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Chromatin accessibility and transcriptomic heterogeneity in human tonsillar B-cell subsets

ABSTRACT: Chromatin accessibility and transcriptomic heterogeneity in human tonsillar B-cell subsets

PROVIDER: PRJNA670166 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12850356.fastq.gz	Fastqsanger.gz
	SRR12850357.fastq.gz	Fastqsanger.gz
	SRR12850358.fastq.gz	Fastqsanger.gz
	SRR12850359.fastq.gz	Fastqsanger.gz
	SRR12850360.fastq.gz	Fastqsanger.gz

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Single-cell characterization of transcriptomic heterogeneity in human tonsillar B-cell subsets

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Project description:In order to assess the miRNA signature of B cells undergoing the germinal center reaction, we isolated three subsets of B cells from tonsils--naive (N), germinal center (GC), and memory (M) and looked at their miRNA profile. We looked at three subsets of B cells, isolated from tonsils obtained from four different donors. Thus, we profiled a total of 12 samples, and each tonsillar subset--N, GC, and M, had four biological replicates.

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Single-cell characterization of transcriptomic heterogeneity in human tonsillar B-cell subsets

Project description:BFL-1 is an understudied anti-apoptotic protein that is upregulated in melanoma, certain forms of leukemias and lymphomas, and Epstein-Barr virus (EBV)-immortalized lymphoblastoid cell lines (LCLs). We have previously shown that BFL-1 is upregulated in LCLs through a viral-mediated chromatin conformation. However, BFL-1 is also highly expressed in uninfected B cells undergoing maturation in the germinal center. We therefore sought to determine the non-viral mechanisms underlying BFL-1 upregulation in B cells. Here, we characterized the chromatin landscape of maturing B cell subsets found in human tonsillar lymphoid tissue. While chromatin accessibility at the BFL-1 locus increases as naïve B cells enter the germinal center reaction, we found that BFL-1 expression during the transition from dark zone to light zone correlates with a significant increase in three-dimensional chromatin association between upstream enhancer regions and the BFL-1 transcriptional start site (TSS). Interestingly, both LCLs and germinal center light zone B cells shared similar chromatin architectures at the BFL-1 TSS, suggesting a conserved mechanism underlying BFL-1 upregulation. Increased BFL-1 in LCLs also protects against FasL and TRAIL-activated extrinsic apoptosis. In addition to BFL-1 expression, LCLs and germinal center light zone B cells share similar patterns of gene expression, suggesting strong evidence that EBV infection phenocopies various aspects of the germinal center reaction. From this, we infer that EBV-infected B cells co-opts strategies from germinal center light zone B cells to upregulate BFL-1 and enhance their survival in establishing long-lived latent infection.

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Chromatin accessibility and transcriptomic heterogeneity in human tonsillar B-cell subsets

Project description:This SuperSeries is composed of the SubSeries listed below.

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Chromatin accessibility profiling of B cell subsets

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Antibody repertoire sequencing of human tonsillar B cell subsets

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Genome-wide analysis of chromatin accessibility in human tonsillar B cell subsets

Project description:We performed ATAC-Seq on three freshly dissociated human tonsils sorted to purity into the following B-cell subsets: CD19+ naïve (IgD+/CD38-), memory (IgD-/CD38-), germinal center light zone (IgD-/CD38mid/CD83+/CXCR4lo), germinal center dark zone (IgD-/CD38mid/CD83lo/CXCR4hi), and plasma cells (IgD-/CD38hi). We used these data to derive differentially accessible sites between B-cell subsets and relative to EBV-immortalized B cell lines (LCLs). These studies revealed similarities between LCLs and both DZ and LZ GC cells at the BCL2A1 (BFL1) locus that formed the impetus for further three-dimensional chromatin studies, which are the focus of the associated manuscript.

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