Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues

Innate lymphoid cells (ILCs) are tissue-resident lymphocytes categorized on the basis of their core regulatory programs and the expression of signature cytokines. Human ILC3s that produce the cytokine interleukin-22 convert into ILC1-like cells that produce interferon-γ in vitro, but whether this conversion occurs in vivo remains unclear. In the present study we found that ILC3s and ILC1s in human tonsils represented the ends of a spectrum that included additional discrete subsets. RNA velocity analysis identified an intermediate ILC3-ILC1 cluster, which had strong directionality toward ILC1s. In humanized mice, the acquisition of ILC1 features by ILC3s showed tissue dependency. Chromatin studies indicated that the transcription factors Aiolos and T-bet cooperated to repress regulatory elements active in ILC3s. A transitional ILC3-ILC1 population was also detected in the human intestine. We conclude that ILC3s undergo conversion into ILC1-like cells in human tissues in vivo, and that tissue factors and Aiolos were required for this process.

Gene Regulatory Programs Conferring Phenotypic Identities to Human NK Cells

Natural killer (NK) cells develop from common progenitors but diverge into distinct subsets, which differ in cytokine production, cytotoxicity, homing, and memory traits. Given their promise in adoptive cell therapies for cancer, a deeper understanding of regulatory modules controlling clinically beneficial NK phenotypes is of high priority. We report integrated "-omics" analysis of human NK subsets, which revealed super-enhancers associated with gene cohorts that may coordinate NK functions and localization. A transcription factor-based regulatory scheme also emerged, which is evolutionarily conserved and shared by innate and adaptive lymphocytes. For both NK and T lineages, a TCF1-LEF1-MYC axis dominated the regulatory landscape of long-lived, proliferative subsets that traffic to lymph nodes. In contrast, effector populations circulating between blood and peripheral tissues shared a PRDM1-dominant landscape. This resource defines transcriptional modules, regulated by feedback loops, which may be leveraged to enhance phenotypes for NK cell-based therapies.

A B-Cell-Specific Enhancer Orchestrates Nuclear Architecture to Generate a Diverse Antigen Receptor Repertoire

The genome is organized into topologically associated domains (TADs) that enclose smaller subTADs. Here, we identify and characterize an enhancer that is located in the middle of the V gene region of the immunoglobulin kappa light chain (Igκ) locus that becomes active preceding the stage at which this locus undergoes V(D)J recombination. This enhancer is a hub of long-range chromatin interactions connecting subTADs in the V gene region with the recombination center at the J genes. Deletion of this element results in a highly altered long-range chromatin interaction pattern across the locus and, importantly, affects individual V gene utilization locus-wide. These results indicate the existence of an enhancer-dependent framework in the Igκ locus and further suggest that the composition of the diverse antibody repertoire is regulated in a subTAD-specific manner. This enhancer thus plays a structural role in orchestrating the proper folding of the Igκ locus in preparation for V(D)J recombination.

The role CTCF and transcription in sculpting the TCRβ repertoire

Primary Tcrb diversification is preceded by distinct changes in chromatin conformation and transcription during the early stages of T-cell development. However, the mechanisms by which these changes occur and how they shape the repertoire remain unclear. We have shown that distal and proximal Trbv segments are distinctly regulated. For instance, a CTCF binding site, known as 5′ PC, mediates long-range interactions that bring distal Trbvs into spatial proximity with the DβJβ segments. The 5′PC and several other CTCF sites in the 3′ end of the locus are oriented in a manner that we predict to facilitate specific contact, and thus recombination, between groups of Trbv segments the DβJβ segments. To specifically test this, we individually deleted key CTCF sites from the mouse Tcrb locus and sequenced Trbv gene usage in DN thymocytes. We find that loss of the 5′ PC results in a repertoire skewed against distal Trbv segments but favors proximal Trbv usage. Deletion of another CTCF site at the 3′ end of the locus, near the DβJβ clusters, does not significantly alter Trbv repertoire, presumably due to functional redundancy with another set of DβJβ-flanking CTCF sites. To test how transcriptional state affects the Trbv repertoire, we deleted an area spanning the Trbv12-2 and Trbv13-2 segments, which displays the highest levels of transcriptional and chromatin activation. We find that Trbv12/13 deletion enhances the usage of neighboring Trbv genes in the primary repertoire. Collectively, these data show that specific CTCF sites and regional transcription, at least in part, shape Tcrb repertoire.

Regulatory circuits governing identity and function of human type 1 ILCs

Innate lymphocytes develop from common progenitors but diverge functionally into a broad range of subsets that comprise a rapid response system to pathogens. In mice, type 1 innate lymphoid cells (ILCs), characterized by IFN-g expression, segregate into two major groups: cytotoxic natural killer (NK) cells and cytokine-producing, helper like ILC1s. In humans, this functional dichotomy is complicated further by heterogenous populations of circulating or tissue-resident NK cells, which exhibit distinct potentials for cytotoxicity or cytokine expression. Although developmental and functional kinships among NK cells have been studied extensively in mice, little is known about the molecular programs governing NK populations in humans. Here, we present integrated “-omics” analysis of human type 1 ILCs from blood and mucosal tissues, which identifies the key factors and biologic pathways establishing cell-type and functional identifies, as well as their underlying gene regulatory programs.

Correlative Recurrent Expression of Predicted Elements (CREPE): A Novel Computational Approach to Predict LncRNA Function

Long non-coding RNAs (lncRNAs) act as transcriptional regulators, scaffolds, and signaling modulators in development, immune response, and oncogenesis. Our -omics study of >100 human Non-Hodgkin Lymphoma (NHL) and normal B cell samples revealed altered expression of lncRNAs in NHL. LncRNAs have not been characterized in NHL or B cells, and there are few guidelines for functional prediction. To address this gap, we developed a novel computational approach: Correlative Recurrent Expression of Predicted Elements (CREPE). This method calculates and tracks the following for each lncRNA: expression, cell-type specificity, subcellular localization, differential expression (eg, tumor/normal), correlation with neighboring gene transcripts (RNAseq); local enhancer and 3D genome interaction landscapes (ChIPseq, Hi-C, ChIA-PET). From this, CREPE calculates a rankable score to predict the likelihood of potential functions, including 1) transcriptional regulation via lncRNA transcript, 2) enhancer-associated regulation, and 3) scaffold/modulator cytoplasmic function. The likelihood score formula incorporates an if-then logic, correlative regression analysis, and statistical significance. Finally, CREPE enables heuristic ranking of lncRNAs by pathway analysis. CREPE identified lncRNAs that may regulate NHL oncogenes and modulate B-cell receptor signaling. CREPE analysis of data from The Cancer Genome Atlas and a CRISPRi lncRNA growth screen validate its ability to identify lncRNAs with oncogenic or growth-promoting potential in diverse studies. In summary, we developed a novel approach that fills an unmet need for predictive modeling of lncRNA function and identified lncRNAs likely to promote lymphomagenesis.

Long Non-Coding RNAs Regulate Transcription of Lymphoma Oncogenes

Non-Hodgkin Lymphoma (NHL) is the most common blood cancer in the U.S. Our analysis of gene regulation in >100 NHL and normal B cell samples revealed a distinct profile of long non-coding RNA (lncRNA) expression. Few lncRNAs have been characterized, and there are no guidelines for functional prediction or categorization. Therefore, we developed a novel computational approach: Correlative Recurrent Expression of Predicted Elements (CREPE), which integrates -omics data to create a correlative regression model to predict lncRNA function. CREPE analysis revealed several NHL-associated lncRNAs that may regulate the expression of signaling proteins downstream of B-cell receptor activation. We highlight a multi-exon lncRNA that is highly expressed in NHL and has a top-ranked CREPE transcriptional regulatory score: AC074289.1. Consistent with a role in regulating transcription, qRT-PCR of subcellular fractions demonstrate nuclear localization and chromatin association (3.5–5X : cytoplasm). Expression of AC074289.1 is cell-type specific with 5–10X higher levels in B lymphoid compared to T or epithelial cell lines. AC074289.1 expression positively correlates with a neighboring gene, PELI1, which encodes Pellino 1, an E3 ubiquitin ligase that modulates NF-κb signaling in immune cells. NF-κb signaling also plays a significant role in NHL pathogenesis. Notably, high PELI1 expression is associated with more aggressive NHL. In summary, our global -omics study of normal and NHL samples identified new gene regulatory connections between lncRNAs and potential NHL oncogenes, including AC074289.1 and PELI1. This novel approach will accelerate our understanding of lncRNA function and may uncover new therapeutic targets in NHL.

Functional dissection of a novel IL-22 super-enhancer

Innate lymphoid cells (ILCs) are an emerging family of immune cells that serve essential roles in initiation, regulation and resolution of different immune responses. ILCs respond promptly to various signals present in their microenvironment by producing an array of cytokines and thereby directing the immune responses. These cells have been categorized as ILC1, ILC2 and ILC3 depending upon the effector cytokines secreted and transcription factors expressed by them. The signature effector cytokines produced by ILC3s are IL-22 and IL-17, providing protective immunity against extracellular pathogens. Another crucial facet of IL-22 function is its maintenance of mucosal homeostasis by modulating processes like tissue repair. However, there is a void of knowledge about genomic regions regulating IL-22 in different immune cells. In this regard, recent studies from our lab revealed a novel super-enhancer (SE), regulatory region composed of a large cluster of conventional enhancers, which likely regulates IL-22 and, perhaps, the neighboring IFNG gene. To dissect ILC3-specific functions of enhancers within the SE regulatory region, we are exploiting a murine cell line, MNK3, which mimics ILC3 functions in vitro and in vivo. We found that CRISPR-Cas9 mediated deletion of 5′ and 3′ end of this novel SE abrogated IL-22 expression in MNK3 cells. Furthermore, to identify cell and/or agonist specific elements of SE we set up a CRISPRi screen for which we generated a stable line of MNK3 expressing Dox inducible KRAB-dCas9. Together, our approach will define the cis-elements that regulate IL-22 in distinct immune cells and hence opening the field for novel therapeutic interventions for inflammatory diseases including autoimmune disorders.

A B Cell Lymphoma-Associated LncRNA Modulates BCR-Mediated Calcium Signaling

Long non-coding RNAs (lncRNA) act as transcriptional regulators, scaffolds, and signaling modulators, but their role in normal or malignant lymphocytes is unknown. We identified lncRNAs with altered expression in >100 human Non-Hodgkin Lymphoma (NHL) and normal B cell samples. One of these lncRNA genes is upstream of PLCG2 and parallels its expression, but the transcript is localized in the cytoplasm, making transcriptional regulation of PLCG2 unlikely. As expected, knock-out (KO), knock-down (KD), or over-expression of lncRNA-PLCG2 did not affect PLCG2 levels. PLCG2 is a B-cell specific phospholipase C enzyme that stimulates Ca2+ signaling after BCR activation. We assessed Ca2+ signaling via IgM stimulation of the BCR in multiple lncRNA-PLCG2 KO/KD NHL cell lines and observed defects in Ca2+ efflux from the ER and influx through Orai channels. To identify lncRNA-PLCG2 interacting proteins, we performed RNA pull-down experiments using sense (S) and anti-sense (AS, control) lncRNA-PLCG2 as bait incubated with B cell lysates. Mass spectrometry of eluted proteins showed several proteins significantly enriched in S versus AS, including PLD1, DICER1 and DHX9; we confirmed these by Western blot. We next performed RNA-binding protein Immunoprecipitation (RIP) using antibodies for PLD1, DHX9 and DICER1, which showed 2–10-fold enrichment of lncRNA-PLCG2 compared to IgG isotype control. Ongoing studies are mapping lncRNA-PLCG2-protein interactions and evaluating the impact of lncRNA-PLCG2 on PLD1 activity. Taken together, these results suggest that lncRNA-PLCG2 modulates BCR-mediated Ca2+ signaling via interaction with BCR downstream signaling proteins, a previously unrecognized mechanism that may promote lymphomagenesis.

cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent

Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression. Indeed, an annotated super-enhancer is dispensable for NEK6 overexpression and for maintaining the architecture of a B cell-specific regulatory hub. A CTCF cluster serves as a chromatin and architectural boundary to block communication of the NEK6 regulatory hub with neighboring genes. Our findings emphasize that validation of predicted cis-regulatory circuits and super-enhancers is needed to prioritize transcriptional control elements as therapeutic targets.

Activation of Mouse Tcrb: Uncoupling RUNX1 Function from Its Cooperative Binding with ETS1

T lineage commitment requires the coordination of key transcription factors (TFs) in multipotent progenitors that transition them away from other lineages and cement T cell identity. Two important TFs for the multipotent progenitors to T lineage transition are RUNX1 and ETS1, which bind cooperatively to composite sites throughout the genome, especially in regulatory elements for genes involved in T lymphopoiesis. Activation of the TCR β (Tcrb) locus in committed thymocytes is a critical process for continued development of these cells, and is mediated by an enhancer, Eβ, which harbors two RUNX-ETS composite sites. An outstanding issue in understanding T cell gene expression programs is whether RUNX1 and ETS1 have independent functions in enhancer activation that can be dissected from cooperative binding. We now show that RUNX1 is sufficient to activate the endogenous mouse Eβ element and its neighboring 25 kb region by independently tethering this TF without coincidental ETS1 binding. Moreover, RUNX1 is sufficient for long-range promoter-Eβ looping, nucleosome clearance, and robust transcription throughout the Tcrb recombination center, spanning both DβJβ clusters. We also find that a RUNX1 domain, termed the negative regulatory domain for DNA binding, can compensate for the loss of ETS1 binding at adjacent sites. Thus, we have defined independent roles for RUNX1 in the activation of a T cell developmental enhancer, as well as its ability to mediate specific changes in chromatin landscapes that accompany long-range induction of recombination center promoters.

The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites

In the mammalian intestine, crypts of Leiberkühn house intestinal epithelial stem/progenitor cells at their base. The mammalian intestine also harbors a diverse array of microbial metabolite compounds that potentially modulate stem/progenitor cell activity. Unbiased screening identified butyrate, a prominent bacterial metabolite, as a potent inhibitor of intestinal stem/progenitor proliferation at physiologic concentrations. During homeostasis, differentiated colonocytes metabolized butyrate likely preventing it from reaching proliferating epithelial stem/progenitor cells within the crypt. Exposure of stem/progenitor cells in vivo to butyrate through either mucosal injury or application to a naturally crypt-less host organism led to inhibition of proliferation and delayed wound repair. The mechanism of butyrate action depended on the transcription factor Foxo3. Our findings indicate that mammalian crypt architecture protects stem/progenitor cell proliferation in part through a metabolic barrier formed by differentiated colonocytes that consume butyrate and stimulate future studies on the interplay of host anatomy and microbiome metabolism.

The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites

In the mammalian intestine, crypts of Leiberkühn house intestinal epithelial stem/progenitor cells at their base. The mammalian intestine also harbors a diverse array of microbial metabolite compounds that potentially modulate stem/progenitor cell activity. Unbiased screening identified butyrate, a prominent bacterial metabolite, as a potent inhibitor of intestinal stem/progenitor proliferation at physiologic concentrations. During homeostasis, differentiated colonocytes metabolized butyrate likely preventing it from reaching proliferating epithelial stem/progenitor cells within the crypt. Exposure of stem/progenitor cells in vivo to butyrate through either mucosal injury or application to a naturally crypt-less host organism led to inhibition of proliferation and delayed wound repair. The mechanism of butyrate action depended on the transcription factor Foxo3. Our findings indicate that mammalian crypt architecture protects stem/progenitor cell proliferation in part through a metabolic barrier formed by differentiated colonocytes that consume butyrate and stimulate future studies on the interplay of host anatomy and microbiome metabolism.

Targeted epigenetic repression of a lymphoma oncogene by sequence-specific histone modifiers induces apoptosis in DLBCL

Alterations to the epigenetic landscape of diffuse large B-cell lymphoma (DLBCL) play a fundamental role in deregulating genes involved in normal lymphocyte differentiation. To determine whether targeted epigenetic therapy could reverse these pathogenic chromatin changes and suppress the expression of a lymphoma oncogene, we focused on BCL6, a transcriptional repressor whose aberrant expression is tightly linked to DLBCL proliferation and survival. We fused zinc-finger (ZF) domains specific for regulatory regions in the BCL6 locus to a repressive epigenetic modifier, the Kruppel-associated box (KRAB) repressor domain. Distinct ZF-KRAB fusions repressed the local chromatin landscape, suppressed BCL6 expression, significantly impaired DLBCL growth, and caused widespread cell death in a BCL6-dependent manner. Importantly, expression of ectopic BCL6 protein rescued ZF-KRAB-induced cell death, demonstrating the modifiers' specificity. We show that sequence-specific epigenetic modifiers can alter oncogene expression and induce apoptosis in cancer cells, underscoring their potential for future development as targeted epigenetic protein therapies.

Distinct Gene Regulatory Pathways for Human Innate versus Adaptive Lymphoid Cells

Innate lymphoid cells (ILCs) serve as sentinels in mucosal tissues, sensing release of soluble inflammatory mediators, rapidly communicating danger via cytokine secretion, and functioning as guardians of tissue homeostasis. Although ILCs have been extensively studied in model organisms, little is known about these "first responders" in humans, especially their lineage and functional kinships to cytokine-secreting T helper (Th) cell counterparts. Here, we report gene regulatory circuitries for four human ILC-Th counterparts derived from mucosal environments, revealing that each ILC subset diverges as a distinct lineage from Th and circulating natural killer cells but shares circuitry devoted to functional polarization with their Th counterparts. Super-enhancers demarcate cohorts of cell-identity genes in each lineage, uncovering new modes of regulation for signature cytokines, new molecules that likely impart important functions to ILCs, and potential mechanisms for autoimmune disease SNP associations within ILC-Th subsets.

NKG2D-NKG2D Ligand Interaction Inhibits the Outgrowth of Naturally Arising Low-Grade B Cell Lymphoma In Vivo

It is now clear that recognition of nascent tumors by the immune system is critical for survival of the host against cancer. During cancer immunoediting, the ability of the tumor to escape immune recognition is important for tumor development. The immune system recognizes tumors via the presence of classical Ags and also by conserved innate mechanisms. One of these mechanisms is the NKG2D receptor that recognizes ligands whose expression is induced by cell transformation. In this study, we show that in NKG2D receptor-deficient mice, increasing numbers of B cells begin to express NKG2D ligands as they age. Their absence in wild-type mice suggests that these cells are normally cleared by NKG2D-expressing cells. NKG2D-deficient mice and mice constitutively expressing NKG2D ligands had increased incidence of B cell tumors, confirming that the inability to clear NKG2D ligand-expressing cells was important in tumor suppression and that NKG2D ligand expression is a marker of nascent tumors. Supporting a role for NKG2D ligand expression in controlling the progression of early-stage B cell lymphomas in humans, we found higher expression of a microRNA that inhibits human NKG2D ligand expression in tumor cells from high-grade compared with low-grade follicular lymphoma patients.

Short-Circuiting Gene Regulatory Networks: Origins of B Cell Lymphoma

B cell lymphomas (BCLs) are characterized by widespread deregulation of gene expression compared with their normal B cell counterparts. Recent epigenomic studies defined cis-regulatory elements (REs) whose activities are altered in BCL to drive some of these pathogenic expression changes. During transformation, multiple mechanisms are employed to alter RE activities, including perturbations in the function of chromatin modifiers, which can lead to revision of the B cell epigenome. Inherited and somatic variants also alter RE function via disruption of transcription factor (TF) binding. Aberrant expression of noncoding RNAs (ncRNAs) deregulates genes involved in B cell differentiation via direct repression and post-transcriptional targeting. These discoveries have established epigenetic etiologies for B cell transformation that are being exploited in novel therapeutic approaches.

Regulation of Tcrb Gene Assembly by Genetic, Epigenetic, and Topological Mechanisms

The adaptive immune system endows mammals with an ability to recognize nearly any foreign invader through antigen receptors that are expressed on the surface of all lymphocytes. This defense network is generated by V(D)J recombination, a set of sequentially controlled DNA cleavage and repair events that assemble antigen receptor genes from physically separated variable (V), joining (J), and sometimes diversity (D) gene segments. The recombination process itself must be stringently regulated to minimize oncogenic translocations involving chromosomes that harbor immunoglobulin and T cell receptor loci. Indeed, V(D)J recombination is controlled at several levels, including tissue-, developmental stage-, allele-, and gene segment-specificity. These levels of control are imposed by a collection of architectural and regulatory elements that are distributed throughout each antigen receptor locus. Together, the genetic elements regulate developmental changes in chromatin, transcription, and locus topology that promote or disfavor long-range recombination. This chapter focuses on the cross talk between these mechanisms at the T cell receptor beta (Tcrb) locus, and how they sculpt a diverse TCRβ repertoire while maintaining monospecificity of this antigen receptor on each mature T lymphocyte. We also discuss how insights obtained from studies of Tcrb are more generally relevant to our understanding of gene regulation strategies employed by mammals.

CYLD and the NEMO Zinc Finger Regulate Tumor Necrosis Factor Signaling and Early Embryogenesis

NF-κB essential modulator (NEMO) and cylindromatosis protein (CYLD) are intracellular proteins that regulate the NF-κB signaling pathway. Although mice with either CYLD deficiency or an alteration in the zinc finger domain of NEMO (K392R) are born healthy, we found that the combination of these two gene defects in double mutant (DM) mice is early embryonic lethal but can be rescued by the absence of TNF receptor 1 (TNFR1). Notably, NEMO was not recruited into the TNFR1 complex of DM cells, and consequently NF-κB induction by TNF was severely impaired and DM cells were sensitized to TNF-induced cell death. Interestingly, the TNF signaling defects can be fully rescued by reconstitution of DM cells with CYLD lacking ubiquitin hydrolase activity but not with CYLD mutated in TNF receptor-associated factor 2 (TRAF2) or NEMO binding sites. Therefore, our data demonstrate an unexpected non-catalytic function for CYLD as an adapter protein between TRAF2 and the NEMO zinc finger that is important for TNF-induced NF-κB signaling during embryogenesis.

Domain-Specific and Stage-Intrinsic Changes in Tcrb Conformation during Thymocyte Development

Considerable cross-talk exists between mechanisms controlling genome architecture and gene expression. AgR loci are excellent models for these processes because they are regulated at both conformational and transcriptional levels to facilitate their assembly by V(D)J recombination. Upon commitment to the double-negative stage of T cell development, Tcrb adopts a compact conformation that promotes long-range recombination between Vβ gene segments (Trbvs) and their DβJβ targets. Formation of a functional VβDβJβ join signals for robust proliferation of double-negative thymocytes and their differentiation into double-positive (DP) cells, where Trbv recombination is squelched (allelic exclusion). DP differentiation also is accompanied by decontraction of Tcrb, which has been thought to separate the entire Trbv cluster from DβJβ segments (spatial segregation-based model for allelic exclusion). However, DP cells also repress transcription of unrearranged Trbvs, which may contribute to allelic exclusion. We performed a more detailed study of developmental changes in Tcrb topology and found that only the most distal portion of the Trbv cluster separates from DβJβ segments in DP thymocytes, leaving most Trbvs spatially available for rearrangement. Preferential dissociation of distal Trbvs is independent of robust proliferation or changes in transcription, chromatin, or architectural factors, which are coordinately regulated across the entire Trbv cluster. Segregation of distal Trbvs also occurs on alleles harboring a functional VβDβJβ join, suggesting that this process is independent of rearrangement status and is DP intrinsic. Our finding that most Trbvs remain associated with DβJβ targets in DP cells revises allelic exclusion models from their current conformation-dominant to a transcription-dominant formulation.

Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma

Most B-cell lymphomas arise in the germinal center (GC), where humoral immune responses evolve from potentially oncogenic cycles of mutation, proliferation, and clonal selection. Although lymphoma gene expression diverges significantly from GC B cells, underlying mechanisms that alter the activities of corresponding regulatory elements (REs) remain elusive. Here we define the complete pathogenic circuitry of human follicular lymphoma (FL), which activates or decommissions REs from normal GC B cells and commandeers enhancers from other lineages. Moreover, independent sets of transcription factors, whose expression was deregulated in FL, targeted commandeered versus decommissioned REs. Our approach revealed two distinct subtypes of low-grade FL, whose pathogenic circuitries resembled GC B or activated B cells. FL-altered enhancers also were enriched for sequence variants, including somatic mutations, which disrupt transcription-factor binding and expression of circuit-linked genes. Thus, the pathogenic regulatory circuitry of FL reveals distinct genetic and epigenetic etiologies for GC B-cell transformation.

Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

Majumder et al. explore the large-scale looping architecture of the Tcrb locus early in murine thymocyte development during the generation of TCRβ diversity. They dissect novel DNA regulatory elements controlling V to D-J recombination and identify within an insulator region a distally located CTCF-containing element functioning as a tether, which facilitates looping of distal Vβ to Dβ-Jβ regions and promotes locus contraction. A second CTCF-containing element, proximal to the Dβ-Jβ region, acts as a boundary, preventing the spread of active chromatin associated with Dβ-Jβ regions. Removal of the proximal boundary element impairs the locus contraction capabilities of the tethering element.

Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers.