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High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [PRO-cap]

ABSTRACT: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [PRO-cap]

PROVIDER: PRJNA834081 | ENA |

REPOSITORIES: ENA

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High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks

Project description:High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks

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Somatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position

Project description:Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation-induced deaminase (AID) is essential for the maturation of protective antibodies. AID preferentially mutates cytosines within WRCH motifs (W=A/T, R=A/G, H=A/C/T), yet WRCH motifs show large but reproducible variations in mutation frequency, highlighting a crucial role for sequence-intrinsic mechanisms (a sequence grammar) in determining mutational outcomes and, therefore, in antibody maturation. Here, we demonstrate that the same sequence context can exert significantly varying effects on the mutability of different WRCH motifs. Furthermore, targeting of SHM to the template and non-template cytosines in palindromic AGCT motifs can be differentially regulated by sequence contexts. Additionally, we provide evidence that the location of a motif within the V region can have a significant impact on its mutability. Therefore, discrete V region mutation patterns arise from a combination of a motif-specific sequence grammar and motif position.

2025-09-01 | GSE283316 | GEO

High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [MutPE]

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Project description:Analysis of chromatin marks, nascent transcription and mutational profiles at AID-target genes in human cell line and mouse

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Somatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position

Project description:Somatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position

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B cell Lymphomas present Immunoglobulin Neoantigens

Project description:Immunoglobulin gene rearrangement and somatic hypermutation have the potential to create neoantigens in non-Hodgkin B cell lymphoma. However, the presentation of these putative immunoglobulin neoantigens by B cell lymphomas has not been proven. We used MHC immunoprecipitation followed by liquid chromatography and tandem mass spectrometry (LC-MS/MS) to define antigens presented by follicular lymphomas (FL), chronic lymphocytic leukemias (CLL), diffuse large B cell lymphoma (DLBCL) and mantle cell lymphomas (MCL). We found presentation of the clonal immunoglobulin molecule, including neoantigens by both class I and class II MHC, though more commonly in class II MHC. To determine whether B cell activation could promote presentation of immunoglobulin neoantigens, we used a toll-like receptor 9 (TLR9) agonists to upregulate expression of MHC-II. This resulted in enhanced class II MHC presentation of the immunoglobulin variable region including neoantigens. These findings demonstrate that immunoglobulin neoantigens are presented across most subtypes of B cell lymphomas. Activation of lymphoma cells to upregulate antigen presentation boosts presentation of immunoglobulin neoantigens and represents a strategy for augmenting lymphoma immunotherapies.

2019-01-07 | PXD010808 | Pride

HIRA-dependent H3.3 deposition and its modification H3.3K36me3 facilitate somatic hypermutation of immunoglobulin genes by maintaining the proper chromatin state and transcription

Project description:The H3.3 histone variant and its chaperone HIRA are involved in active transcription but their detailed roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells is not yet fully understood. In this study we show that, knockout (KO) of HIRA significantly decreased SHM and changed the mutation pattern of the variable region of immunoglobulin heavy chain (IGH) in the human Ramos B cell line without changing the levels of AID and other major proteins known to be involved in SHM. Except for H3K79me2/3, many factors related to active transcription, including H3.3, were substantively decreased in HIRA KO cells and this was accompanied by decreased nascent transcription in IGH locus. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the Ig locus was also reduced in the HIRA KO. Somewhat surprisingly HIRA loss increased the chromatin accessibility of Ig V region locus. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit both the trimethylation of H3.3K36 and the recruitment of ZMYND11 significantly reduced SHM in Ramos cells, while the H3.3K79M did not. Consistent with HIRA KO, the H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on the IGH variable and downstream switching regions. Our results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and extend our knowledge of how transcription coupled chromatin structure and accessibility contribute to SHM in human B cells.

2021-07-29 | GSE180899 | GEO

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