Structure and Expression of Germ Line Immunoglobulin Heavy-Chain ε Transcripts: Interleukin-4 Plus Lipopolysaccharide-Directed Switching to Cε

Rothman, Paul B.; Chen, Y Y; Lutzker, Stuart; Li, S C; Stewart, Victoria; Coffman, Robert L.; Alt, Frederick W.

doi:10.1128/mcb.10.4.1672-1679.1990

Cited by 6 publications

(2 citation statements)

References 39 publications

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“…We first clarified the exact genomic position of TSS for the sterile transcript for every human and mouse IgH C gene with the exception of IgD where sterile transcription is not well understood. We collected from the literature a set of DNA genomic sequences isolated using traditional molecular cloning and restriction enzyme analysis, of the promoter region of sterile transcripts observed in experimental and/or clinical models of CSR [46][47][48][83][84][85][86][87][88][89] . These sequences are mapped to the hg38 (for human) /mm10 (for mouse) reference genomes using BLAT 90…”

Section: Methodsmentioning

confidence: 99%

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

Garcia

Stewart

et al. 2023

Preprint

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Class-switch recombination (CSR) is an integral part of B cell maturation. Steady-state analyses of isotype distribution (e.g. B cell receptor [BCR] repertoire analysis of snapshots during an immune response) do not directly measure CSR dynamics, which is crucial in understanding how B cell maturation is regulated across time. We present sciCSR (pronounced 'scissor', single-cell inference of class switch recombination), a computational pipeline which analyses CSR events and dynamics of B cells from single-cell RNA-sequencing (scRNA-seq) experiments. sciCSR re-analyses transcriptomic sequence alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline "sterile" transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built by the pipeline to infer the dynamics and direction of CSR. Applying sciCSR on SARS-CoV-2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier timepoint in the collected time-course, the isotype distribution of BCR repertoires of subsequent timepoints with high accuracy (cosine similarity approximately 0.9). sciCSR also recapitulates CSR patterns in mouse models where B cell maturation was perturbed using gene knockouts. sciCSR infers cell state transitions using processes specific to B cells, identifies transitions which are often missed by conventional RNA velocity analyses, and can reveal insights into the regulation of CSR and the dynamics of B cell maturation during an immune response.

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Section: Methodsmentioning

confidence: 99%

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

Garcia

Stewart

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…We first clarified the exact genomic position of TSS for the sterile transcript for every human and mouse IgH C gene with the exception of IgD where sterile transcription is not well understood. We collected from the literature a set of DNA genomic sequences isolated using traditional molecular cloning and restriction enzyme analysis, of the promoter region of sterile transcripts observed in experimental and/ or clinical models of CSR [51][52][53][55][56][57][58][59][60][61] . These sequences are mapped to the hg38 (for human)/mm10 (for mouse) reference genomes using BLAT 62 (v.36×4).…”

Section: Mapping Positions Of Sterile Transcription At the Igh Genomi...mentioning

confidence: 99%

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

Ng,

Montamat Garcia,

Stewart

et al. 2023

Nat Methods

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Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced ‘scissor’, single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline ‘sterile’ transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.

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Identification of a Conserved Lipopolysaccharide-Plus-Interleukin-4-Responsive Element Located at the Promoter of Germ Line ε Transcripts

Rothman

Gorham

et al. 1991

Molecular and Cellular Biology

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Treatment of splenic B lymphocytes and certain B-lineage cell lines with the mitogen lipopolysaccharide (LPS) and the lymphokine interleukin-4 (IL-4) induces expression of germ line immunoglobulin C epsilon transcripts and class switching to the C epsilon gene. We show that LPS-plus-IL-4 induction of germ line epsilon transcripts (termed I epsilon transcripts) occurs at the transcriptional level in an Abelson murine leukemia virus-transformed pre-B-cell line. A 1.1-kb region of DNA surrounding the I epsilon promoter endows inducible transcription to a heterologous reporter gene stably transfected into these cells; such inducible expression depends on combined treatment with LPS and IL-4. Analyses of constructs transiently introduced into a B-cell lymphoma line demonstrated that LPS-plus-IL-4-inducible expression can be conferred by a 179-bp segment of DNA spanning the I epsilon transcriptional initiation site. Mutational analyses demonstrated that this expression depended on DNA sequences within a conserved region directly upstream from the I epsilon transcriptional initiation region. One nuclear protein that is constitutively expressed in normal B cells binds to the downstream end of the conserved sequence; its binding specificity correlates with the functional effect of several mutations. Two additional proteins, which are induced by IL-4 treatment of splenic B cells, bind to the transcription initiation sites of I epsilon. These proteins are indistinguishable in binding assays from proteins previously shown to bind an enhancer region of the class II major histocompatibility complex gene A alpha.

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Structure and Expression of Germ Line Immunoglobulin Heavy-Chain ε Transcripts: Interleukin-4 Plus Lipopolysaccharide-Directed Switching to Cε

Cited by 6 publications

References 39 publications

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

Identification of a Conserved Lipopolysaccharide-Plus-Interleukin-4-Responsive Element Located at the Promoter of Germ Line ε Transcripts

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