CapStarr-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms.

show abstract

“…The P5424 cell line is originated from early developing T cells and resembles DP thymocytes at phenotypic and transcriptomic levels (ref. 8 and Supplementary Fig. 1a,b).…”

Section: Resultsmentioning

confidence: 99%

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Three different types of murine cell lines, representative of three different lineage and developmental contexts, were analyzed: a RAG2 Ϫ͞Ϫ Abelson virus transformed Pro B cell line (32), a RAG1 Ϫ͞Ϫ p53 Ϫ͞Ϫ Pro T cell line (33), and NIH 3T3 cells, a fibroblast line. The use of cell lines ensured we were analyzing a homogeneous population of cells at a discrete developmental stage and that adequate material could be obtained for analysis.…”

Section: Resultsmentioning

confidence: 99%

“…RAG2-deficient Abelson murine leukemia virusderived Pro B cells (32) and RAG1-deficient, p53-deficient Pro T cells (33) were maintained in RPMI medium 1640 supplemented with 20% FBS and 0.05 mM 2-mercaptoethanol. NIH 3T3 cells were maintained in DMEM supplemented with 10% calf serum.…”

Section: Methodsmentioning

confidence: 99%

Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4

Morshead

Ciccone

Taverna

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

175

170

View full text Add to dashboard Cite

In the earliest stages of antigen receptor assembly, D and J segments of the Ig heavy chain and T cell receptor ␤ loci are recombined in B and T cells, respectively, whereas the V segments are not. Distinct distribution patterns of various histone modifications and the nucleosome-remodeling factor BRG1 are found at ''active'' (DJ) and ''inactive'' (V) regions. Striking ''hotspots'' of histone H3 dimethylated at lysine 4 (di-Me H3-K4) are localized at the ends of the active DJ domains of both the Ig heavy chain and T cell receptor ␤ loci. BRG1 is not localized to specific sequences, as it is with transcriptional initiation, but rather associates with the entire active locus in a pattern that mirrors acetylation of histone H3. Within some inactive loci marked by H3-K9 dimethylation, two distinct levels of methylation are found in a nonrandom genesegment-specific pattern. We suggest that the hotspots of di-Me H3-K4 are important marks for locus accessibility. The specific patterns of modification imply that the regulation of V(D)J recombination involves recruitment of specific methyltransferases in a localized manner.T he chromatin in the nucleus of eukaryotic cells is regulated to permit or exclude access of the enzymatic machinery for processes such as transcription and recombination. Specific regulatory sequences in the DNA are ultimately responsible for this regulation, serving as binding sites for proteins or protein complexes that recruit specific chromatin-modifying activities. In the case of transcriptional regulation, specific DNA-binding activators or repressors recruit histone-modifying enzymes and nucleosome remodeling complexes, generating localized modifications of the chromatin that govern the access of the transcription machinery (reviewed in refs. 1 and 2). In addition to such localized chromatin modifications, there are developmentally regulated large-scale reorganizations of chromatin structure into active and inactive domains [e.g., ␤-globin genes in chickens (3) and the mating-type locus in Schizosaccharomyces pombe (4)] (reviewed in ref. 5).A variety of covalent histone modifications are associated with active or inactive chromatin (6-8). Acetylation of histones H3 and H4 is well known to mark transcriptionally active chromatin. Dimethylation of histone H3 on lysine 4 (di-Me H3-K4) is often observed at active loci in yeast (4), Tetrahymena (9), and chicken (3), although associations with silent loci have also been reported (10). In contrast, dimethylation of histone H3 on lysine 9 (di-Me H3-K9) is often, if not always, correlated with regions of silent inactive chromatin (11).Coordination of the series of DNA rearrangement events required to assemble Ig and TCR genes from component V, D, and J segments presents a highly complex regulatory problem (reviewed in refs. 12 and 13). There are seven structurally unique antigen receptor loci, some spanning 3 or 4 megabases, each composed of multiple V, J, and sometimes D segments, along with nonrearranging constant (C) gene segments. Rearrangement is ...

show abstract

“…Thymoma line 4b was derived from a DP thymocyte of a mouse deficient in both p53 and TCR␣ (41). Thymoma EL4 was derived from a CD4 ϩ thymocyte.…”

Section: Dna Probes and Plasmids-a 780-bpmentioning

confidence: 99%

A Nuclear Matrix Attachment Region Upstream of the T Cell Receptor β Gene Enhancer Binds Cux/CDP and SATB1 and Modulates Enhancer-dependent Reporter Gene Expression but Not Endogenous Gene Expression

Chattopadhyay

Whitehurst

Chen

1998

Journal of Biological Chemistry

View full text Add to dashboard Cite

We have previously identified a DNase I-hypersensitive site in the T cell receptor ␤ locus, designated HS1, that is located 400 base pairs upstream of the transcriptional enhancer E ␤ and is induced during CD4 ؊ CD8 ؊ to CD4 ؉ CD8؉ thymocyte differentiation. Using electrophoretic mobility shift assays, we show that HS1 induction correlates with increased binding of two nuclear factors, Cux/CDP and SATB1, to a 170-base pair DNA sequence within HS1. Furthermore, we demonstrate that HS1 is a nuclear matrix attachment region, referred to as MAR ␤ . These findings demonstrate that an analogous organization of cis-regulatory elements in which a nuclear matrix attachment region is in close proximity to an enhancer is conserved in the immunoglobulin and T cell receptor loci. In addition, we show that MAR expressed by an individual T cell (4, 5). After V ␤ D ␤ J ␤ rearrangement, a mature transcript is initiated from the V ␤ promoter in a T cell-specific manner (6). To achieve the lineage-, stage-, and allele-specific TCR␤ gene rearrangement and transcription, many cis-acting elements and their associated transacting factors are likely to be involved (4, 5).To date, the TCR␤ gene enhancer (E ␤ ) is the only cis-regulatory element demonstrated to be required for both the lineage-and stage-specific transcription and rearrangement of the TCR␤ gene (7-12). Although the V ␤ promoter is required for lineage-specific TCR␤ transcription, its role in regulating V ␤ gene rearrangement remains unclear (13-17). In addition to V ␤ promoters and E ␤ , there are likely other cis-regulatory elements involved in the control of various aspects of TCR␤ gene rearrangement and transcription. In particular, nuclear matrix attachment regions (MAR) are a class of cis-regulatory elements found in many genetic loci that are distinct from transcriptional promoters and enhancers, and yet are often closely associated with these regulatory elements (18 -20). MARs are typically AT-rich DNA sequences that bind to the nuclear matrix, often contain topoisomerase II cleavage sites, and exhibit a propensity for base unpairing when subjected to superhelical strain (21, 22). They have been proposed to be involved in transcription, DNA recombination, replication, and repair (23). In the immunoglobulin heavy chain (IgH) locus, MARs flank the intronic enhancer E and are in close proximity to V H promoters (22)(23)(24)(25)(26). Reporter gene assays in cell lines and transgenic mice have suggested that these MARs exert both positive and negative effects on IgH gene transcription and promote long range chromatin accessibility (27-31). A highly conserved MAR is also found 200 base pairs (bp) upstream of the intronic immunoglobulin (Ig) enhancer in mouse, human, and rabbit (22,32). Together, the Ig MAR and enhancer promote demethylation, transcription, recombination, and somatic hypermutation of the locus although no specific function has been attributed to the MAR alone (33-36). The presence of MARs at other antigen receptor loci has not been reported.To characteriz...

show abstract

Characterization of immature thymocyte lines derived from T-cell receptor or recombination activating gene 1 and p53 double mutant mice.

Cited by 44 publications

References 31 publications

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4

A Nuclear Matrix Attachment Region Upstream of the T Cell Receptor β Gene Enhancer Binds Cux/CDP and SATB1 and Modulates Enhancer-dependent Reporter Gene Expression but Not Endogenous Gene Expression

Contact Info

Product

Resources

About