Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs

Bortnick, A., He, Z., Aubrey, M., Chandra, V., Denholtz, M., Chen, K., Lin, Y.C. and Murre, C.

Cell Reports, 31(1)


Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program

Denholtz, M., Zhu, Y., He, Z., Lu, H., Isoda, T., Döhrmann, S., Nizet, V. and Murre, C.

Genes & Development, 34(1–17)




Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nature communications, 10(1), pp.1-13.

Khanna, N., Zhang, Y., Lucas, J.S., Dudko, O.K. and Murre, C.

Nature Communication, 10(1), 1-13


A B-Cell-Specific Enhancer Orchestrates Nuclear Architecture to Generate a Diverse Antigen Receptor Repertoire
Barajas-Mora, E.M., Kleiman, E., Xu, J., Carrico, N.C., Lu, H., Oltz, E.M., Murre, C. and Feeney, A.J.
Molecular cell, 73(1), 48-60.


Helix–loop–helix proteins and the advent of cellular diversity: 30 years of discovery
Murre, C.
Genes & development, 33(1-2), 6-25.




Nuclear Architecture Controls the Timescales of Genomic Interactions
Zhang, Y., Khanna, N., Dudko, O., & Murre, C.
Biophysical Journal, 114(3), 30a.


mTECs Aire on the side of caution
Bortnick, A. and Murre, C.
Nature immunology, 19(2), 100.




Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate
Isoda, T., Moore, A.J., He, Z., Chandra, V., Aida, M., Denholtz, M., van Hamburg, J.P., Fisch, K.M., Chang, A.N., Fahl, S.P. and Wiest, D.L. and Murre, C.
Cell 171(1), 103-119.

The E-Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development
Miyazaki, M., Miyazaki, K., Chen, K., Jin, Y., Turner, J., Moore, A.J., Saito, R., Yoshida, K., Ogawa, S., Rodewald, H.R. and Lin, Y.C. and Murre, C.
Immunity 46(5), 818-834.

ccctc-binding Factor Translates Interleukin 2-and α-ketoglutarate-sensitive Metabolic Changes in T Cells into Context-dependent Gene Programs
Chisolm, D.A., Savic, D., Moore, A.J., Ballesteros-Tato, A., León, B., Crossman, D.K., Murre, C., Myers, R.M. and Weinmann, A.S.
Immunity 47(2), 251-267.

Comprehensive characterization of neutrophil genome topology
Zhu, Y., Gong, K., Denholtz, M., Chandra, V., Kamps, M.P., Alber, F. and Murre, C.
Genes & Development 31(2), 141-153.




Id3 Orchestrates Germinal Center B Cell Development
Chen, S., Miyazaki, M., Chandra, V., Fisch, K.M., Chang, A.N. and Murre, C.
Molecular and cellular biology, 36(20), 2543-2552.

Cellular and chromatin dynamics of antibody‐secreting plasma cells
Bortnick, A. and Murre, C.
Wiley Interdisciplinary Reviews: Developmental Biology, 5(2), 136-149.




A common mechanism that underpins antibody diversification

Murre, C.

Cell 163, 1055-1056


The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth

Bossen, Murre, C.S., Chang, A.N., Mansson, R., Rodewald, H.R. and Murre, C.

Nat. Immunol 16, 775-784

The E-Id protein axis modulates the activities of the PI3K-AKT-mTORC1-Hif1a and c-myc/p19Arf pathways to suppress innate variant

TFH cell development, thymocyte expansion and lymphomagenesis

Miyazaki. M., Miyazaki, K., Chen, S.Y., Chandra, V., Agata, Y., Chang, A., Kawamoto, H. and Murre, C.

Genes Dev 29, 409-425

New roles for DNA cytosine modification, eRNA, anchors and superanchors in developing B cell progenitors

Benner, C., Isoda, T and Murre, C.

Proc. Natl. Acad. Sci USA 112, 12776-12781




B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity

Qian, J., Wang, Q., Dose, M., Pruett N., Kieffer-Kwon, K.R., Resch, W., Liang, G., Tang, Z., Mathé, E., Benner, C., Duboi, W., Nelson, S.,

Vian, L., Oliveira, T.Y., Jankovic, M., Hakim, O., Gazumyan, A., Pavri, R., Awasthi, P., Song, B., Liu, G., Chen, L., Zhu, S., Feigenbaum, L.,

Staudt, L., Murre, C., Ruan, Y., Robbiani, D.F., Pan-Hammarstr?m, Q., Nussenzweig, M.C. and Casellas, R.

Cell 18, 1524-1537


The 3-D trajectories adopted by coding and regulatory DNA elements: First-passage times and long-range genomic interactions

Lucas JS, Zhang J, Dudko OS, Murre C

Cell 158, 339-352


Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease

Miyazaki M, Miyazaki K, Chen SY, Itoi M, Miller M, Lu L-F, Varki N, Chang A, Broide DH, Murre C

Nat Immunol 15, 767-776


The establishment of B versus T cell identity

Miyazaki K, Miyazaki M, Murre C

Trends Immunol 35, 205-210





Boosting lymphocyte production

Murre C

Immunity 38, 1081-1083


Nuclear location and the control of developmental progression

Lin YC, Murre C

Curr Opion Genet Dev 23, 104-108


A HESitant decision for T cells

Bortnick A, Murre C

Nat Immunol 14, 1209-1210





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

Lin YC, Benner C, Mansson R, Heinz S, Miyazaki M, Miyazaki K, Chancera V, Bossen C, Glass CK, Murre C

Nat Immunol 12,1196-1204


Chromatin topology and the regulation of antigen receptor assembly

Bossen C, Mansson R, Murre C

Annual Rev Immunol 30, 337-356


Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate

Mansson R, Welinder E, Ashber J, Lin YC, Benner C, Glass CK, Sigvardsson M, Murre C

Proc Natl Acad. Sci USA 108, 17402-17407





Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineage in hematopoietic progenitors

Mercer EM, Lin YC, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C

Immunity 35, 413-425   


The opposing roles of the transcription factor E2A and its antagonist Id3 that orchestrate and enforce the naïve fate of T cells

Miyazaki M, Rivera RR, Miyazaki K, Lin YC, Agata Y, Murre C

Nat Immunol 12, 992-1001


E2A and HEB act in concert to induce the expression of FOXO1 in the common lymphoid progenitor

Welinder E, Mansson R, Mercer EM, Bryder D, Sigvardsson M, Murre C

Proc Natl Acad Sci USA 108, 17402-17407


CTCF-binding elements mediate control of V(D)J recombination

Guo C, Yoon HS, Franklin A, Jain S, Ebert A, Cheng HL, Hansen E, Despo O, Bossen C, Vettermann C, Bates JG, Richards N, Myers D, Patel H, Gallagher M, Schlissel MS, Murre C, Busslinger M, Giallourakis CC, Alt FW

Nature 477, 424-430


Transcription and recombination factories:  Common features? 

Lucas JL, Bossen C, Murre C

Curr Opin Cell Biol 23, 318-324


Ldb1, a new guardian of hematopoietic stem cell maintenance

Welinder E, Murre C

Nat Immunol 12, 113-114


CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells

Degner SC, Verma-Gaur J, Wong TP, Bossen C, Iverson GM, Torkamani A, Vettermann C, Lin YC, Ju Z, Schulz D, Murre CS, Birshtein BK, Schork NJ, Schlissel MS, Riblet R, Murre C, Feeney AJ

Proc Natl Acad Sci USA 108, 9566-9571


Factors and networks that underpin early hematopoiesis

Mercer EM, Lin YC, Murre C

Semin Immunol 5, 317-325





A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza A, Dutkowski J, Ideker T, Glass CK, Murre C

Nat Immunol 11, 635-643


Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK

Mol Cell 38, 576-89





Chromatin architecture and the generation of antigen receptor diversity

Jhunjhunwala S, van Zelm MC, Peak M, Murre C

Cell 138, 435-448


Distinct roles for E12 and E47 in B cell specification and the sequential rearrangement of immunoglobulin light chain loci

Beck K, Peak M, Ota T, Nemazee D. Murre C

J Exp Med 206, 2271-2284


E2A proteins maintain the hematopoietic stem cell pool and promote the maturation of myelolymphoid and myeloerythroid progenitors

Semerad CL, Mercer EM, Inlay MA, Weissman IL, Murre C

Proc Natl Acad Sci USA 106, 1930-1935


Developmental trajectories in early hematopoiesis

Murre C

Genes Devel 15, 2366-2370


--Publication before 2009 (txt file)--