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Allelic exclusion

Allelic exclusion is a fundamental genetic regulatory mechanism observed in B and T lymphocytes as well as certain sensory neurons that ensures the monoallelic expression of immunoglobulin (Ig) and T-cell receptor (TCR) genes in immune cells, and odorant receptor genes in olfactory neurons, resulting in each cell producing a single receptor specificity to maintain diversity and prevent autoreactivity.^[1] This process occurs during lymphocyte development in the bone marrow and thymus, where V(D)J recombination stochastically rearranges gene segments on one allele first, and successful assembly of a functional receptor chain triggers feedback inhibition to suppress rearrangement on the homologous allele.^[2] In B cells, allelic exclusion applies to the heavy chain (IgH) locus, initiating at the pro-B cell stage, followed by light chain (Igκ or Igλ) loci at the pre-B cell stage, with efficiency rates of approximately 99% for IgH and 93-99% for light chains, ensuring the "one B cell-one antibody" rule.^[2] For T cells, it primarily governs TCRβ and TCRγ loci through similar feedback mechanisms, though TCRα exhibits lower exclusion (about 90% efficiency) due to ongoing rearrangements.^[1] The importance of allelic exclusion lies in generating a polyclonal repertoire of monospecific lymphocytes, which supports effective pathogen recognition while minimizing the risk of dual-specificity cells that could promote autoimmunity or dilute immune responses.^[3] Mechanistically, allelic exclusion integrates stochastic initiation of recombination—controlled by low recombinase efficiency and asynchronous replication timing—with instructive feedback from the pre-BCR or pre-TCR, which signals via pathways like ATM kinase to halt further V(D)J activity.^[2] Epigenetic factors, including asynchronous replication, nuclear compartmentalization, histone modifications (e.g., H3K9 methylation for repression), and DNA methylation, further enforce monoallelic accessibility, positioning one allele in euchromatin for active rearrangement while the other remains condensed and inaccessible.^[3] Although incomplete exclusion occurs at low frequencies (1-10% for most loci), peripheral tolerance mechanisms mitigate potential risks from biallelic expression.^[1]

Overview

Definition and principles

Allelic exclusion is a genetic regulatory process in lymphocytes in which only one of the two homologous alleles of an antigen receptor gene is productively expressed, while the other remains silenced, ensuring monoallelic expression.^[2] In the context of the immune system, this mechanism applies to antigen receptor genes, where it guarantees that individual lymphocytes produce a single functional receptor specificity from one allele.^[1] The phenomenon was first observed in the 1950s and 1960s through studies on immunoglobulin allotypes in rabbits, notably by Pernis et al. (1965), who used immunofluorescence to demonstrate that plasma cells in heterozygous animals express immunoglobulins bearing only one of the two possible allelic allotypic specificities, indicating cellular restriction to a single allele.^[4] The core principles of allelic exclusion involve V(D)J recombination, a somatic DNA rearrangement process that assembles functional antigen receptor genes by joining variable (V), diversity (D, for some loci), and joining (J) gene segments in a developmentally ordered manner.^[2] This recombination is mediated by the RAG1 and RAG2 endonucleases, which recognize recombination signal sequences (RSS) flanking the gene segments, adhering to the 12/23 rule to ensure compatible joining.^[2] To prevent biallelic expression, epigenetic mechanisms such as DNA methylation and histone modifications silence the unrearranged or nonproductive allele; for instance, the unrearranged allele maintains high levels of repressive histone marks like H3K9me3 and DNA methylation, while the active allele undergoes demethylation and acquisition of activating marks such as H3K4me3.^[3] Transcriptional regulation further enforces this by limiting germline transcription and locus accessibility to one allele at a time.^[2] At a general level, the mechanism begins with monoallelic accessibility, where epigenetic factors like asynchronous replication timing and nuclear localization render one allele euchromatic and transcriptionally active, while the other remains condensed in heterochromatin.^[3] Successful V(D)J recombination on the accessible allele generates a functional protein that signals to inhibit further rearrangements on the homologous allele through recombination checkpoints.^[2] This ordered process, combining initial stochastic choice with feedback enforcement, ensures the exclusion of the second allele.^[5]

Biological significance

Allelic exclusion plays a central role in adaptive immunity by ensuring that each lymphocyte expresses a single antigen receptor specificity, thereby upholding the "one cell, one receptor" principle essential for precise immune recognition and response.^[1] This monospecificity prevents the co-expression of multiple receptors on a single cell, which could dilute the immune response or promote self-reactivity, and facilitates clonal selection where only cells bearing receptors specific to a given antigen proliferate.^[1] By limiting receptor expression to one functional allele, allelic exclusion enhances the overall diversity of the immune repertoire while maintaining specificity, allowing for effective discrimination between self and non-self antigens through central and peripheral tolerance mechanisms.^[1]^[6] Failure of allelic exclusion, resulting in biallelic expression or allelic inclusion, has significant pathological consequences, including increased risk of autoimmunity and lymphoid malignancies. For instance, incomplete exclusion in T cell receptor β genes accelerates spontaneous autoimmune arthritis in mouse models by allowing autoreactive T cells to escape clonal deletion.^[7] Similarly, allelic inclusion of T cell receptor α genes can lead to low-level expression of autospecific receptors, enabling their escape from tolerance checkpoints and triggering autoimmune diseases such as diabetes in transgenic models.^[8] Defects in exclusion also heighten the risk of oncogenic translocations due to accumulated DNA breaks from recombination, contributing to B cell lymphomas.^[1] From an evolutionary perspective, allelic exclusion confers a key advantage by balancing immense receptor diversity with monospecificity, a feature conserved across vertebrates from jawless species like lampreys to jawed vertebrates including sharks.^[6]^[9] In sharks, for example, B cells exhibit exclusion at immunoglobulin heavy chain loci despite a clustered gene organization, demonstrating the mechanism's ancient origins and role in generating a diverse yet specific adaptive immune system.^[9] This conservation underscores its importance in promoting pathogen-specific responses without compromising cellular focus. Beyond immunity, allelic exclusion has broader implications for cellular economy and identity, preventing wasteful gene expression by restricting output to a single functional allele and avoiding the energetic cost of producing multiple specificities.^[2] Analogous to monoallelic expression in olfactory sensory neurons, where one odorant receptor per neuron ensures precise sensory discrimination, this process maintains lymphocyte identity in stochastic developmental contexts, optimizing resource allocation during repertoire formation.^[2]

Allelic exclusion in lymphocytes

In B lymphocytes

In B lymphocytes, allelic exclusion ensures the monospecificity of antibodies by restricting V(D)J recombination to one allele at the immunoglobulin loci during development in the bone marrow. This process begins in pro-B cells, where the immunoglobulin heavy chain (IgH) locus undergoes sequential rearrangements: first, D segments join to J segments on one allele, followed by V segment addition to form a complete VDJ rearrangement. A productive VDJ rearrangement, which occurs with approximately one-third probability per allele due to reading frame constraints, expresses a μ heavy chain protein that pairs with surrogate light chain components (VpreB and λ5) to form the pre-B cell receptor (pre-BCR).^[10]^[2] The successful assembly and surface expression of the pre-BCR triggers a feedback signal that proliferates the cell and inhibits further IgH rearrangements on the second allele, enforcing heavy chain allelic exclusion at this checkpoint. Approximately 60% of pro-B cells successfully produce a functional heavy chain from at least one allele, allowing them to advance to the pre-B cell stage, while nonproductive attempts or failures lead to cell death or secondary attempts on the other allele. In pre-B cells, light chain loci (κ or λ) then undergo VJ recombination following a similar monoallelic pattern, with checkpoints ensuring only one productive light chain pairs with the heavy chain to form a complete B cell receptor (BCR).^[11]^[12] This ordered exclusion mechanism results in each mature B cell expressing a BCR of unique specificity, contributing to the diversity of the humoral immune response. Experimental evidence from flow cytometry analyses of bone marrow and peripheral B cells confirms high fidelity, with 95–99% of mature B cells displaying monoallelic surface immunoglobulin expression and only 1–3% showing biallelic heavy chain inclusion.80472-0)^[2]

In T lymphocytes

Allelic exclusion in T lymphocytes occurs during T cell development in the thymus, where the T cell receptor (TCR) genes undergo V(D)J recombination to generate diverse antigen receptors. The process begins with the β-chain locus in CD4⁻CD8⁻ double-negative (DN) thymocytes, where initial Dβ-to-Jβ joining precedes Vβ-to-DJβ rearrangement on one allele.^[1] Successful β-chain rearrangement pairs with the invariant pre-Tα chain to form the pre-TCR complex, which delivers signals that enforce allelic exclusion by inhibiting further rearrangement on the second β allele and promoting progression to the CD4⁺CD8⁺ double-positive (DP) stage.^[1] This β-selection checkpoint ensures that only one functional TCRβ chain is expressed per cell.^[13] In contrast, TCRα-chain rearrangement occurs later in DP thymocytes, involving direct Vα-to-Jα joining without a D segment.^[1] Unlike the β chain, α-chain exclusion is less stringent, as continued rearrangement can occur even after a productive α gene is formed, leading to secondary rearrangements that replace the initial product.^[1] This process is coupled to positive and negative selection in the thymus, where functional TCRαβ complexes are tested for MHC restriction and self-reactivity.^[14] A key distinction from B lymphocytes lies in the regulation and fidelity of exclusion: while immunoglobulin heavy and light chains exhibit near-absolute monoallelic expression, TCRβ exclusion is highly stringent (1–3% allelic inclusion), but TCRα allows greater biallelic expression (~30% of mature T cells bear two in-frame α rearrangements, though only ~10% express dual α chains on the surface due to pairing limitations).^[1] Additionally, T cell development involves a lineage choice between αβ and γδ T cells; successful γδ rearrangement diverts cells from the αβ pathway, but in αβ-committed cells, β exclusion remains dominant.90453-J) Regulatory factors include the recombination-activating genes (RAG1 and RAG2) enzymes, which initiate V(D)J recombination, and locus accessibility controlled by enhancers such as the TCRβ enhancer (Eβ), which directs monoallelic opening of chromatin.^[1] The transcription factor GATA3 plays a pivotal role in promoting monoallelic Vβ choice by modulating recombination propensity; low GATA3 levels favor exclusion (94% monoallelic in DN4 cells), while higher abundance can lead to biallelic recombination.^[15] Evidence from single-cell sequencing confirms the efficiency of β-chain exclusion, with >95% of mature peripheral T cells displaying monoallelic TCRβ expression, underscoring the pre-TCR's role in preventing dual specificity.^[1]

Regulatory mechanisms

Stochastic model

The stochastic model of allelic exclusion proposes that monoallelic expression of antigen receptor genes arises from the inherently low probability of productive V(D)J recombination at each allele, rendering simultaneous success on both alleles rare without requiring coordinated regulation. During V(D)J recombination, the joining of variable (V), diversity (D, where applicable), and joining (J) gene segments must occur in-frame to produce a functional protein; since there are three possible reading frames, only about one-third of rearrangements yield a productive outcome.^[1] This probabilistic inefficiency ensures that, in most cells, only one allele assembles a functional receptor chain by chance, thereby establishing exclusion passively.^[10] The mathematical foundation of the model derives from these recombination probabilities. For immunoglobulin heavy chain (IgH) or TCRβ loci involving VDJ joining, the success rate per allele is approximately \frac{1}{3}. Thus, for diploid cells with two alleles, the probability of biallelic productive rearrangement is \left( \frac{1}{3} \right)^2 = \frac{1}{9} \approx 11\%. However, actual rates of biallelic expression in mature B and T cells are far lower, typically under 1%, indicating that stochastic chance alone predicts a higher incidence of inclusion than observed and necessitating supplementary mechanisms for stringent control.^[2] Supporting evidence emerges from RAG-deficient mouse models, where V(D)J recombination is impaired until conditionally restored; in such systems, especially with pre-rearranged transgenes to bypass early checkpoints, locus activation and rearrangement occur randomly across alleles, resulting in predominantly monoallelic productive outcomes due to the low per-allele success rate.^[16] This stochastic pattern holds for both immunoglobulin and TCR loci, as demonstrated by independent, probabilistic initiation of V-to-DJ joining in developing thymocytes lacking directed allelic preference.^[17] Although foundational, the stochastic model is insufficient to explain the near-absolute exclusion observed in vivo, as its predicted biallelic frequency exceeds empirical data, underscoring the requirement for its integration with other regulatory processes to fully enforce monoallelic expression.^[2]

Asynchronous recombination model

The asynchronous recombination model posits that allelic exclusion arises from temporal disparities in the accessibility and recombination timing of homologous alleles, ensuring that only one allele undergoes V(D)J rearrangement at a time during lymphocyte development. This model emphasizes epigenetic and chromatin-based mechanisms that create asynchronous windows for recombination, preventing simultaneous activity on both alleles. Within this framework, two main subtypes are distinguished: the probabilistic subtype, where one allele is randomly selected to recombine first due to inherently low recombination efficiency, and the instructive subtype, where a specific allele is preferentially chosen based on cellular signals that dictate epigenetic timing. Asynchrony is primarily driven by epigenetic factors, such as differential replication timing and chromatin looping, which render one allele accessible before the other. For instance, one allele may initiate looping to nearby enhancers earlier, facilitating RAG enzyme access and recombination initiation.^[18] In pro-B cells, the mechanism unfolds sequentially for the immunoglobulin heavy chain (IgH) locus: initial D-to-J recombination occurs biallelically, but subsequent V-to-DJ recombination is restricted to one allele due to its prior chromatin contraction and enhancer engagement, leaving the second allele in a contracted, inaccessible state if the first rearrangement succeeds. This temporal staggering limits the opportunity for biallelic productive rearrangements, as the recombination machinery is not equally available to both alleles simultaneously.^[19] Supporting evidence comes from chromosome conformation capture (3C) and Hi-C studies in the 2010s, which revealed monoallelic interactions between IgH promoters and enhancers, such as the intronic enhancer Eμ, in developing B cells. These techniques demonstrated that chromatin looping is allele-specific, with one IgH allele forming loops to regulatory elements while the other remains excluded, correlating with asynchronous replication and subnuclear repositioning.^[20] For example, Hi-C data in B cell lines showed preferential enhancer-promoter contacts on the productively rearranging allele, underscoring the role of 3D chromatin architecture in enforcing temporal differences.^[20] This model accounts for the high efficiency of allelic exclusion, observed at approximately 90-99% in mature B cells, which exceeds what would be expected from purely stochastic recombination probabilities alone. By integrating probabilistic elements with regulated timing, it provides a mechanistic explanation for the robust monoallelic outcome beyond chance.^[21]

Feedback inhibition model

The feedback inhibition model posits that a successful V(D)J recombination event on one allele produces a functional immunoglobulin or T cell receptor (TCR) chain protein that signals to prevent rearrangement on the homologous allele, thereby enforcing monoallelic expression.^[2] In B cell development, this process is exemplified by the formation of the pre-B cell receptor (pre-BCR), where a productively rearranged immunoglobulin heavy chain (IgH, μ) pairs with a surrogate light chain (comprising VpreB and λ5) and the signaling molecules Igα and Igβ.^[12] The pre-BCR then transmits signals through phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs) on Igα/Igβ, activating kinases such as SYK and adaptor proteins like BLNK, which culminate in the downregulation of recombination-activating genes (RAG1 and RAG2).^[2] This suppression halts further IgH locus recombination, ensuring allelic exclusion.^[22] At the molecular level, these signals induce transcriptional repression of unrearranged alleles via factors including Pax5, which binds to IgH regulatory elements to limit accessibility, and NF-κB, which modulates RAG expression and promotes cellular survival.^[2] Additionally, RAG2 protein levels are reduced through cyclin A/CDK2-mediated phosphorylation and subsequent ubiquitination by the Skp2-SCF complex, providing a post-transcriptional layer of inhibition.^[2] For light chain loci (Igκ and Igλ), feedback inhibition operates sequentially after successful μ heavy chain pairing in the pre-BCR; the absence of pre-BCR signaling allows biallelic light chain rearrangements, as demonstrated in mice with targeted disruption of the μ heavy chain transmembrane exon, where allelic exclusion is lost and dual light chain expression increases.^[12]^[23] Evidence supporting this model comes from genetic studies, such as pre-BCR component knockouts (e.g., λ5-deficient mice), which exhibit impaired suppression of RAG expression and partial loss of IgH exclusion, confirming the pre-BCR's role in signal-dependent inhibition.^[24] A parallel mechanism operates in T cell development via the pre-TCR, where a functional TCRβ chain associates with pre-Tα and CD3 subunits to activate similar SYK-dependent signals, downregulating RAG1/2 and enforcing TCRβ allelic exclusion; knockouts of pre-TCR components like pTα result in biallelic TCRβ rearrangements.^[1]^[25] Two variants of this model exist: the classic direct inhibition, where pre-BCR or pre-TCR signals immediately repress RAG activity and locus accessibility, and an indirect mechanism involving signal-induced proliferation, which dilutes unrearranged alleles by expanding cells with a successful rearrangement before secondary recombination can occur.^[2]^[1]

Allelic exclusion at immunoglobulin loci

Heavy chain genes

The immunoglobulin heavy chain (IgH) locus is located on the long arm of human chromosome 14 at band 14q32.33, spanning approximately 1.25 megabases and comprising multiple variable (V_H), diversity (D_H), joining (J_H), and constant (C_H) gene segments.^[26] In pro-B cells, V(D)J recombination at the IgH locus initiates with D_H-to-J_H joining, which occurs simultaneously on both alleles to generate D_J intermediates, enhancing the probability of productive rearrangement.^[2] This biallelic D-J phase is followed by monoallelic V_H-to-DJ_H joining, which establishes allelic exclusion and ensures that only one allele typically progresses to a functional μ heavy chain.^[2] Allelic exclusion at the IgH locus is enforced through a feedback inhibition mechanism triggered by successful VDJ recombination on one allele, leading to the assembly and surface expression of the pre-B cell receptor (pre-BCR) containing the μ heavy chain paired with surrogate light chains.^[11] Pre-BCR signaling rapidly halts further V_H-to-DJ_H rearrangements on the second allele by downregulating recombination-activating gene (RAG) expression and altering locus accessibility, thereby preventing biallelic expression.^[11] This process critically involves the intronic enhancer Eμ, which promotes high-level transcription of the rearranged VDJ segment to amplify pre-BCR signaling, and the 3' regulatory region (3'RR), which coordinates locus contraction and nuclear positioning to favor monoallelic recombination.^[27]^[28] The efficiency of IgH allelic exclusion is exceptionally high, exceeding 95% in mature B cells, as failures in achieving a productive rearrangement on at least one allele typically result in apoptosis of the pro-B cell, while rare dual rearrangements lead to either editing attempts or cell elimination.^[1] Sequencing studies of peripheral B cells confirm that allelic inclusion at the IgH locus is uncommon, occurring in approximately 1% or fewer cells, underscoring the robustness of the exclusion mechanism in generating monospecific B cell receptors.^[2]^[1]

Light chain genes (Igκ and Igλ)

In B lymphocyte development, following successful rearrangement and expression of the immunoglobulin heavy chain, light chain gene rearrangement initiates at the κ (Igκ) loci before proceeding to the λ (Igλ) loci if necessary. The human Igκ locus is situated on the short arm of chromosome 2 at band 2p11.2, spanning approximately 1.8 Mb and containing 76 Vκ gene segments (31-36 functional in common haplotypes), 5 Jκ segments, and a single Cκ constant region gene.^[29]^[30] In contrast, the Igλ locus resides on the long arm of chromosome 22 at band 22q11.2, spanning approximately 1.05 Mb with 73-74 Vλ genes (29-33 functional, depending on haplotype), 7-11 Jλ-Cλ clusters (4-5 functional), and 7-11 Cλ genes arranged in tandem.^[31]^[32] This sequential and hierarchical strategy ensures that κ rearrangement is attempted first on both alleles, with intra-allelic exclusion occurring at one allele (productive VJ joining leading to a functional transcript) before inter-allelic exclusion suppresses the second allele.^[2] The primary mechanism enforcing allelic exclusion at these light chain loci involves feedback inhibition triggered by a functional B cell receptor (BCR). A productively rearranged κ chain pairs with the pre-existing μ heavy chain to form a surface BCR, which delivers survival and maturation signals that downregulate recombination-activating gene (RAG) enzymes and halt further VJ recombination at both Igκ and Igλ loci.^[2] If rearrangement at both Igκ alleles yields nonproductive outcomes (e.g., out-of-frame or stop codon insertions, occurring in ~2/3 of attempts due to random joining), the cell proceeds to Igλ rearrangement, again following intra- then inter-allelic exclusion.^[16] This process maintains monospecificity, as biallelic expression is rare and typically arises from incomplete inhibition or secondary editing events.^[33] Allelic exclusion operates with differing efficiencies at the Igκ and Igλ loci, reflecting variations in recombination signal sequence (RSS) strength and chromatin accessibility. The Igκ locus exhibits stricter exclusion, mediated by more efficient 12/23 RSS spacer compatibility (Vκ RSS with 12-bp spacer pairing to Jκ RSS with 23-bp spacer), which promotes rapid, ordered recombination and near-complete allelic silencing upon success.^[2] In comparison, Igλ recombination is less efficient due to weaker RSS signals and more asynchronous activation, resulting in a modestly higher incidence of biallelic inclusion (up to 5-10% in some contexts, though overall dual κ/λ expression remains <1%).^[34] These differences contribute to species-specific κ/λ usage ratios: in humans, ~60% of mature B cells express κ light chains (monoallelically) and ~40% express λ, while in mice, >95% express κ and only ~5% express λ.^[34]^[35] Studies in human and mouse models, including transgenic and knockout approaches, confirm this hierarchy and exclusion dynamics. For instance, targeted disruption of Igκ enhancers increases λ usage to near 100% in mice, demonstrating the default progression to λ upon κ failure, while flow cytometric analyses of peripheral B cells reveal the low dual-expression rates that underscore effective inhibition.^[36]^[37]

Allelic exclusion in neurons

Olfactory sensory neurons

In olfactory sensory neurons of the main olfactory epithelium, allelic exclusion manifests as the monoallelic expression of one odorant receptor (OR) gene chosen from approximately 1,100 such genes in the mouse genome, ensuring each neuron detects a specific subset of odorants.^[38] This process involves an initial stochastic selection of a single OR allele for low-level transcription, followed by a negative feedback signal from the nascent OR protein that amplifies expression from the chosen allele while repressing all others, thereby stabilizing the choice and preventing multigenic or biallelic expression in mature neurons. The resulting "one neuron, one receptor" rule generates vast neuronal diversity, enabling fine-grained odor discrimination and precise wiring of olfactory axons to the bulb.^[39]^[40] The underlying mechanism relies on epigenetic regulation rather than DNA recombination, distinct from immune receptor loci. Transcriptional activation of the selected allele occurs through interactions with distant enhancers, such as the multiple Greek islands elements, which loop to the promoter and recruit activating factors. Non-selected alleles, along with the vast majority of the OR repertoire, are maintained in a silenced state via heterochromatin marks like H3K9me3 and H4K20me3, with additional involvement of Polycomb group proteins; for instance, the Eed subunit of Polycomb repressive complex 2 establishes allele-specific epigenetic differences required for exclusion. This combinatorial silencing ensures genome-wide repression, with only the chosen allele escaping to achieve high-fidelity monoallelic output.^[41]^[42] Key evidence for this process derives from mouse genetic studies using targeted insertions of lacZ reporters into OR loci to visualize expressing neurons. In seminal work, Shykind et al. (2004) demonstrated that individual OSNs express only one tagged OR allele, with rare switching events in immature neurons but stable monoallelic commitment in mature ones, confirming the feedback-dependent stabilization. Single-cell RNA sequencing further supports this, demonstrating tight monoallelic expression (>99.7% allele-specific) in analyzed OSNs, underscoring the efficiency of exclusion despite occasional low-level biallelic transcription in developing neurons.^[43]^[44] This neuronal allelic exclusion parallels the feedback inhibition model observed in immune cells, where successful receptor expression halts further rearrangement or activation of alternative alleles.^[39]

Vomeronasal sensory neurons

Allelic exclusion in vomeronasal sensory neurons (VSNs) of the vomeronasal organ (VNO) manifests as the monoallelic and monogenic expression of vomeronasal type 1 receptor (V1R) genes, ensuring that each neuron transcribes a single V1R allele chosen stochastically from a repertoire of approximately 240 functional V1R genes in the mouse genome. This process restricts expression to one functional receptor per neuron, enabling specialized detection of pheromones that mediate social and reproductive behaviors. Unlike the main olfactory system, V1R expression in the VNO is tailored to non-volatile peptide and small molecule pheromones, with neurons zoned apically in the VNO epithelium.^[45] The mechanism underlying this exclusion involves a negative feedback loop initiated by the transcription of the chosen V1R gene, which signals to the nucleus to suppress all other V1R alleles and loci. Experimental evidence from gene-targeted mice demonstrates that expressing a single functional V1R, such as V1rb2, prevents coexpression of any other V1R in the same neuron; in one study, analysis of over 6,000 V1rb2-expressing neurons across multiple mice revealed zero instances of V1R coexpression.^[46] This feedback is receptor-dependent, as substitution with a non-functional allele or an unrelated odorant receptor disrupts exclusion, leading to biallelic or multigenic expression in a subset of neurons.^[46] Epigenetic modifications, including localized histone changes at the expressed locus, reinforce this silencing, though the precise nuclear signaling pathway remains under investigation. The significance of V1R allelic exclusion lies in its role in generating a diverse array of pheromone-sensitive VSNs, each tuned to a specific ligand, which supports discrete neural mapping in the accessory olfactory bulb and behavioral responses to conspecific cues. While V1R exclusion is highly efficient, with biallelic expression occurring in less than 1% of neurons, V2R-expressing VSNs in the basal VNO layer exhibit a distinct pattern, coexpressing two V2R genes from different subfamilies in a non-random, monoallelic manner per gene.^[46]^[47] This organization enhances the VNO's capacity for detecting complex social signals without compromising neuronal specificity.

Recent developments

Advances in T cell regulation

Recent research has elucidated the role of recombination signal sequences (RSSs) in enforcing allelic exclusion at the T cell receptor β (TCRβ) locus. In 2020, studies demonstrated that the inherently poor quality of Vβ RSSs stochastically limits the frequency of Vβ-to-DJβ recombination, thereby promoting monoallelic bias and preventing biallelic expression of functional TCRβ chains before feedback inhibition can occur. This mechanism ensures that only one productive TCRβ allele is typically assembled per T cell, with experimental replacement of low-quality Vβ RSSs leading to a significant increase in biallelic rearrangements, up to 27-fold in certain models. Single-cell RNA sequencing (scRNA-seq) analyses have further supported the influence of RSS quality on TCRβ allelic exclusion. A 2024 study using high-throughput sequencing (HTS) and scRNA-seq across mammalian species, including humans and mice, revealed that the location and RSS quality of rearranged Vβ genes directly impact the bias toward monoallelic expression in thymocytes.^[48] Poor RSSs were associated with reduced recombination efficiency on the second allele, reinforcing stochastic monoallelic dominance at the transcriptional level in developing T cells.^[48] Advances in 2025 have confirmed allelic exclusion mechanisms in engineered T cells derived from transgenic hematopoietic stem and progenitor cells (HSPCs). In a study published in Nature Communications, single-nucleus RNA sequencing of peripheral blood mononuclear cells from patients treated with transgenic HSPCs expressing a tumor-specific TCR showed predominant allelic exclusion, with heatmaps of TRBC1 and TRBC2 expression indicating that 63% of lentiviral-positive T cells exclusively expressed the transgenic TCR, while 37% co-expressed it with endogenous chains.^[49] This partial but effective exclusion was observed in both CD4+ and CD8+ T cell clusters, validating the process in clinically relevant human models.^[49] These findings hold implications for chimeric antigen receptor T (CAR-T) cell therapies, where maintaining uniform TCR expression through allelic exclusion enhances the consistency and efficacy of engineered T cells. In transgenic HSPC-derived TCR T cells, observed exclusion minimizes dual-specificity risks, potentially improving antitumor persistence and reducing off-target effects in adoptive immunotherapies.^[49]

Emerging molecular insights

CTCF and cohesin play roles in chromatin organization relevant to allelic exclusion. Single-cell omics approaches have provided insights into allele-specific dynamics during allelic exclusion in B cells and neuronal cells. In olfactory sensory neurons, stochastic monoallelic activation precedes stable exclusion via feedback reinforcement. Emerging models integrate stochastic recombination with feedback inhibition to predict exclusion outcomes across systems. Recent 2022 studies have addressed longstanding gaps in λ chain regulation, revealing that allelic exclusion at the Igλ locus relies on distinct enhancer-promoter interactions compared to κ chains, with reduced feedback efficiency leading to higher rates of biallelic inclusion in autoimmune contexts like lupus. These findings, derived from high-throughput sequencing of light chain repertoires, indicate that λ-specific CTCF sites and surrogate light chain pairing enforce exclusion less stringently, allowing dual expression in ~5-10% of mature B cells under pathological conditions.^[50]

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Distinct Signaling Requirements for Dμ Selection, IgH Allelic ...
The accumulation of pre-BCRhigh pre-B cells in the double mutant mice allowed us to analyze directly the status of IgH allelic exclusion on the surface of the ...
[23]
Loss of Precursor B Cell Expansion but Not Allelic Exclusion in ...
Surprisingly, IgH allelic exclusion is functioning in λ5−/− mice 25. One hypothesis to explain this finding is that a pre-BII cell can make a modified pre-BCR ...
[24]
Essential Role of the Pre-T Cell Receptor in Allelic Exclusion of the T ...
This may indicate that the pre-TCR is approximately 40% of cells gave results that might be expected from a TCRß+ CD25+ cell, namely, two or more not needed for ...
[25]
IMGT Repertoire (IG and TR) 1. Locus and genes
Sep 21, 2001 · The human IGH locus is located on the chromosome 14 [1], at band 14q32.33, at the telomeric extremity of the long arm.
[26]
A role for the IgH intronic enhancer Eμ in enforcing allelic exclusion
It is through components of the preBCR that developing B cells sense successful assembly of an Igμ gene on one allele and signal arrest of any further assembly ...
[27]
Core enhancers of the 3′RR optimize IgH nuclear position and ...
Oct 16, 2024 · We conclude that the 3′RR core enhancers are necessary and sufficient to pre-organize the position and conformation of IgH loci in resting B-cell nuclei.
[28]
IGK immunoglobulin kappa locus [Homo sapiens (human)] - NCBI
Aug 19, 2025 · Location. RS_2025_08, current, GRCh38.p14 (GCF_000001405.40), 2 ... Chromosome 2 Reference GRCh38.p14 Primary Assembly, NW_012132915.1 ...
[29]
Human (Homo sapiens) IGK - IMGT Repertoire (IG and TR)
The human IGK locus is located on the chromosome 2 [1], on the short arm, at band 2p11.2 [2]. The list of human IGK genes is available at IMGT/GENE-DB.DNA · Human IGK locus at 2p11.2 · Total number of human IGK... · Nomenclature
[30]
IGL immunoglobulin lambda locus [Homo sapiens (human)] - Gene
Assignment of the genes for human lambda immunoglobulin chains to chromosome 22. Erikson J, et al. Nature, 1981 Nov 12. PMID 6795508 ...
[31]
Human IGL locus at 22q11.2 - IMGT Repertoire (IG and TR)
Overview. The human IGL locus is located on the chromosome 22 [1], on the long arm, at band 22q11. 2 [2]. IGL orphons have been identified on chromosomes 8 and ...
[32]
Igκ allelic inclusion is a consequence of receptor editing - PMC
Variegated transcriptional activation of the immunoglobulin kappa locus in pre-b cells contributes to the allelic exclusion of light-chain expression. Cell ...Missing: review | Show results with:review
[33]
A Human Immunoglobulin λ Locus Is Similarly Well Expressed in ...
Analysis of bone marrow cells showed that human Igλ and mouse Igκ were expressed at similar levels throughout B cell development, suggesting that the Igλ ...
[34]
The kappa/lambda ratio in surface immunoglobulin molecules on B ...
The majority (91%-97%) of the IgM+ B cells express kappa chains, but a very small percentage (3.1%-5.0%) express lambda. A similarly high kappa/lambda ratio was ...
[35]
Mice with megabase humanization of their immunoglobulin genes ...
The accompanying paper describes the precise, in situ replacement of six megabases of mouse immune genes with the corresponding human immune genes.
[36]
kappa+lambda+ dual receptor B cells are present in the human ...
By three-color staining with anti-CD19, anti-kappa, and anti-lambda antibodies we could estimate that 0.2-0.5% of peripheral blood B cells from healthy adults ...
[37]
Regulation of odorant receptors: one allele at a time
Each olfactory sensory neuron chooses just one OR from the more than 1000 possibilities encoded in the genome and transcribes it from just one allele.
[38]
A feedback mechanism regulates monoallelic odorant receptor ...
Each olfactory neuron expresses only one allele of an individual OR gene from >1,000 related genes dispersed throughout the genome, a process termed monoallelic ...
[39]
https://academic.oup.com/hmg/article/14/suppl_1/R33/560829
[40]
Differences between homologous alleles of olfactory receptor genes ...
Oct 22, 2007 · Differences between homologous alleles of olfactory receptor genes require the Polycomb Group protein Eed ... Allelic exclusion of Ly49 ...
[41]
Gene Switching and the Stability of Odorant Receptor Gene Choice
We observe that immature olfactory sensory neurons that express a given odorant receptor can switch receptor expression, albeit at low frequency.
[42]
Hierarchical deconstruction of mouse olfactory sensory neurons
Dec 16, 2015 · We show that 98.9% of intact olfactory receptor (OR) genes are expressed in mature OSNs. We uncover a hitherto unknown bipartition among mature ...
[43]
https://www.sciencedirect.com/science/article/pii/S009286740400529X
[44]
https://www.nature.com/articles/srep18178
[45]
HTS and scRNA-seq revealed that the location and RSS quality of ...
Oct 29, 2024 · Poor quality Vβ recombination signal sequences stochastically enforce TCRβ allelic exclusion. J Exp Med 2020, 217(9). Wu C, Bassing CH, Jung ...
[46]
Human cancer-targeted immunity via transgenic hematopoietic stem ...
Jul 1, 2025 · Heatmap for expression of pLenti TCR, TRBC2, and TRBC1 per nucleus for pLenti+ T cells revealed allelic exclusion in the majority of nuclei. 45% ...Missing: HSPC | Show results with:HSPC
[47]
Recent advances in universal chimeric antigen receptor T cell therapy
Aug 29, 2025 · In recent years, CAR T cell therapy has shown remarkable efficacy in treating relapsed or refractory (r/r) hematological malignancies, such as B ...
[48]
Genetic analysis of cancer drivers reveals cohesin and CTCF as ...
Feb 11, 2022 · We utilized genetic screening with a curated library of 500 tumor suppressor genes to identify cohesin subunits and CTCF among the most significant suppressors ...
[49]
Learning antibody sequence constraints from allelic inclusion - bioRxiv
Oct 25, 2024 · We demonstrate that these B cells can be used to learn constraints on antibody sequence. Using large-scale single-cell sequencing data from humans.Missing: ATAC- 2023-2025
[50]
Single-cell genomics details the maturation block in BCP-ALL and ...
Sep 26, 2024 · Epigenetic profiling by scATAC-seq of 41 892 nuclei revealed a cellular BCP-ALL landscape closely mirroring the transcriptomic landscape (Figure ...
[51]
RNA-mediated symmetry breaking enables singular olfactory ...
Dec 20, 2023 · We propose a physics-based symmetry-breaking model where the self-affinity of GI hub-binding factors in a single prevailing cluster results in ...
[52]
Elevated Detection of Dual Antibody B Cells Identifies Lupus ...
Feb 3, 2022 · Allelic exclusion at the immunoglobulin (Ig) loci is a fundamental tenet of immunology that is considered essential for achieving immune ...