Portal de Periódicos da CAPES

T Cell LEGO: Identifying the Master Builders and What They Do

2018; Cell Press; Volume: 48; Issue: 2 Linguagem: Inglês

10.1016/j.immuni.2018.02.004

1097-4180

Jasmine Li, Stephen T. Turner,

Epigenetics and DNA Methylation

Understanding how cell fate decisions are made during cellular differentiation and the mechanisms that drive them is a holy grail of cell biology. In this issue of Immunity, Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar and Johnson et al., 2018Johnson J.L. Georgakilas G. Petrovic J. Kurachi M. Cai S. Harly C. Pear W.S. Bhandoola A. Wherry E.J. Vahedi G. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cell development.Immunity. 2018; 48 (this issue): 243-257Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar demonstrate that key transcriptional regulators and global changes in nuclear architecture underlie differentiation decisions during T cell development. Understanding how cell fate decisions are made during cellular differentiation and the mechanisms that drive them is a holy grail of cell biology. In this issue of Immunity, Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar and Johnson et al., 2018Johnson J.L. Georgakilas G. Petrovic J. Kurachi M. Cai S. Harly C. Pear W.S. Bhandoola A. Wherry E.J. Vahedi G. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cell development.Immunity. 2018; 48 (this issue): 243-257Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar demonstrate that key transcriptional regulators and global changes in nuclear architecture underlie differentiation decisions during T cell development. In The LEGO Movie, "master builders" are special characters that cooperate to build different aspects of the LEGO universe. Similarly, the generation of distinct mammalian cells is controlled by specific transcription factors (TFs) or master builders that, when expressed at appropriate times, contribute to shaping cell fate during differentiation. This is the case for the generation of T cells, where master builders such as the TFs TCF-1 (encoded by Tcf-7), BCL11B, GATA3, and the RUNX family members are critical for T cell lineage commitment (Yui and Rothenberg, 2014Yui M.A. Rothenberg E.V. Developmental gene networks: a triathlon on the course to T cell identity.Nat. Rev. Immunol. 2014; 14: 529-545Crossref PubMed Scopus (217) Google Scholar). In this issue of Immunity, Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar and Johnson et al., 2018Johnson J.L. Georgakilas G. Petrovic J. Kurachi M. Cai S. Harly C. Pear W.S. Bhandoola A. Wherry E.J. Vahedi G. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cell development.Immunity. 2018; 48 (this issue): 243-257Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar provide insight into the mechanisms by which two master builders, TCF-1 and BCL11B, drive T cell differentiation decisions by remodeling nuclear architecture to generate a new gene transcriptional landscape. To regulate gene transcription, TFs need to gain access to their DNA sequence motifs. Binding to regulatory regions in the genome is something controlled by the chromatin structure. Just as with LEGOs, the genome is made up of DNA/nucleosomal building blocks (termed chromatin) that are packaged into spatially distinct structures. Large genomic regions within chromosomes are compartmentalized into either transcriptionally active (termed A compartments) or transcriptionally repressed domains (termed B compartments) (Lieberman-Aiden et al., 2009Lieberman-Aiden E. van Berkum N.L. Williams L. Imakaev M. Ragoczy T. Telling A. Amit I. Lajoie B.R. Sabo P.J. Dorschner M.O. et al.Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Science. 2009; 326: 289-293Crossref PubMed Scopus (4855) Google Scholar) (Figure 1). Within these compartments, the genome is further divided into spatially segregated regions (termed "topologically associated domains" or TADs) where bundles of looped chromatin are in close contact with one another (Figure 1) (Dekker and Heard, 2015Dekker J. Heard E. Structural and functional diversity of topologically associating domains.FEBS Lett. 2015; 589: 2877-2884Crossref PubMed Scopus (179) Google Scholar). The ability to activate or shut down gene transcription is dependent on the ability to reorganize chromatin structures, either by globally changing their A/B compartment status and/or by altering chromatin contacts within TADs into either transcriptionally permissive (accessible) or transcriptionally silent (inaccessible) states (Kouzarides, 2007Kouzarides T. Chromatin modifications and their function.Cell. 2007; 128: 693-705Abstract Full Text Full Text PDF PubMed Scopus (8024) Google Scholar). Early stages of T cell maturation involve commitment of hematopoietic stem cells to T cell progenitors, termed the double-negative (DN1, DN2, DN3, DN4) stage, as these T cell progenitors do not express the CD4 or CD8 co-receptors. T cell lineage commitment occurs during the DN2-DN3 transition (Yui and Rothenberg, 2014Yui M.A. Rothenberg E.V. Developmental gene networks: a triathlon on the course to T cell identity.Nat. Rev. Immunol. 2014; 14: 529-545Crossref PubMed Scopus (217) Google Scholar) and leads to T cell receptor (TCR) β chain gene rearrangement, a key checkpoint termed β selection. Success in passing this checkpoint enables maturation to the double-positive (DP) stage, where immature T cells express both CD4 and CD8 co-receptors. At this point, there is TCRα gene rearrangement, and cells able to express a functional TCRαβ heterodimer, capable of recognizing host major histocompatibility complex (MHC) antigens (a process termed positive selection), can then differentiate into mature T cells. Previous studies have also shown that there are broad and dynamic changes in transcription and chromatin modifications associated with T cell development (Zhang et al., 2012Zhang J.A. Mortazavi A. Williams B.A. Wold B.J. Rothenberg E.V. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.Cell. 2012; 149: 467-482Abstract Full Text Full Text PDF PubMed Scopus (264) Google Scholar). It has also been long appreciated that changes in chromatin structure contribute to T cell development. For example, successful TCR gene rearrangement requires the formation of chromatin loops (Skok et al., 2007Skok J.A. Gisler R. Novatchkova M. Farmer D. de Laat W. Busslinger M. Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes.Nat. Immunol. 2007; 8: 378-387Crossref PubMed Scopus (119) Google Scholar). Further, transcriptional activation of the master builder, Bcl11b, requires nuclear reposition of a locus control region (Isoda et al., 2017Isoda T. Moore A.J. He Z. Chandra V. Aida M. Denholtz M. Piet van Hamburg J. Fisch K.M. Chang A.N. Fahl S.P. et al.Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer-promoter communication and T cell fate.Cell. 2017; 171 (e18): 103-119Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar). Beyond changes to specific gene loci, it is not yet apparent if there are global changes in higher-order chromatin structures and whether this is necessary for establishment of T cell identity. To assess the global changes in chromatin structure during T cell development, both Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar and Johnson et al., 2018Johnson J.L. Georgakilas G. Petrovic J. Kurachi M. Cai S. Harly C. Pear W.S. Bhandoola A. Wherry E.J. Vahedi G. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cell development.Immunity. 2018; 48 (this issue): 243-257Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar profiled chromatin accessibility across 8 distinct stages of T cell development using either single-cell DNase sequencing or ATAC-seq, respectively. Both groups showed that dynamic changes in chromatin accessibility occurred throughout the genome during T cell differentiation. Accessible genomic regions (primarily at non-coding genomic regions) were associated with T cell-lineage-specific gene loci, with significant enrichment of binding motifs at these regions for TCF-1, known to be key for T cell maturation and classified as one of the earliest T cell lineage markers (Yui and Rothenberg, 2014Yui M.A. Rothenberg E.V. Developmental gene networks: a triathlon on the course to T cell identity.Nat. Rev. Immunol. 2014; 14: 529-545Crossref PubMed Scopus (217) Google Scholar). A striking finding was that waves of chromatin accessibility were observed as developing cells progressed through T cell differentiation. Particularly, Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar identified an abrupt change in chromatin accessibility when β selection occurred and just prior to positive selection, the two key checkpoints for T cell maturation. Interestingly, many of the regions that had undergone dramatic chromatin remodeling during the DN4-DP transition overlapped with regions that had already experienced prior remodeling at the first DN2-DN3 checkpoint. This suggests that perhaps positive selection serves not only to ensure MHC restriction but also to reinforce cell fate decisions by cementing architectural changes made at early stages of T cell differentiation. HiC is an approach that combines chemical cross-linking of nuclei and high-throughput sequencing to capture long-range chromatin-chromatin interactions. Using this approach, Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar asked whether the observed changes in chromatin accessibility during T cell maturation were associated with global changes in higher-order chromatin structures. They demonstrated that changes in chromatin accessibility correlated with changes in intra-TAD chromatin interactions, concordant with higher-order chromatin compartment reorganization. For example, genes involved in T cell commitment (e.g., Bcl11b, Ets1, Tcf1, and Cd3 signaling components), initially located within a repressed B compartment in hematopoietic progenitors, exhibited few intra-TAD contacts and an inaccessible chromatin structure. However, in DP cells, this same region exhibited extensive accessibility and greater intra-TAD connectivity and was now located within an A compartment. These early changes in higher-order chromatin structure, which serve to activate T cell-lineage-specific gene transcription, occurred in a stepwise and unidirectional fashion, i.e., they were not reversed at later stages of differentiation. Hence, the authors propose that such dramatic changes in the higher-order chromatin structures during development serve as an "energy barrier" that effectively locks in T cell lineage. In this way, the fate of a T cell progenitor is sealed. Do T cell specific master builders play a role in driving changes to higher-order chromatin structure? Bcl11b was a likely candidate as it is expressed at the DN2-DN3 transition, is essential for T cell lineage commitment (Yui and Rothenberg, 2014Yui M.A. Rothenberg E.V. Developmental gene networks: a triathlon on the course to T cell identity.Nat. Rev. Immunol. 2014; 14: 529-545Crossref PubMed Scopus (217) Google Scholar), and is part of the SWI/SNF chromatin remodeling complex (Kadoch et al., 2013Kadoch C. Hargreaves D.C. Hodges C. Elias L. Ho L. Ranish J. Crabtree G.R. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy.Nat. Genet. 2013; 45: 592-601Crossref PubMed Scopus (821) Google Scholar). Surprisingly, Bcl11b deficiency exerted no effect on the dramatic changes in chromatin accessibility observed during T cell differentiation; however, there was evidence of decreased intra-TAD contacts within mature T cells. Hence, BCL11B is important for maintaining higher-order chromatin structures, not initiating chromatin accessibility at the time of T cell lineage commitment. So, what drives T cell-specific chromatin accessibility at that first checkpoint? Johnson et al., 2018Johnson J.L. Georgakilas G. Petrovic J. Kurachi M. Cai S. Harly C. Pear W.S. Bhandoola A. Wherry E.J. Vahedi G. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cell development.Immunity. 2018; 48 (this issue): 243-257Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar found that 70% of the accessible chromatin linked to T cell-lineage-specific loci was bound by TCF-1 at early stages of differentiation. TCF-1-deficient mice exhibited a decrease in chromatin accessibility at early stages of T cell maturation, showing that initiation of chromatin remodeling was in fact TCF-1 dependent. This was particularly evident for the Bcl11b locus, indicating that TCF-1 acts upstream of this master builder. Most interestingly, single-cell ATAC-seq of DP cells showed that TCF-1 acts on the majority of progenitors to "synchronize" changes in chromatin accessibility. Hence, early TCF-1 expression is the initial checkpoint for the T cell lineage commitment process (Figure 1). So, what does the chromatin landscape look like in progenitors prior to TCF-1 binding? The limiting number of T cell progenitors makes it technically difficult to address this question. However, insights were provided by ectopic expression of TCF-1 in a terminally differentiated fibroblast cell line. TCF-1 could bind to T cell-lineage-specific gene loci associated with transcriptionally repressed, heterochromatic structures and initiate chromatin remodeling, increasing accessibility, with a subsequent transcriptional upregulation of several genes associated with T cell lineage commitment, e.g., Bcl11b. Thus, TCF-1 has an unequivocal role as a definitive master builder reconfiguring the chromatin landscape in progenitor cells to specifically support the T cell expression program. It should be noted that overexpression of TCF-1 alone was not sufficient to transform fibroblasts into cells with T cell function. It would seem that the molecular lockdown evident during T cell development, described by Hu et al., 2018Hu G. Cui K. Fang D. Hirose S. Wang X. Wangsa D. Jin W. Ried T. Liu P. Zhu J. et al.Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells.Immunity. 2018; 48 (this issue): 227-242Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar, likely has corollaries in other cell types. This also indicates TCF-1 potentially requires other, as yet unidentified, master builders to sculpt chromatin into a landscape that will support effective T cell function. Despite T cell fate being determined at an early stage, immature T cells still exhibit plasticity in their fate at positive selection where RUNX3 and ThPOK dictate commitment to either the CD8 or CD4 T cell lineage, respectively (Egawa and Littman, 2008Egawa T. Littman D.R. ThPOK acts late in specification of the helper T cell lineage and suppresses Runx-mediated commitment to the cytotoxic T cell lineage.Nat. Immunol. 2008; 9: 1131-1139Crossref PubMed Scopus (158) Google Scholar). This is also the case for mature, naive T cells where specific TFs control fate decisions into distinct functional states. Do these later fate decisions involve further changes in higher chromatin structures and locking in of these fates? Or does it represent fine tuning of small regions of a genome that is already preconfigured? Do these principals of locking in fate determination via modulation of higher-order chromatin structures apply to other immune cell lineages? Given the interest in "reprogramming" immune cells for immunotherapies, providing answers to these fundamental questions will be critical for ensuring success. Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T CellsHu et al.ImmunityFebruary 20, 2018In BriefCellular differentiation and cell-fate choice involve substantial chromatin reorganization. Through an integrative analysis of the regulome, 3D nucleome, and transcriptome, Hu and Cui et al. uncover abrupt global changes in the regulome and 3D nucleome at the DN2-to-DN3 transition, establishing a chromatin barrier to lock cell fate into the T lineages. Full-Text PDF Open ArchiveLineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T CellsJohnson et al.ImmunityFebruary 20, 2018In BriefIt is known that TCF-1 is required for T cell development, but the mechanism by which it controls the T cell lineage remains unclear. Johnson et al. reveal that TCF-1 controls T cell fate through its ability to create de novo open chromatin, establishing the epigenetic identity of T cells. Full-Text PDF Open Archive