Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate b cell fate

ABSTRACT The genome is folded into domains located in compartments that are either transcriptionally inert or transcriptionally permissive. Here we used genome-wide strategies to

characterize domains during B cell development. Structured interaction matrix analysis showed that occupancy by the architectural protein CTCF was associated mainly with intradomain

interactions, whereas sites bound by the histone acetyltransferase p300 or the transcription factors E2A or PU.1 were associated with intra- and interdomain interactions that are

developmentally regulated. We identified a spectrum of genes that switched nuclear location during early B cell development. In progenitor cells, the transcriptionally inactive locus

encoding early B cell factor (_Ebf1_) was sequestered at the nuclear lamina, which thereby preserved their multipotency. After development into the pro-B cell stage, _Ebf1_ and other genes

switched compartments to establish new intra- and interdomain interactions associated with a B lineage–specific transcription signature. Access through your institution Buy or subscribe This

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DECOUPLES ENHANCER-MEDIATED GENE ACTIVATION FROM CHROMATIN HUB FORMATION Article Open access 13 May 2025 WIDESPREAD REORGANISATION OF PLURIPOTENT FACTOR BINDING AND GENE REGULATORY

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EMBRYONIC LINEAGES Article 05 December 2023 ACCESSION CODES PRIMARY ACCESSIONS GENE EXPRESSION OMNIBUS * GSE40173 REFERENCES * Sedat, J. & Manuelidis, L. A direct approach to the

structure of eukaryotic chromosomes. _Cold Spring Harb. Symp. Quant. Biol._ 42, 331–350 (1977). Article  Google Scholar  * Rattner, J.B. & Lin, C.C. Radial loops and helixcal coils

coexist in metaphase chromosomes. _Cell_ 42, 291–296 (1985). Article  CAS  PubMed  Google Scholar  * Paulson, J.R. & Laemmli, U.K. The structure of histone depleted metaphase

chromosomes. _Cell_ 12, 817–828 (1977). Article  CAS  PubMed  Google Scholar  * Pienta, K.J. & Coffey, D.S. A structural analysis of the nuclear matrix and DNA loops in the organization

of the nucleus and chromosome. _J. Cell Sci._ (suppl. 1), 123–135 (1984). * Munkel, C. & Langowski, J. Chromosome structure described by a polymer model. _Phys. Rev. E Stat. Phys.

Plasmas Fluids Relat. Interdiscip. Topics_ 575B, 5888–5896 (1998). Google Scholar  * Jhunjhunwala, S. et al. The 3D-structure of the immunoglobulin heavy chain locus: Implications for

long-range genomic interactions. _Cell_ 133, 265–279 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  * Bau., D. et al. The three-dimensional folding of the α-globin gene domain

reveals formation of chromatin globules. _Nat. Struct. Mol. Biol._ 18, 107–114 (2011). Article  CAS  PubMed  Google Scholar  * Guo, C. et al. Two forms of loops generate the chromatin

conformation of the immunoglobulin heavy chain locus. _Cell_ 147, 332–343 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Peric-Hupkes, D. et al. Molecular maps of the

reorganization of genome-nuclear lamina interactions during differentiation. _Mol. Cell_ 38, 603–613 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Schneider, R. &

Grosschedl, R. Dynamics and interplay of nuclear architecture, genome organization and gene expression. _Genes Dev._ 21, 3027–3043 (2007). Article  CAS  PubMed  Google Scholar  * Brown,

K.E., Baxtger, J., Graf, D., Merkenschlager, M. & Fisher, A.G. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. _Mol. Cell_ 3, 207–217 (1999).

Article  CAS  PubMed  Google Scholar  * Kosak, S.T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. _Science_ 296, 158–162 (2002). Article  CAS 

PubMed  Google Scholar  * Fuxa, M. et al. Pax5 induces V-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. _Genes Dev._ 18, 411–422 (2004). Article  CAS  PubMed

  PubMed Central  Google Scholar  * Roldán, E. et al. Locus 'decontraction' and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene.

_Nat. Immunol._ 6, 31–41 (2005). Article  CAS  PubMed  Google Scholar  * Hewitt, S.L., Chaumeil, J. & Skok, J.A. Chromosome dynamics and the regulation of V(D)J recombination. _Immunol.

Rev._ 237, 43–54 (2010). Article  CAS  PubMed  Google Scholar  * Goldmit, M. et al. Epigenetic ontogeny of the IgK locus during B cell development. _Nat. Immunol._ 6, 198–203 (2005). Article

  CAS  PubMed  Google Scholar  * Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. _Science_ 326, 289–293 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar  * Fullwood, M.J. et al. An oestrogen-receptor-α-bound human chromatin interactome. _Nature_ 462, 58–64 (2009). Article  CAS  PubMed 

PubMed Central  Google Scholar  * Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. & Chen, L. Genome architectures revealed by tethered chromosome conformation capture and

population-based modeling. _Nat. Biotechnol._ 30, 90–98 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Sexton, T. et al. Three-dimensional folding and functional

organization principles of the _Drosophila_ genome. _Cell_ 148, 458–472 (2012). Article  CAS  PubMed  Google Scholar  * Li, G. et al. Extensive promoter-centered chromatin interactions

provide a topological basis for transcription regulation. _Cell_ 148, 84–98 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Zhang, Y. et al. Spatial organization of the mouse

genome and its role in recurrent chromosomal translocations. _Cell_ 148, 908–921 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Dixon, J.R. et al. Topological domains in

mammalian genomes identified by analysis of chromatin interactions. _Nature_ 485, 376–380 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Siepel, A. et al. Evolutionarily

conserved elements in vertebrate, insect, worm, and yeast genomes. _Genome Res._ 15, 1034–1050 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Dawson, M.A. & Kouzarides,

T. Cancer epigenetics: from mechanism to therapy. _Cell_ 150, 12–27 (2012). Article  CAS  PubMed  Google Scholar  * Schmidt, D. et al. Waves of retrotransposon expansion remodel genome

organization and CTCF binding in multiple mammalian lineages. _Cell_ 148, 335–348 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ochiai, K. et al. A self-reinforcing

regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. _Nat. Immunol._ 13, 300–307 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  *

Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. _Cell_ 133, 1106–1117 (2008). Article  CAS  PubMed  Google Scholar 

* Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. _Mol. Cell_ 38, 576–589

(2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Lin, Y.C. et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.

_Nat. Immunol._ 11, 635–643 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Iborra, F.J., Pombo, A., Jackson, D.A. & Cook, P.R. Active RNA polymerase are localized within discrete

transcription factories in human nuclei. _J. Cell Sci._ 109, 142–2436 (1996). Google Scholar  * Edelman, L.B. & Fraser, F. Transcription factories: genetic programming in three

dimensions. _Curr. Opin. Gen. Dev._ 22, 110–114 (2012). Article  CAS  Google Scholar  * Corcoran, A.E. The epigenetic role of non-coding RNA transcription and nuclear organization in

immunoglobulin repertoire generation. _Semin. Immunol._ 6, 353–361 (2010). Article  CAS  Google Scholar  * Simonis, M. et al. Nuclear organization of active and inactive chromatin domains

uncovered by chromosome capture-on-chip (4C). _Nat. Genet._ 38, 1348–1354 (2006). Article  CAS  PubMed  Google Scholar  * Jhunjhunwala, S., van Zelm, M.C., Peak, M. & Murre, C. Chromatin

architecture and the generation of antigen receptor diversity. _Cell_ 138, 435–448 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  * Inlay, M.A., Tina, H., Lin, T. & Xu,

Y. Important roles for E protein binding sites within the immunoglobulin kappa chain intronic enhancer in activating Vκ to Jκ rearrangement. _J. Exp. Med._ 200, 1205–1211 (2004). Article 

CAS  PubMed  PubMed Central  Google Scholar  * Romanow, W.J. et al. E2A and EBF act in synergy with the V(D)J recombinase to generate a diverse immunoglobulin repertoire in non-lymphoid

cells. _Mol. Cell_ 5, 343–353 (2000). Article  CAS  PubMed  Google Scholar  * Sakamoto, S. et al. E2A and CBP/p300 act in synergy to promote chromatin accessibility of the immunoglobulin κ

locus. _J. Immunol._ 188, 5547–5560 (2012). Article  CAS  PubMed  Google Scholar  * Bossen, C., Mansson, R. & Murre, C. Chromatin topology and the regulation of antigen receptor

assembly. _Annu. Rev. Immunol._ 30, 337–356 (2012). Article  CAS  PubMed  Google Scholar  * Li, L., Leid, M. & Rothenberg, E.V. An early T cell lineage commitment checkpoint dependent on

the transcription factor Bcl11b. _Science_ 329, 89–93 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Ikawa, T. et al. An essential developmental checkpoint for production

of the T cell lineage. _Science_ 329, 93–96 (2010). Article  CAS  PubMed  Google Scholar  * Li, P. et al. Reprogamming of T cells to natural killer-like cells upon Bcl11b deletion. _Science_

329, 85–89 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Welinder, E. et al. E2A and HEB act in concert to induce the expression of FOXO1 in the common lymphoid

progenitor. _Proc. Natl. Acad. Sci. USA_ 108, 17402–17407 (2011). Article  PubMed  PubMed Central  Google Scholar  * Seet, C.S., Brumbaugh, R.L. & Kee, B.L. Early B cell factor promotes

B lymphopoiesis with reduced interleukin 7 responsiveness in the absence of E2A. _J. Exp. Med._ 199, 1689–1700 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  * Semerad, C.L.,

Mercer, E.M., Inlay, M.A., Weissman, I.L. & Murre, C. E2A proteins maintain the hematopoietic stem cell pool and promote the maturation of myelolymphoid and myeloerythroid progenitors.

_Proc. Natl. Acad. Sci. USA_ 106, 1930–1935 (2009). Article  PubMed  PubMed Central  Google Scholar  * Zullo, J.M. et al. DNA sequence-dependent compartmentalization and silencing of

chromatin at the nuclear lamina. _Cell_ 149, 1474–1487 (2012). Article  CAS  PubMed  Google Scholar  * Ikawa, T., Kawamoto, H., Wright, L.Y. & Murre, C. Long-term cultured E2A-deficient

hematopoietic progenitor cells are pluripotent. _Immunity_ 20, 349–360 (2004). Article  CAS  PubMed  Google Scholar  * Sayegh, C.E., Jhunjhunwala, S., Riblet, R. & Murre, C.

Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells. _Genes Dev._ 22, 322–327 (2005). Article  CAS  Google Scholar  Download references

ACKNOWLEDGEMENTS We thank G. Hardiman, C. Ludka, L. Edsall, S. Kuan, C. Espinoza, U. Wagner, J. Sprague and Z. Ye for help with Solexa DNA sequencing; J. Dixon for help during the initial

phase of Hi-C analysis; B. Wold for suggesting fixation with ethylene glycol bis(succinimidylsuccinate); B. Ren for access to the Illumina Hi-Seq; and members of the Murre laboratory for

comments on the manuscript. Supported by the American Recovery and Reinvestment Act (ARRA PHS 3RO1AI082850 to Y.C.L.), the European Molecular Biology Organization (C.Bo.), the Swiss National

Science Foundation (C.Bo.), the University of California San Diego, Cancer Center (P30 CA23100) and the US National Institutes of Health (AI082850A and AI00880 to C.K.G. and C.M.). AUTHOR

INFORMATION Author notes * Yin C Lin and Christopher Benner: These authors contributed equally to this work. AUTHORS AND AFFILIATIONS * Department of Molecular Biology, University of

California San Diego, La Jolla, California, USA., Yin C Lin, Robert Mansson, Kazuko Miyazaki, Masaki Miyazaki, Vivek Chandra, Claudia Bossen & Cornelis Murre * Department of Cellular and

Molecular Medicine, University of California San Diego, La Jolla, California, USA., Christopher Benner, Sven Heinz & Christopher K Glass * Integrative Genomics and Bioinformatics Core,

Salk Institute for Biological Studies, La Jolla, California, USA Christopher Benner Authors * Yin C Lin View author publications You can also search for this author inPubMed Google Scholar *

Christopher Benner View author publications You can also search for this author inPubMed Google Scholar * Robert Mansson View author publications You can also search for this author

inPubMed Google Scholar * Sven Heinz View author publications You can also search for this author inPubMed Google Scholar * Kazuko Miyazaki View author publications You can also search for

this author inPubMed Google Scholar * Masaki Miyazaki View author publications You can also search for this author inPubMed Google Scholar * Vivek Chandra View author publications You can

also search for this author inPubMed Google Scholar * Claudia Bossen View author publications You can also search for this author inPubMed Google Scholar * Christopher K Glass View author

publications You can also search for this author inPubMed Google Scholar * Cornelis Murre View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS

R.M. and S.H. contributed equally to this work. Y.C.L., R.M. and S.H. designed and did most of the experiments; S.H. did Gro-Seq analysis; C.Be. did the bioinformatics analysis, analyzed

data, suggested new approaches and developed SIMA; M.M., K.M. and V.C. did chromatin immunoprecipitation followed by deep sequencing; C.Bo. provided insight into the topology of the _Igk_

locus; Y.C.L., C.Be. and C.M. wrote the manuscript with contributions from C.K.G., R.M. and S.H.; and C.K.G. and C.M. supervised the study. CORRESPONDING AUTHORS Correspondence to

Christopher Benner, Christopher K Glass or Cornelis Murre. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION

SUPPLEMENTARY TEXT AND FIGURES Supplementary Figures 1–7 and Tables 1–3 and Supplementary Methods (PDF 8652 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS

ARTICLE Lin, Y., Benner, C., Mansson, R. _et al._ Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. _Nat

Immunol_ 13, 1196–1204 (2012). https://doi.org/10.1038/ni.2432 Download citation * Received: 06 July 2012 * Accepted: 27 August 2012 * Published: 14 October 2012 * Issue Date: December 2012

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