Clonally stable Vκ allelic choice instructs Igκ repertoire

Levin‐Klein, Rena; Fraenkel, Shira; Lichtenstein, Michal; Matheson, Louise S.; Bartok, Osnat; Nevo, Yuval; Kadener, Sebastián; Corcoran, Anne E.; Cedar, Howard; Bergman, Yehudit

doi:10.1038/ncomms15575

Cited by 11 publications

(20 citation statements)

References 42 publications

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“…This need for heterogeneity could suggest that long-range loops are constantly forming and reassembling in each precursor lymphocyte to create a structure in which different V genes are closest to the (D)J genes at different times, and there is evidence that CTCF binding, and by inference chromatin looping, is very dynamic ( 24 ). Alternatively, it could be that there is extensive heterogeneity within the population of lymphocyte precursors of long-range loops that might be somewhat more stable, as was suggested in studies on long-term cultured pre-B cells ( 95 ). The fact that the height of most of the bound CTCF peaks in the AgR loci are low might suggest that only a subset of the millions of cells analyzed in a ChIP-seq have CTCF bound at those individual sites at any given time, possibly due to weaker affinity for specific CTCF sites.…”

Section: Discussionmentioning

confidence: 98%

Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci

et al. 2018

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CCCTC-binding factor (CTCF) is largely responsible for the 3D architecture of the genome, in concert with the action of cohesin, through the creation of long-range chromatin loops. Cohesin is hypothesized to be the main driver of these long-range chromatin interactions by the process of loop extrusion. Here, we performed ChIP-seq for CTCF and cohesin in two stages each of T and B cell differentiation and examined the binding pattern in all six antigen receptor (AgR) loci in these lymphocyte progenitors and in mature T and B cells, ES cells, and fibroblasts. The four large AgR loci have many bound CTCF sites, most of which are only occupied in lymphocytes, while only the CTCF sites at the end of each locus near the enhancers or J genes tend to be bound in non-lymphoid cells also. However, despite the generalized lymphocyte restriction of CTCF binding in AgR loci, the Igκ locus is the only locus that also shows significant lineage-specificity (T vs. B cells) and developmental stage-specificity (pre-B vs. pro-B) in CTCF binding. We show that cohesin binding shows greater lineage- and stage-specificity than CTCF at most AgR loci, providing more specificity to the loops. We also show that the culture of pro-B cells in IL7, a common practice to expand the number of cells before ChIP-seq, results in a CTCF-binding pattern resembling pre-B cells, as well as other epigenetic and transcriptional characteristics of pre-B cells. Analysis of the orientation of the CTCF sites show that all sites within the large V portions of the Igh and TCRβ loci have the same orientation. This suggests either a lack of requirement for convergent CTCF sites creating loops, or indicates an absence of any loops between CTCF sites within the V region portion of those loci but only loops to the convergent sites at the D-J-enhancer end of each locus. The V region portions of the Igκ and TCRα/δ loci, by contrast, have CTCF sites in both orientations, providing many options for creating CTCF-mediated convergent loops throughout the loci. CTCF/cohesin loops, along with transcription factors, drives contraction of AgR loci to facilitate the creation of a diverse repertoire of antibodies and T cell receptors.

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Section: Discussionmentioning

confidence: 98%

Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci

et al. 2018

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“…However, considering that ASF1a has been reported to be necessary for maintenance of pluripotency and cellular reprogramming 70 and that ASF1a and ASF1b are involved in multiple pathways 28 , the role of ASF1 in differentiation is likely distinct from CAF-1 and awaits further investigation. In particular, in contexts such as the establishment of monoallelic expression—where early replication of the expressed allele coincides with chromatin accessibility 71 —it would be interesting to know whether ASF1 and the distribution of histone variants affect replication timing and, in turn, the differentiation program.…”

Section: Discussionmentioning

confidence: 99%

High-resolution visualization of H3 variants during replication reveals their controlled recycling

et al. 2018

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DNA replication is a challenge for the faithful transmission of parental information to daughter cells, as both DNA and chromatin organization must be duplicated. Replication stress further complicates the safeguard of epigenome integrity. Here, we investigate the transmission of the histone variants H3.3 and H3.1 during replication. We follow their distribution relative to replication timing, first in the genome and, second, in 3D using super-resolution microscopy. We find that H3.3 and H3.1 mark early- and late-replicating chromatin, respectively. In the nucleus, H3.3 forms domains, which decrease in density throughout replication, while H3.1 domains increase in density. Hydroxyurea impairs local recycling of parental histones at replication sites. Similarly, depleting the histone chaperone ASF1 affects recycling, leading to an impaired histone variant landscape. We discuss how faithful transmission of histone variants involves ASF1 and can be impacted by replication stress, with ensuing consequences for cell fate and tumorigenesis.

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“…Notably, we did not observe a significant contribution of non-coding transcription to either RF model, suggesting that transcription does not play a predictive role in Vκ recombination. A previous study proposed that transcription causes the eviction of H2A/H2B around Vκ RSSs ( 75 ), and non-coding transcription has also been shown to mark recombinationally active domains of the Vκ region ( 16 ). Together, these findings suggest that, in common with histone H3 and H4 acetylation, non-coding transcription may play a priming role for all Vκ genes, setting the stage for the features we have described here to specifically activate Vκ genes for recombination with a range of frequencies.…”

Section: Discussionmentioning

confidence: 99%

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination

et al. 2017

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V(D)J recombination is essential for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa (Igκ) light chain recombination follows immunoglobulin heavy chain (Igh) recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS) of VH genes are highly predictive of recombination in mouse pro-B cells. It is unknown whether local chromatin states contribute to Vκ gene choice during Igκ recombination. Here we adapt VDJ-seq to profile the Igκ VκJκ repertoire and present a comprehensive readout in mouse pre-B cells, revealing highly variable Vκ gene usage. Integration with genome-wide datasets for histone modifications, DNase hypersensitivity, transcription factor binding and germline transcription identified PU.1 binding at the RSS, which was unimportant for Igh, as highly predictive of whether a Vκ gene will recombine or not, suggesting that it plays a binary, all-or-nothing role, priming genes for recombination. Thereafter, the frequency with which these genes recombine was shaped both by the presence and level of enrichment of several other chromatin features, including H3K4 methylation and IKAROS binding. Moreover, in contrast to the Igh locus, the chromatin landscape of the promoter, as well as of the RSS, contributes to Vκ gene recombination. Thus, multiple facets of local chromatin features explain much of the variation in Vκ gene usage. Together, these findings reveal shared and divergent roles for epigenetic features and transcription factors in AgR V(D)J recombination and provide avenues for further investigation of chromatin signatures that may underpin V(D)J-mediated chromosomal translocations.

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Clonally stable Vκ allelic choice instructs Igκ repertoire

Cited by 11 publications

References 42 publications

Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci

Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci

High-resolution visualization of H3 variants during replication reveals their controlled recycling

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination

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