1
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Patta I, Zand M, Lee L, Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang HY, Cheng CS, Fisch KM, Hu M, Murre C. Nuclear morphology is shaped by loop-extrusion programs. Nature 2024; 627:196-203. [PMID: 38355805 PMCID: PMC11052650 DOI: 10.1038/s41586-024-07086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/17/2024] [Indexed: 02/16/2024]
Abstract
It is well established that neutrophils adopt malleable polymorphonuclear shapes to migrate through narrow interstitial tissue spaces1-3. However, how polymorphonuclear structures are assembled remains unknown4. Here we show that in neutrophil progenitors, halting loop extrusion-a motor-powered process that generates DNA loops by pulling in chromatin5-leads to the assembly of polymorphonuclear genomes. Specifically, we found that in mononuclear neutrophil progenitors, acute depletion of the loop-extrusion loading factor nipped-B-like protein (NIPBL) induced the assembly of horseshoe, banded, ringed and hypersegmented nuclear structures and led to a reduction in nuclear volume, mirroring what is observed during the differentiation of neutrophils. Depletion of NIPBL also induced cell-cycle arrest, activated a neutrophil-specific gene program and conditioned a loss of interactions across topologically associating domains to generate a chromatin architecture that resembled that of differentiated neutrophils. Removing NIPBL resulted in enrichment for mega-loops and interchromosomal hubs that contain genes associated with neutrophil-specific enhancer repertoires and an inflammatory gene program. On the basis of these observations, we propose that in neutrophil progenitors, loop-extrusion programs produce lineage-specific chromatin architectures that permit the packing of chromosomes into geometrically confined lobular structures. Our data also provide a blueprint for the assembly of polymorphonuclear structures, and point to the possibility of engineering de novo nuclear shapes to facilitate the migration of effector cells in densely populated tumorigenic environments.
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Affiliation(s)
- Indumathi Patta
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Maryam Zand
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Shreya Mishra
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Alexandra Bortnick
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Hanbin Lu
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Arpita Prusty
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Huan-You Wang
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Cheng
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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2
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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3
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Pham PD, Lu H, Han H, Zhou JJ, Madan A, Wang W, Murre C, Cho KWY. Transcriptional network governing extraembryonic endoderm cell fate choice. Dev Biol 2023; 502:20-37. [PMID: 37423592 PMCID: PMC10550205 DOI: 10.1016/j.ydbio.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
The mechanism by which transcription factor (TF) network instructs cell-type-specific transcriptional programs to drive primitive endoderm (PrE) progenitors to commit to parietal endoderm (PE) versus visceral endoderm (VE) cell fates remains poorly understood. To address the question, we analyzed the single-cell transcriptional signatures defining PrE, PE, and VE cell states during the onset of the PE-VE lineage bifurcation. By coupling with the epigenomic comparison of active enhancers unique to PE and VE cells, we identified GATA6, SOX17, and FOXA2 as central regulators for the lineage divergence. Transcriptomic analysis of cXEN cells, an in vitro model for PE cells, after the acute depletion of GATA6 or SOX17 demonstrated that these factors induce Mycn, imparting the self-renewal properties of PE cells. Concurrently, they suppress the VE gene program, including key genes like Hnf4a and Ttr, among others. We proceeded with RNA-seq analysis on cXEN cells with FOXA2 knockout, in conjunction with GATA6 or SOX17 depletion. We found FOXA2 acts as a potent suppressor of Mycn while simultaneously activating the VE gene program. The antagonistic gene regulatory activities of GATA6/SOX17 and FOXA2 in promoting alternative cell fates, and their physical co-bindings at the enhancers provide molecular insights to the plasticity of the PrE lineage. Finally, we show that the external cue, BMP signaling, promotes the VE cell fate by activation of VE TFs and repression of PE TFs including GATA6 and SOX17. These data reveal a putative core gene regulatory module that underpins PE and VE cell fate choice.
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Affiliation(s)
- Paula Duyen Pham
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Hanbin Lu
- School of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, 92039, USA
| | - Han Han
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Jeff Jiajing Zhou
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Aarushi Madan
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Cornelis Murre
- School of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, 92039, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA.
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4
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Russ BE, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, Barugahare A, See M, Nussing S, Morey AE, Udupa VA, Bennett T.J, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naïvety through regulation of global genome architecture. bioRxiv 2023:2023.02.26.530139. [PMID: 36909629 PMCID: PMC10002700 DOI: 10.1101/2023.02.26.530139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The differentiation of naïve CD8+ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naïve, effector and memory virus-specific CD8+ T cells. We observed that the architecture of the naive CD8+ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naïve chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naïve CD8+ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naïve chromatin state.
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Affiliation(s)
- Brendan E. Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
- Department of Molecular Biology, University of California, San Diego, USA
| | - Jason K. C. Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, USA
| | - Paul F. Harrison
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Michael See
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | | | - Alison E. Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Vibha A. Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Taylah .J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Ananda W. Goldrath
- Department of Biological Sciences, University of California, San Diego, USA
| | - Stephen J. Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
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5
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Barajas-Mora EM, Lee L, Lu H, Valderrama JA, Bjanes E, Nizet V, Feeney AJ, Hu M, Murre C. Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens. Nat Immunol 2023; 24:320-336. [PMID: 36717722 PMCID: PMC10917333 DOI: 10.1038/s41590-022-01402-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/06/2022] [Indexed: 01/31/2023]
Abstract
Antigen receptor loci are organized into variable (V), diversity (D) and joining (J) gene segments that rearrange to generate antigen receptor repertoires. Here, we identified an enhancer (E34) in the murine immunoglobulin kappa (Igk) locus that instructed rearrangement of Vκ genes located in a sub-topologically associating domain, including a Vκ gene encoding for antibodies targeting bacterial phosphorylcholine. We show that E34 instructs the nuclear repositioning of the E34 sub-topologically associating domain from a recombination-repressive compartment to a recombination-permissive compartment that is marked by equivalent activating histone modifications. Finally, we found that E34-instructed Vκ-Jκ rearrangement was essential to combat Streptococcus pneumoniae but not methicillin-resistant Staphylococcus aureus or influenza infections. We propose that the merging of Vκ genes with Jκ elements is instructed by one-dimensional epigenetic information imposed by enhancers across Vκ and Jκ genomic regions. The data also reveal how enhancers generate distinct antibody repertoires that provide protection against lethal bacterial infection.
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Affiliation(s)
| | - Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Hanbin Lu
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - J Andrés Valderrama
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elisabet Bjanes
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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6
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Aubrey M, Warburg ZJ, Murre C. Helix-Loop-Helix Proteins in Adaptive Immune Development. Front Immunol 2022; 13:881656. [PMID: 35634342 PMCID: PMC9134016 DOI: 10.3389/fimmu.2022.881656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The E/ID protein axis is instrumental for defining the developmental progression and functions of hematopoietic cells. The E proteins are dimeric transcription factors that activate gene expression programs and coordinate changes in chromatin organization. Id proteins are antagonists of E protein activity. Relative levels of E/Id proteins are modulated throughout hematopoietic development to enable the progression of hematopoietic stem cells into multiple adaptive and innate immune lineages including natural killer cells, B cells and T cells. In early progenitors, the E proteins promote commitment to the T and B cell lineages by orchestrating lineage specific programs of gene expression and regulating VDJ recombination of antigen receptor loci. In mature B cells, the E/Id protein axis functions to promote class switch recombination and somatic hypermutation. E protein activity further regulates differentiation into distinct CD4+ and CD8+ T cells subsets and instructs mature T cell immune responses. In this review, we discuss how the E/Id proteins define the adaptive immune system lineages, focusing on their role in directing developmental gene programs.
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Affiliation(s)
- Megan Aubrey
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Zachary J Warburg
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Cornelis Murre
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
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7
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Abstract
It is well established that the helix-loop-helix proteins, E2A and E2-2, promote B cell activation. Here, we examined how during the course of B cell activation E2A and E2-2 gene expression is regulated. We found that E2A and E2-2 mRNA abundance concomitantly increased in activated B cells. The increase in E2A and E2-2 mRNA abundance correlated with increased cell growth. Elevated E2A and E2-2 mRNA abundance was instructed by increased transcriptional bursting frequencies and elevated E2A and E2-2 mRNA half-lives. The increase in E2A and E2-2 bursting frequencies often occurred at shared interchromosomal transcriptional hubs. We suggest that in naïve B cells low E2A and E2-2 bursting frequencies and high E2A and E2-2 mRNA decay rates instruct noisy gene expression that allows a clonal and swift response to invading pathogens whereas in activated B cells increased transcriptional bursting and low mRNA decay rates dictate an activated B lineage gene program.
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Affiliation(s)
- Yi Zhou
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Cornelis Murre
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92039, USA
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8
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Pongubala JMR, Murre C. Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development. Front Immunol 2021; 12:633825. [PMID: 33854505 PMCID: PMC8039525 DOI: 10.3389/fimmu.2021.633825] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Higher-order spatial organization of the genome into chromatin compartments (permissive and repressive), self-associating domains (TADs), and regulatory loops provides structural integrity and offers diverse gene regulatory controls. In particular, chromatin regulatory loops, which bring enhancer and associated transcription factors in close spatial proximity to target gene promoters, play essential roles in regulating gene expression. The establishment and maintenance of such chromatin loops are predominantly mediated involving CTCF and the cohesin machinery. In recent years, significant progress has been made in revealing how loops are assembled and how they modulate patterns of gene expression. Here we will discuss the mechanistic principles that underpin the establishment of three-dimensional (3D) chromatin structure and how changes in chromatin structure relate to alterations in gene programs that establish immune cell fate.
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Affiliation(s)
| | - Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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9
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Delpoux A, Marcel N, Hess Michelini R, Katayama CD, Allison KA, Glass CK, Quiñones-Parra SM, Murre C, Loh L, Kedzierska K, Lappas M, Hedrick SM, Doedens AL. FOXO1 constrains activation and regulates senescence in CD8 T cells. Cell Rep 2021; 34:108674. [PMID: 33503413 DOI: 10.1016/j.celrep.2020.108674] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/25/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022] Open
Abstract
Naive and memory T cells are maintained in a quiescent state, yet capable of rapid response and differentiation to antigen challenge via molecular mechanisms that are not fully understood. In naive cells, the deletion of Foxo1 following thymic development results in the increased expression of multiple AP-1 family members, rendering T cells less able to respond to antigenic challenge. Similarly, in the absence of FOXO1, post-infection memory T cells exhibit the characteristics of extended activation and senescence. Age-based analysis of human peripheral T cells reveals that levels of FOXO1 and its downstream target, TCF7, are inversely related to host age, whereas the opposite is found for AP-1 factors. These characteristics of aging also correlate with the formation of T cells manifesting features of cellular senescence. Our work illustrates a role for FOXO1 in the active maintenance of stem-like properties in T cells at the timescales of acute infection and organismal life span.
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Affiliation(s)
- Arnaud Delpoux
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Nimi Marcel
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Rodrigo Hess Michelini
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Carol D Katayama
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Karmel A Allison
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Sergio M Quiñones-Parra
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Cornelis Murre
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Martha Lappas
- Obstetrics, Nutrition, and Endocrinology Group, Department of Obstetrics & Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Stephen M Hedrick
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA.
| | - Andrew L Doedens
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA.
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10
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Zhu Y, Denholtz M, Lu H, Murre C. Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization. Genes Dev 2020; 35:65-81. [PMID: 33334824 PMCID: PMC7778268 DOI: 10.1101/gad.343475.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/22/2020] [Indexed: 12/18/2022]
Abstract
In this study, Zhu et al. sought to understand the signaling pathways and epigenetic control of nuclear architecture during developmental progression of immune cells. They found that in activated neutrophils calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of active enhancers and promoters to dictate widespread changes in compartment segregation. During developmental progression the genomes of immune cells undergo large-scale changes in chromatin folding. However, insights into signaling pathways and epigenetic control of nuclear architecture remain rudimentary. Here, we found that in activated neutrophils calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of active enhancers and promoters to dictate widespread changes in compartment segregation. NIPBL recruitment to enhancers and promoters occurred with distinct kinetics. The induction of NIPBL-binding was coordinate with increased P300, BRG1 and RNA polymerase II occupancy. NIPBL-bound enhancers were associated with NFAT, PU.1, and CEBP cis elements, whereas NIPBL-bound promoters were enriched for GC-rich DNA sequences. Using an acute degradation system, we found that the histone acetyltransferases P300 and CBP maintained H3K27ac abundance and facilitated NIPBL occupancy at enhancers and that active transcriptional elongation is essential to maintain H3K27ac abundance. Chromatin remodelers, containing either of the mutually exclusive BRG1 and BRM ATPases, promoted NIPBL recruitment at active enhancers. Conversely, at active promoters, depletion of BRG1 and BRM showed minimal effect on NIPBL occupancy. Finally, we found that calcium signaling in both primary innate and adaptive immune cells swiftly induced NIPBL occupancy. Collectively, these data reveal how transcriptional regulators, histone acetyltransferases, chromatin remodelers, and transcription elongation promote NIPBL occupancy at active enhancers while the induction of NIPLB occupancy at promoters is primarily associated with GC-rich DNA sequences.
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Affiliation(s)
- Yina Zhu
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Matthew Denholtz
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Hanbin Lu
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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11
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Boland BS, He Z, Tsai MS, Olvera JG, Omilusik KD, Duong HG, Kim ES, Limary AE, Jin W, Milner JJ, Yu B, Patel SA, Louis TL, Tysl T, Kurd NS, Bortnick A, Quezada LK, Kanbar JN, Miralles A, Huylebroeck D, Valasek MA, Dulai PS, Singh S, Lu LF, Bui JD, Murre C, Sandborn WJ, Goldrath AW, Yeo GW, Chang JT. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses. Sci Immunol 2020; 5:5/50/eabb4432. [PMID: 32826341 PMCID: PMC7733868 DOI: 10.1126/sciimmunol.abb4432] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal mucosal immune systems in health and ulcerative colitis (UC). UC was associated with an increase in IgG1+ plasma cells in colonic tissue, increased colonic regulatory T cells characterized by elevated expression of the transcription factor ZEB2, and an enrichment of a γδ T cell subset in the peripheral blood. Moreover, we observed heterogeneity in CD8+ tissue-resident memory T (TRM) cells in colonic tissue, with four transcriptionally distinct states of differentiation observed across health and disease. In the setting of UC, there was a marked shift of clonally related CD8+ TRM cells toward an inflammatory state, mediated, in part, by increased expression of the T-box transcription factor Eomesodermin. Together, these results provide a detailed atlas of transcriptional changes occurring in adaptive immune cells in the context of UC and suggest a role for CD8+ TRM cells in IBD.
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Affiliation(s)
- Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Matthew S Tsai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Han G Duong
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Eleanor S Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abigail E Limary
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - J Justin Milner
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Bingfei Yu
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shefali A Patel
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiani L Louis
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nadia S Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alexandra Bortnick
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lauren K Quezada
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jad N Kanbar
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ara Miralles
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Danny Huylebroeck
- Department of Development and Regeneration, University of Leuven, Leuven, Belgium.,Department of Cell Biology, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, Netherlands
| | - Mark A Valasek
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Siddharth Singh
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Li-Fan Lu
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jack D Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA, USA
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12
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Bortnick A, He Z, Aubrey M, Chandra V, Denholtz M, Chen K, Lin YC, Murre C. Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs. Cell Rep 2020; 31:107876. [PMID: 32610145 DOI: 10.1016/j.celrep.2020.107876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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13
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Kurd NS, He Z, Louis TL, Milner JJ, Omilusik KD, Jin W, Tsai MS, Widjaja CE, Kanbar JN, Olvera JG, Tysl T, Quezada LK, Boland BS, Huang WJ, Murre C, Goldrath AW, Yeo GW, Chang JT. Early precursors and molecular determinants of tissue-resident memory CD8 + T lymphocytes revealed by single-cell RNA sequencing. Sci Immunol 2020; 5:eaaz6894. [PMID: 32414833 PMCID: PMC7341730 DOI: 10.1126/sciimmunol.aaz6894] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023]
Abstract
During an immune response to microbial infection, CD8+ T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (TRM) cells that mediate potent protection within nonlymphoid tissues. Here, we used single-cell RNA sequencing to examine the gene expression patterns of individual CD8+ T cells in the spleen and small intestine intraepithelial lymphocyte (siIEL) compartment throughout the course of their differentiation in response to viral infection. These analyses revealed previously unknown transcriptional heterogeneity within the siIEL CD8+ T cell population at several stages of differentiation, representing functionally distinct TRM cell subsets and a subset of TRM cell precursors within the tissue early in infection. Together, these findings may inform strategies to optimize CD8+ T cell responses to protect against microbial infection and cancer.
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Affiliation(s)
- Nadia S Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tiani L Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J Justin Milner
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Jad N Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren K Quezada
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy J Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA, USA
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14
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Bortnick A, He Z, Aubrey M, Chandra V, Denholtz M, Chen K, Lin YC, Murre C. Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs. Cell Rep 2020; 31:107470. [PMID: 32268089 PMCID: PMC10871151 DOI: 10.1016/j.celrep.2020.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/31/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
The transition from the follicular B to the plasma cell stage is associated with large-scale changes in cell morphology. Here, we examine whether plasma cell development is also associated with changes in nuclear architecture. We find that the onset of plasma cell development is concomitant with a decline in remote genomic interactions; a gain in euchromatic character at loci encoding for factors that specify plasma cell fate, including Prdm1 and Atf4; and establishment of de novo inter-chromosomal hubs. We find that, in developing plasma cells and concurrent with transcriptional silencing, the Ebf1 locus repositions from an euchromatic to peri-centromeric heterochromatic environment. Finally, we find that inter-chromosomal hubs are enriched for the deposition of either H3K27Ac or H3K27me3. These data indicate that plasma cell fate is orchestrated by elaborate changes in genome topology and that epigenetic marks, linked with super-enhancers or transcriptionally repressed regions, are enriched at inter-chromosomal hubs.
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Affiliation(s)
- Alexandra Bortnick
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoren He
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan Aubrey
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vivek Chandra
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Denholtz
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kenian Chen
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246, USA
| | - Yin C Lin
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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15
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Denholtz M, Zhu Y, He Z, Lu H, Isoda T, Döhrmann S, Nizet V, Murre C. Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program. Genes Dev 2020; 34:149-165. [PMID: 31919189 PMCID: PMC7000913 DOI: 10.1101/gad.333708.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/12/2019] [Indexed: 01/03/2023]
Abstract
Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 h) repositioned the ensemble of proinflammatory genes toward the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape, permitting an immediate transcriptional response upon bacterial exposure. We found that activated enhancers, marked by increased deposition of H3K27Ac, were highly enriched for cistromic elements associated with PU.1, CEBPB, TFE3, JUN, and FOSL2 occupancy. These data reveal how upon microbial challenge the cohesin machinery is recruited to an activated enhancer repertoire to instruct changes in chromatin folding, nuclear architecture, and to activate an inflammatory gene program.
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Affiliation(s)
- Matthew Denholtz
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA
| | - Yina Zhu
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA
| | - Zhaoren He
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA
| | - Hanbin Lu
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA
| | - Takeshi Isoda
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA
| | - Simon Döhrmann
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA
| | - Victor Nizet
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA
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16
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Abstract
This Outlook by Murre discusses two new studies in this issue of Genes & Development by Miyai et al. and Li et al. These studies provide new and unprecedented insights into the genetic and epigenetic mechanisms that establish B-cell identity. Earlier studies have identified transcription factors that specify B-cell fate, but the underlying mechanisms remain to be revealed. Two new studies by Miyai and colleagues (pp. 112–126) and Li and colleagues (pp. 96–111) in this issue of Genes & Development provide new and unprecedented insights into the genetic and epigenetic mechanisms that establish B-cell identity.
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Affiliation(s)
- Cornelis Murre
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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17
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Khanna N, Zhang Y, Lucas JS, Dudko OK, Murre C. Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nat Commun 2019; 10:2771. [PMID: 31235807 PMCID: PMC6591236 DOI: 10.1038/s41467-019-10628-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/20/2019] [Indexed: 11/08/2022] Open
Abstract
Diverse antibody repertoires are generated through remote genomic interactions involving immunoglobulin variable (VH), diversity (DH) and joining (JH) gene segments. How such interactions are orchestrated remains unknown. Here we develop a strategy to track VH-DHJH motion in B-lymphocytes. We find that VH and DHJH segments are trapped in configurations that allow only local motion, such that spatially proximal segments remain in proximity, while spatially remote segments remain remote. Within a subset of cells, however, abrupt changes in VH-DHJH motion are observed, plausibly caused by temporal alterations in chromatin configurations. Comparison of experimental and simulated data suggests that constrained motion is imposed by a network of cross-linked chromatin chains characteristic of a gel phase, yet poised near the sol phase, a solution of independent chromatin chains. These results suggest that chromosome organization near the sol-gel phase transition dictates the timing of genomic interactions to orchestrate gene expression and somatic recombination.
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Affiliation(s)
- Nimish Khanna
- Division of Biological Sciences, 0377, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yaojun Zhang
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ, 08544, USA
| | - Joseph S Lucas
- Division of Biological Sciences, 0377, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olga K Dudko
- Department of Physics, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Cornelis Murre
- Division of Biological Sciences, 0377, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
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18
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Arends T, Dege C, Bortnick A, Danhorn T, Knapp JR, Jia H, Harmacek L, Fleenor CJ, Straign D, Walton K, Leach SM, Feeney AJ, Murre C, O'Connor BP, Hagman JR. CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis. Proc Natl Acad Sci U S A 2019; 116:10927-10936. [PMID: 31085655 PMCID: PMC6561196 DOI: 10.1073/pnas.1821301116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cell lineage specification is a tightly regulated process that is dependent on appropriate expression of lineage and developmental stage-specific transcriptional programs. Here, we show that Chromodomain Helicase DNA-binding protein 4 (CHD4), a major ATPase/helicase subunit of Nucleosome Remodeling and Deacetylase Complexes (NuRD) in lymphocytes, is essential for specification of the early B cell lineage transcriptional program. In the absence of CHD4 in B cell progenitors in vivo, development of these cells is arrested at an early pro-B-like stage that is unresponsive to IL-7 receptor signaling and unable to efficiently complete V(D)J rearrangements at Igh loci. Our studies confirm that chromatin accessibility and transcription of thousands of gene loci are controlled dynamically by CHD4 during early B cell development. Strikingly, CHD4-deficient pro-B cells express transcripts of many non-B cell lineage genes, including genes that are characteristic of other hematopoietic lineages, neuronal cells, and the CNS, lung, pancreas, and other cell types. We conclude that CHD4 inhibits inappropriate transcription in pro-B cells. Together, our data demonstrate the importance of CHD4 in establishing and maintaining an appropriate transcriptome in early B lymphopoiesis via chromatin accessibility.
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Affiliation(s)
- Tessa Arends
- Program in Molecular Biology, University of Colorado Denver, Aurora, CO 80045
| | - Carissa Dege
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045
| | - Alexandra Bortnick
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
| | - Thomas Danhorn
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Jennifer R Knapp
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Haiqun Jia
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Courtney J Fleenor
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Desiree Straign
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Kendra Walton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
| | - Sonia M Leach
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Ann J Feeney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Cornelis Murre
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
| | - Brian P O'Connor
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - James R Hagman
- Program in Molecular Biology, University of Colorado Denver, Aurora, CO 80045;
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
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19
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Abstract
In this review from Murre, the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed. Helix–loop–helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer–promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.
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Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92903, USA
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20
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Barajas-Mora EM, Kleiman E, Xu J, Carrico NC, Lu H, Oltz EM, Murre C, Feeney AJ. A B-Cell-Specific Enhancer Orchestrates Nuclear Architecture to Generate a Diverse Antigen Receptor Repertoire. Mol Cell 2018; 73:48-60.e5. [PMID: 30449725 DOI: 10.1016/j.molcel.2018.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/16/2018] [Accepted: 10/08/2018] [Indexed: 12/20/2022]
Abstract
The genome is organized into topologically associated domains (TADs) that enclose smaller subTADs. Here, we identify and characterize an enhancer that is located in the middle of the V gene region of the immunoglobulin kappa light chain (Igκ) locus that becomes active preceding the stage at which this locus undergoes V(D)J recombination. This enhancer is a hub of long-range chromatin interactions connecting subTADs in the V gene region with the recombination center at the J genes. Deletion of this element results in a highly altered long-range chromatin interaction pattern across the locus and, importantly, affects individual V gene utilization locus-wide. These results indicate the existence of an enhancer-dependent framework in the Igκ locus and further suggest that the composition of the diverse antibody repertoire is regulated in a subTAD-specific manner. This enhancer thus plays a structural role in orchestrating the proper folding of the Igκ locus in preparation for V(D)J recombination.
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Affiliation(s)
- E Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eden Kleiman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Xu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy C Carrico
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hanbin Lu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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21
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Zhang Y, Khanna N, Dudko O, Murre C. Nuclear Architecture Controls the Timescales of Genomic Interactions. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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22
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Roy S, Moore AJ, Love C, Reddy A, Rajagopalan D, Dave SS, Li L, Murre C, Zhuang Y. Id Proteins Suppress E2A-Driven Invariant Natural Killer T Cell Development prior to TCR Selection. Front Immunol 2018; 9:42. [PMID: 29416542 PMCID: PMC5787561 DOI: 10.3389/fimmu.2018.00042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/08/2018] [Indexed: 02/01/2023] Open
Abstract
A family of transcription factors known as E proteins, and their antagonists, Id proteins, regulate T cell differentiation at critical developmental checkpoints. Id proteins promote the differentiation of conventional αβ T cells and suppress the expansion of innate-like αβ T cells known as invariant natural killer T (iNKT) cells. However, it remains to be determined whether Id proteins differentially regulate these distinct lineage choices in early stages of T cell development. In this manuscript, we report that in Id-deficient mice, uninhibited activity of the E protein family member E2A mediates activation of genes that support iNKT cell development and function. There is also biased rearrangement in Id-deficient DP cells that promotes selection into the iNKT lineage in these mice. The observed expansion of iNKT cells is not abrogated by blocking pre-TCR signaling, which is required for conventional αβ T cell development. Finally, E2A is found to be a key transcriptional regulator of both iNKT and γδNKT lineages, which appear to have shared lineage history. Therefore, our study reveals a previously unappreciated role of E2A in coordinating the development of the iNKT lineage at an early stage, prior to their TCR-mediated selection alongside conventional αβ T cells.
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Affiliation(s)
- Sumedha Roy
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Amanda J Moore
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, United States
| | - Cassandra Love
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC, United States
| | - Anupama Reddy
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC, United States
| | - Deepthi Rajagopalan
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC, United States
| | - Sandeep S Dave
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC, United States
| | - Leping Li
- Biostatistics and Computational Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Durham, NC, United States
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, United States
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
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23
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Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C. Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. Cell 2017; 171:103-119.e18. [PMID: 28938112 DOI: 10.1016/j.cell.2017.09.001] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/24/2017] [Accepted: 08/30/2017] [Indexed: 01/01/2023]
Abstract
It is now established that Bcl11b specifies T cell fate. Here, we show that in developing T cells, the Bcl11b enhancer repositioned from the lamina to the nuclear interior. Our search for factors that relocalized the Bcl11b enhancer identified a non-coding RNA named ThymoD (thymocyte differentiation factor). ThymoD-deficient mice displayed a block at the onset of T cell development and developed lymphoid malignancies. We found that ThymoD transcription promoted demethylation at CTCF bound sites and activated cohesin-dependent looping to reposition the Bcl11b enhancer from the lamina to the nuclear interior and to juxtapose the Bcl11b enhancer and promoter into a single-loop domain. These large-scale changes in nuclear architecture were associated with the deposition of activating epigenetic marks across the loop domain, plausibly facilitating phase separation. These data indicate how, during developmental progression and tumor suppression, non-coding transcription orchestrates chromatin folding and compartmentalization to direct with high precision enhancer-promoter communication.
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Affiliation(s)
- Takeshi Isoda
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amanda J Moore
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoren He
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vivek Chandra
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Masatoshi Aida
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Denholtz
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jan Piet van Hamburg
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Institute for Genomic Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aaron N Chang
- Center for Computational Biology & Bioinformatics, Institute for Genomic Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shawn P Fahl
- Blood Cell Development and Function, Fox Chase Cancer Center, 333 Cottman Avenue, PA, Philadelphia, PA 19111, USA
| | - David L Wiest
- Blood Cell Development and Function, Fox Chase Cancer Center, 333 Cottman Avenue, PA, Philadelphia, PA 19111, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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Zhu Y, Gong K, Denholtz M, Chandra V, Kamps MP, Alber F, Murre C. Comprehensive characterization of neutrophil genome topology. Genes Dev 2017; 31:141-153. [PMID: 28167501 PMCID: PMC5322729 DOI: 10.1101/gad.293910.116] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 12/18/2022]
Abstract
Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil differentiation was not associated with large-scale changes in the number and sizes of topologically associating domains (TADs). However, neutrophil genomes were enriched for long-range genomic interactions that spanned multiple TADs. Population-based simulation of spherical and toroid genomes revealed declining radii of gyration for neutrophil chromosomes. We found that neutrophil genomes were highly enriched for heterochromatic genomic interactions across vast genomic distances, a process named supercontraction. Supercontraction involved genomic regions located in the heterochromatic compartment in both progenitors and neutrophils or genomic regions that switched from the euchromatic to the heterochromatic compartment during neutrophil differentiation. Supercontraction was accompanied by the repositioning of centromeres, pericentromeres, and long interspersed nuclear elements (LINEs) to the neutrophil nuclear lamina. We found that Lamin B receptor expression was required to attach centromeric and pericentromeric repeats but not LINE-1 elements to the lamina. Differentiating neutrophils also repositioned ribosomal DNA and mininucleoli to the lamina-a process that was closely associated with sharply reduced ribosomal RNA expression. We propose that large-scale chromatin reorganization involving supercontraction and recruitment of heterochromatin and nucleoli to the nuclear lamina facilitates the folding of the neutrophil genome into a confined geometry imposed by a multilobed nuclear architecture.
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Affiliation(s)
- Yina Zhu
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Ke Gong
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Matthew Denholtz
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Vivek Chandra
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Mark P Kamps
- Department of Pathology, University of California at San Diego, La Jolla, California 92093, USA
| | - Frank Alber
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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25
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Abstract
Targeting of AID to antibody variable (V) regions results in somatic hypermutation, whereas its recruitment to switch (S) regions leads to class-switch recombination. Yeap et al. find that the mechanism by which variable and switch regions recruit AID essentially is the same but that the two regions differ in the density of double-stranded DNA breaks that are generated. These lead to either point mutations in V exons in somatic hypermutation or deletion of intervening DNA sequences during class switch recombination.
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Affiliation(s)
- Cornelis Murre
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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26
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Rother MB, Palstra RJ, Jhunjhunwala S, van Kester KAM, van IJcken WFJ, Hendriks RW, van Dongen JJM, Murre C, van Zelm MC. Nuclear positioning rather than contraction controls ordered rearrangements of immunoglobulin loci. Nucleic Acids Res 2016; 44:175-86. [PMID: 26384565 PMCID: PMC4705691 DOI: 10.1093/nar/gkv928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/05/2015] [Accepted: 09/07/2015] [Indexed: 12/31/2022] Open
Abstract
Progenitor-B cells recombine their immunoglobulin (Ig) loci to create unique antigen receptors. Despite a common recombination machinery, the Ig heavy and Ig light chain loci rearrange in a stepwise manner. We studied pre-pro-B cells and Rag(-/-) progenitor-B cells to determine whether Ig locus contraction or nuclear positioning is decisive for stepwise rearrangements. We found that both Ig loci were contracted in pro-B and pre-B cells. Igh relocated from the nuclear lamina to central domains only at the pro-B cell stage, whereas, Igκ remained sequestered at the lamina, and only at the pre-B cell stage located to central nuclear domains. Finally, in vitro induced re-positioning of Ig alleles away from the nuclear periphery increased germline transcription of Ig loci in pre-pro-B cells. Thus, Ig locus contraction juxtaposes genomically distant elements to mediate efficient recombination, however, sequential positioning of Ig loci away from the nuclear periphery determines stage-specific accessibility of Ig loci.
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Affiliation(s)
- Magdalena B Rother
- Department of Immunology, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Suchit Jhunjhunwala
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Kevin A M van Kester
- Department of Immunology, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Cornelis Murre
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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Zhu Y, Murre C. Abstract A182: Zbtb7b is involved in the association of EBF1 enhancer to the nuclear lamina during early B cell commitment. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-a182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
It is well established that E2A proteins activate the expression of tumor suppressors, EBF1, PAX5 and FOXO1, to promote the B cell fate. E2A and EBF1 are frequently mutated either by chromosomal translocations, point mutations or gene deletions in B-cell precursor acute lymphoblastic leukemia. However, it remains an enigma why EBF1 is not transcribed in multipotent progenitors, in which E2A is expressed at high levels. It has been shown that, by HiC and 3D-fluorescence in situ hybridization (3D-FISH), in multipotent progenitors the EBF1 locus was located at the nuclear lamina, in pro-B cells the EBF1 locus was located away from the lamina. In this study, using gain-of-function approaches, we show that enforced Zbtb7b expression inhibited B cell differentiation and caused rapid loss of EBF1 and Pax5 mRNA. Notably, Using 3D-FISH, we found enforced expression of Zbtb7b sequestered EBF1 locus to the nuclear lamina, and using live cell imaging, we show that, Zbtb7b primarily localized at nuclear lamina. We are now investigating whether and how the nuclear envelope and its interaction with the genome change during early B cell commitment using Damseq; and anti-Zbtb7b ChIP-seq provide fine mapping of potential interaction regions with nuclear lamina. These data indicate a novel role of Zbtb7b in B cell lineage commitment and potentially link EBF1 and Zbtb7b into a common pathway. Experiments are ongoing to further examine how sequestration of genes to the nuclear lamina relates to the development of lymphoid cells.
Citation Format: Yina Zhu, Cornelis Murre. Zbtb7b is involved in the association of EBF1 enhancer to the nuclear lamina during early B cell commitment. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A182.
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Affiliation(s)
- Yina Zhu
- University of California, San Diego, CA
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28
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Bortnick A, Murre C. Cellular and chromatin dynamics of antibody-secreting plasma cells. Wiley Interdiscip Rev Dev Biol 2015; 5:136-49. [PMID: 26488117 DOI: 10.1002/wdev.213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/10/2015] [Accepted: 08/15/2015] [Indexed: 12/12/2022]
Abstract
Plasma cells are terminally differentiated B cells responsible for maintaining protective serum antibody titers. Despite their clinical importance, our understanding of the linear genomic features and chromatin structure of plasma cells is incomplete. The plasma cell differentiation program can be triggered by different signals and in multiple, diverse peripheral B cell subsets. This heterogeneity raises questions about the gene regulatory circuits required for plasma cell specification. Recently, new regulators of plasma cell differentiation have been identified and the enhancer landscapes of naïve B cells have been described. Other studies have revealed that the bone marrow niche harbors heterogeneous plasma cell subsets. Still undefined are the minimal requirements to become a plasma cell and what molecular features make peripheral B cell subsets competent to become antibody-secreting plasma cells. New technologies promise to reveal underlying chromatin configurations that promote efficient antibody secretion. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alexandra Bortnick
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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29
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Abstract
Activation-induced cytidine deaminase (AID) mediates cytosine deamination and underlies two central processes in antibody diversification: somatic hypermutation and class-switch recombination. AID deamination is not exclusive to immunoglobulin loci; it can instigate DNA lesions in non-immunoglobulin genes and thus stringent checks are in place to constrain and restrict its activity. Recent findings have provided new insights into the mechanisms that target AID activity to specific genomic regions, revealing an involvement for noncoding RNAs associated with polymerase pausing and with enhancer transcription as well as genomic architecture. We review these findings and integrate them into a model for multilevel regulation of AID expression and targeting in immunoglobulin and non-immunoglobulin loci. Within this framework we discuss gaps in understanding, and outline important areas of further research.
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Affiliation(s)
- Vivek Chandra
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA
| | - Alexandra Bortnick
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA
| | - Cornelis Murre
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA.
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30
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Miyazaki M, Miyazaki K, Chen S, Chandra V, Wagatsuma K, Agata Y, Rodewald HR, Saito R, Chang AN, Varki N, Kawamoto H, Murre C. 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. Genes Dev 2015; 29:409-25. [PMID: 25691468 PMCID: PMC4335296 DOI: 10.1101/gad.255331.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Miyazaki et al. show that Id2 and Id3 suppress the development and expansion of innate variant TFH cells by acting upstream of the Hif1a/Foxo/AKT/mTORC1 pathway as well as the c-myc/p19Arf module. Mice depleted for Id2 and Id3 expression developed colitis and αβ T-cell lymphomas, and the transcription signatures of Id2- and Id3-depleted lymphomas revealed similarities to genetic deficiencies associated with Burkitt lymphoma. It is now well established that the E and Id protein axis regulates multiple steps in lymphocyte development. However, it remains unknown how E and Id proteins mechanistically enforce and maintain the naïve T-cell fate. Here we show that Id2 and Id3 suppressed the development and expansion of innate variant follicular helper T (TFH) cells. Innate variant TFH cells required major histocompatibility complex (MHC) class I-like signaling and were associated with germinal center B cells. We found that Id2 and Id3 induced Foxo1 and Foxp1 expression to antagonize the activation of a TFH transcription signature. We show that Id2 and Id3 acted upstream of the Hif1a/Foxo/AKT/mTORC1 pathway as well as the c-myc/p19Arf module to control cellular expansion. We found that mice depleted for Id2 and Id3 expression developed colitis and αβ T-cell lymphomas. Lymphomas depleted for Id2 and Id3 expression displayed elevated levels of c-myc, whereas p19Arf abundance declined. Transcription signatures of Id2- and Id3-depleted lymphomas revealed similarities to genetic deficiencies associated with Burkitt lymphoma. We propose that, in response to antigen receptor and/or cytokine signaling, the E–Id protein axis modulates the activities of the PI3K–AKT–mTORC1–Hif1a and c-myc/p19Arf pathways to control cellular expansion and homeostatic proliferation.
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Affiliation(s)
- Masaki Miyazaki
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Kazuko Miyazaki
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Shuwen Chen
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Vivek Chandra
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Keisuke Wagatsuma
- Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan
| | - Yasutoshi Agata
- Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Rintaro Saito
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Aaron N Chang
- Center for Computational Biology, Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Nissi Varki
- Department of Pathology, University of California at San Diego, La Jolla, California 92093, USA
| | - Hiroshi Kawamoto
- Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Cornelis Murre
- Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA;
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32
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Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, Liang G, Tang Z, Mathé E, Benner C, Dubois W, Nelson S, Vian L, Oliveira TY, 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 DF, Pan-Hammarström Q, Nussenzweig MC, Casellas R. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell 2014; 159:1524-37. [PMID: 25483777 DOI: 10.1016/j.cell.2014.11.013] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/26/2014] [Accepted: 10/30/2014] [Indexed: 02/07/2023]
Abstract
The antibody gene mutator activation-induced cytidine deaminase (AID) promiscuously damages oncogenes, leading to chromosomal translocations and tumorigenesis. Why nonimmunoglobulin loci are susceptible to AID activity is unknown. Here, we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome but are predominantly grouped within super-enhancers and regulatory clusters. Unexpectedly, in these domains, AID deaminates active promoters and eRNA(+) enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing, we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment.
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Affiliation(s)
- Jason Qian
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marei Dose
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA.
| | | | | | - Wolfgang Resch
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Genqing Liang
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Zhonghui Tang
- Department of Genetic and Development Biology, Jackson Laboratory for Genomic Medicine, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Ewy Mathé
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Christopher Benner
- The Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wendy Dubois
- Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Laura Vian
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Ofir Hakim
- Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Rushad Pavri
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Doktor Bohr Gasse 7, Vienna 1030, Austria
| | - Parirokh Awasthi
- Science Applications International Corporation/Frederick, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
| | - Bin Song
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Geng Liu
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Longyun Chen
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Shida Zhu
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Lionel Feigenbaum
- Science Applications International Corporation/Frederick, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
| | - Louis Staudt
- Metabolism Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yijun Ruan
- Department of Genetic and Development Biology, Jackson Laboratory for Genomic Medicine, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Pan-Hammarström
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, 14186 Stockholm, Sweden
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; HHMI, The Rockefeller University, New York, NY 10065, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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Miyazaki M, Miyazaki K, Chen S, Itoi M, Miller M, Lu LF, Varki N, Chang AN, Broide DH, Murre C. Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease. Nat Immunol 2014; 15:767-76. [PMID: 24973820 PMCID: PMC4365819 DOI: 10.1038/ni.2928] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 05/22/2014] [Indexed: 12/15/2022]
Abstract
Regulatory T (Treg) cells suppress the development of inflammatory disease, but our knowledge of transcriptional regulators that control this function remains incomplete. Here we show that expression of Id2 and Id3 in Treg cells was required to suppress development of fatal inflammatory disease. We found that T cell antigen receptor (TCR)-driven signaling initially decreased the abundance of Id3, which led to the activation of a follicular regulatory T (TFR) cell-specific transcription signature. However, sustained lower abundance of Id2 and Id3 interfered with proper development of TFR cells. Depletion of Id2 and Id3 expression in Treg cells resulted in compromised maintenance and localization of the Treg cell population. Thus, Id2 and Id3 enforce TFR cell checkpoints and control the maintenance and homing of Treg cells.
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Affiliation(s)
- Masaki Miyazaki
- 1] Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA. [2]
| | - Kazuko Miyazaki
- 1] Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA. [2]
| | - Shuwen Chen
- 1] Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA. [2]
| | - Manami Itoi
- Department of Immunology and Microbiology, Meiji University of Integrative Medicine, Hiyoshi-cho, Kyoto, Japan
| | - Marina Miller
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Li-Fan Lu
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA
| | - Nissi Varki
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Aaron N Chang
- Center for Computational Biology, Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - David H Broide
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA
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34
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Lucas JS, Zhang Y, Dudko OK, Murre C. 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Cell 2014; 158:339-352. [PMID: 24998931 DOI: 10.1016/j.cell.2014.05.036] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/19/2014] [Accepted: 05/01/2014] [Indexed: 12/01/2022]
Abstract
During B lymphocyte development, immunoglobulin heavy-chain variable (VH), diversity (DH), and joining (JH) segments assemble to generate a diverse antigen receptor repertoire. Here, we have marked the distal VH and DH-JH-Eμ regions with Tet-operator binding sites and traced their 3D trajectories in pro-B cells transduced with a retrovirus encoding Tet-repressor-EGFP. We found that these elements displayed fractional Langevin motion (fLm) due to the viscoelastic hindrance from the surrounding network of proteins and chromatin fibers. Using fractional Langevin dynamics modeling, we found that, with high probability, DHJH elements reach a VH element within minutes. Spatial confinement emerged as the dominant parameter that determined the frequency of such encounters. We propose that the viscoelastic nature of the nuclear environment causes coding elements and regulatory elements to bounce back and forth in a spring-like fashion until specific genomic interactions are established and that spatial confinement of topological domains largely controls first-passage times for genomic interactions.
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Affiliation(s)
- Joseph S Lucas
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yaojun Zhang
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olga K Dudko
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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35
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Abstract
In B cell progenitors, E-proteins E2A and HEB (HeLa E-box binding protein) are crucial for the induction of a B lineage-specific program of gene expression and for orchestrating the assembly of the immunoglobulin loci. In the thymus E2A and HEB act differently, activating the expression of genes closely associated with the establishment of T cell identity and promoting the rearrangement of T cell receptor (TCR) loci. These findings have raised the question as to how E-proteins exert these different activities. We review here the distinct regulatory networks that establish B versus T cell identity, and how genomic architecture and location of genes is modulated in these lineage decisions. We conclude by proposing a model wherein stochasticity in the nuclear location of the early B cell factor 1 (Ebf1) locus in multipotent progenitors determines this lineage choice.
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Affiliation(s)
- Kazuko Miyazaki
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Masaki Miyazaki
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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36
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Bortnick A, Murre C. A HESitant decision for T cells. Nat Immunol 2013; 14:1209-10. [PMID: 24240153 DOI: 10.1038/ni.2765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alexandra Bortnick
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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37
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Murre C. The epigenetics of early lymphocyte development. Cold Spring Harb Symp Quant Biol 2013; 78:43-49. [PMID: 24092471 DOI: 10.1101/sqb.2013.78.020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The mammalian genome is highly structured, both spatially and functionally. Chromosomes are organized into specific territories, which are further folded into euchromatic or heterochromatic compartments. The euchromatic compartment often contains domains decorated with activating epigenetic marks, whereas heterochromatic regions lack activating marks or bear repressive ones. During lymphocyte development, gene segments move between these compartments. Additionally, some genes undergoing changes in transcriptional activity also display elaborate alterations in chromatin folding. Lineage-specific transcription factors help mediate these reconfigurations. Herein, I describe how genetic loci encoding for key regulators switch nuclear neighborhoods and reorganize their 3D structures to drive cell fate.
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Affiliation(s)
- C Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093
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38
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Abstract
How lymphoid cell fate is orchestrated in early hematopoietic progenitors remains poorly understood. In this issue of Immunity, Satoh et al. (2013) show that the chromatin remodeler Satb1 promotes lymphocyte differentiation in both young and aged stem cells.
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Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA.
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39
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Miyazaki M, Rivera RR, Miyazaki K, Lin YC, Agata Y, Murre C. Erratum: Corrigendum: The opposing roles of the transcription factor E2A and its antagonist Id3 that orchestrate and enforce the naive fate of T cells. Nat Immunol 2013. [DOI: 10.1038/ni0413-413e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Kreslavsky T, Gleimer M, Miyazaki M, Choi Y, Gagnon E, Murre C, Sicinski P, von Boehmer H. β-Selection-induced proliferation is required for αβ T cell differentiation. Immunity 2013; 37:840-53. [PMID: 23159226 DOI: 10.1016/j.immuni.2012.08.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 08/02/2012] [Indexed: 10/27/2022]
Abstract
Proliferation and differentiation are tightly coordinated to produce an appropriate number of differentiated cells and often exhibit an antagonistic relationship. Developing T cells, which arise in the thymus from a minute number of bone-marrow-derived progenitors, undergo a major expansion upon pre-T cell receptor (TCR) expression. The burst of proliferation coincides with differentiation toward the αβ T cell lineage-but the two processes were previously thought to be independent from one another, although both were driven by signaling from pre-TCR and Notch receptors. Here we report that proliferation at this step was not only absolutely required for differentiation but also that its ectopic activation was sufficient to substantially rescue differentiation in the absence of Notch signaling. Consistently, pharmacological inhibition of the cell cycle machinery also blocked differentiation in vivo. Thus the proliferation step is strictly required prior to differentiation of immature thymocytes.
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Affiliation(s)
- Taras Kreslavsky
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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41
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Lin YC, Murre C. Nuclear location and the control of developmental progression. Curr Opin Genet Dev 2012; 23:104-8. [PMID: 23266214 DOI: 10.1016/j.gde.2012.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/09/2012] [Accepted: 11/19/2012] [Indexed: 11/30/2022]
Abstract
It is now well established that the mammalian genome is highly organized. Chromosomes are structured as territories that only sporadically intermingle. Chromosome territories themselves are segregated into distinct environments, that is, the transcriptionally inert/repressive (heterochromatic) and permissive (euchromatic) compartments. The transcriptionally permissive compartment is organized into domains (∼0.5-3 Mb) that consist of bundles of loops, are gene-rich and closely associated by activating epigenetic marks. During ontogeny and developmental progression chromatin states are highly dynamic. Recent studies have shown that loci and domains readily switch compartments. Switching nuclear neighborhoods is closely associated with changes in transcriptional activity and extensive chromatin reorganization. Here we discuss the implications of a dynamic genome and how it relates to the control of developmental progression.
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Affiliation(s)
- Yin C Lin
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, United States
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42
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Sakamoto S, Wakae K, Anzai Y, Murai K, Tamaki N, Miyazaki M, Miyazaki K, Romanow WJ, Ikawa T, Kitamura D, Yanagihara I, Minato N, Murre C, Agata Y. E2A and CBP/p300 Act in Synergy To Promote Chromatin Accessibility of the Immunoglobulin κ Locus. J I 2012; 188:5547-60. [DOI: 10.4049/jimmunol.1002346] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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43
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Abstract
During an organism's ontogeny and in the adult, each B and T lymphocyte generates a unique antigen receptor, thereby creating the organism's ability to respond to a vast number of different antigens. The antigen receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions. In this review, we discuss the epigenetic modifications that take place in the different antigen receptor loci, the chromatin structure adopted by the antigen receptor loci to allow recombination of elements separated by large genomic distances, and the relationship between epigenetics and chromatin structure and how they relate to the generation of antigen receptor diversity.
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Affiliation(s)
- Claudia Bossen
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093-0377, USA
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44
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Yang CY, Best JA, Knell J, Yang E, Sheridan AD, Jesionek AK, Li HS, Rivera RR, Lind KC, D'Cruz LM, Watowich SS, Murre C, Goldrath AW. The transcriptional regulators Id2 and Id3 control the formation of distinct memory CD8+ T cell subsets. Nat Immunol 2011; 12:1221-9. [PMID: 22057289 PMCID: PMC3872000 DOI: 10.1038/ni.2158] [Citation(s) in RCA: 293] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/06/2011] [Indexed: 12/14/2022]
Abstract
During infection, naive CD8(+) T cells differentiate into effector cells, which are armed to eliminate pathogens, and memory cells, which are poised to protect against reinfection. The transcriptional program that regulates terminal differentiation into short-lived effector-memory versus long-lived memory cells is not clearly defined. Through the use of mice expressing reporters for the DNA-binding inhibitors Id2 and Id3, we identified Id3(hi) precursors of long-lived memory cells before the peak of T cell population expansion or upregulation of cell-surface receptors that indicate memory potential. Deficiency in Id2 or Id3 resulted in loss of distinct CD8(+) effector and memory populations, which demonstrated unique roles for these inhibitors of E-protein transcription factors. Furthermore, cytokines altered the expression of Id2 and Id3 differently, which provides insight into how external cues influence gene expression.
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Affiliation(s)
- Cliff Y Yang
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
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45
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Abstract
Multiple trajectories have recently been described through which hematopoietic progenitor cells travel prior to becoming lineage-committed effectors. A wide spectrum of transcription factors has recently been identified that modulate developmental progression along such trajectories. Here we describe how distinct families of transcription factors act and are linked together to orchestrate early hematopoiesis.
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Affiliation(s)
- Elinore M Mercer
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, United States.
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46
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Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity 2011; 35:413-25. [PMID: 21903424 DOI: 10.1016/j.immuni.2011.06.013] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 05/25/2011] [Accepted: 06/22/2011] [Indexed: 11/16/2022]
Abstract
Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the expression of the E-protein antagonist Id2. Hematopoietic progenitors that express Id2 are multipotent and readily differentiate upon withdrawal of Id2 expression into committed B lineage cells, thus indicating a causative role for E2A (Tcf3) in promoting the B cell fate. Genome-wide analyses revealed that a substantial fraction of lymphoid and myeloid enhancers are premarked by the poised or active enhancer mark H3K4me1 in multipotent progenitors. Thus, in hematopoietic progenitors, multilineage priming of enhancer elements precedes commitment to the lymphoid or myeloid cell lineages.
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Affiliation(s)
- Elinore M Mercer
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
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47
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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. CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells. Proc Natl Acad Sci U S A 2011; 108:9566-71. [PMID: 21606361 PMCID: PMC3111298 DOI: 10.1073/pnas.1019391108] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Compaction and looping of the ~2.5-Mb Igh locus during V(D)J rearrangement is essential to allow all V(H) genes to be brought in proximity with D(H)-J(H) segments to create a diverse antibody repertoire, but the proteins directly responsible for this are unknown. Because CCCTC-binding factor (CTCF) has been demonstrated to be involved in long-range chromosomal interactions, we hypothesized that CTCF may promote the contraction of the Igh locus. ChIP sequencing was performed on pro-B cells, revealing colocalization of CTCF and Rad21 binding at ~60 sites throughout the V(H) region and 2 other sites within the Igh locus. These numerous CTCF/cohesin sites potentially form the bases of the multiloop rosette structures at the Igh locus that compact during Ig heavy chain rearrangement. To test whether CTCF was involved in locus compaction, we used 3D-FISH to measure compaction in pro-B cells transduced with CTCF shRNA retroviruses. Reduction of CTCF binding resulted in a decrease in Igh locus compaction. Long-range interactions within the Igh locus were measured with the chromosomal conformation capture assay, revealing direct interactions between CTCF sites 5' of DFL16 and the 3' regulatory region, and also the intronic enhancer (Eμ), creating a D(H)-J(H)-Eμ-C(H) domain. Knockdown of CTCF also resulted in the increase of antisense transcription throughout the D(H) region and parts of the V(H) locus, suggesting a widespread regulatory role for CTCF. Together, our findings demonstrate that CTCF plays an important role in the 3D structure of the Igh locus and in the regulation of antisense germline transcription and that it contributes to the compaction of the Igh locus.
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MESH Headings
- Animals
- Binding Sites/genetics
- Blotting, Western
- CCCTC-Binding Factor
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line
- Cells, Cultured
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA, Antisense/genetics
- DNA-Binding Proteins
- Enhancer Elements, Genetic/genetics
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Precursor Cells, B-Lymphoid/metabolism
- Protein Binding
- RNA Interference
- RNA, Antisense/genetics
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription, Genetic
- Cohesins
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Affiliation(s)
- Stephanie C. Degner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Jiyoti Verma-Gaur
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Timothy P. Wong
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Claudia Bossen
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | | | - Ali Torkamani
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037
| | - Christian Vettermann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
| | - Yin C. Lin
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Zhongliang Ju
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Danae Schulz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
| | - Caroline S. Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Barbara K. Birshtein
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Nicholas J. Schork
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037
| | - Mark S. Schlissel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
| | - Roy Riblet
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121
| | - Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Ann J. Feeney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
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48
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Murre C. Global approaches to identify novel participants that modulate intestinal epithelial cell development. Dev Cell 2010; 19:647-8. [PMID: 21074714 DOI: 10.1016/j.devcel.2010.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Combinatorial control of lineage-specific gene expression is commonly mediated by suites of diverse transcriptional regulators. In this issue of Developmental Cell, Verzi et al. (2010) use an unbiased global and computational approach to identify distinct partners and functions of CDX2 in intestinal epithelial cell differentiation.
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Affiliation(s)
- Cornelis Murre
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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49
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Lucas JS, Bossen C, Murre C. Transcription and recombination factories: common features? Curr Opin Cell Biol 2010; 23:318-24. [PMID: 21169003 DOI: 10.1016/j.ceb.2010.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 11/24/2010] [Accepted: 11/29/2010] [Indexed: 12/20/2022]
Abstract
There is now substantial evidence that the eukaryotic nucleus consists of highly organized structures. Among such structures are transcription factories that consist of an ensemble of genes recruited by the RNA polymerase machinery. Here we suggest that antigen receptor variable regions are similarly organized. Specifically, we propose that the immunoglobulin heavy chain locus variable gene segments are anchored to the base of rosettes, wrapping around a cavity that contains the recombination machinery. We suggest that the folding of the chromatin fiber into rosettes underpins a crucial mechanism by which antigen receptor diversity is generated.
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Affiliation(s)
- Joseph S Lucas
- Division of Biological Sciences, 0377 Department of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
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50
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Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010; 38:576-89. [PMID: 20513432 PMCID: PMC2898526 DOI: 10.1016/j.molcel.2010.05.004] [Citation(s) in RCA: 7944] [Impact Index Per Article: 567.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 04/02/2010] [Accepted: 05/03/2010] [Indexed: 02/06/2023]
Abstract
Genome-scale studies have revealed extensive, cell type-specific colocalization of transcription factors, but the mechanisms underlying this phenomenon remain poorly understood. Here, we demonstrate in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions. PU.1 binding initiates nucleosome remodeling, followed by H3K4 monomethylation at large numbers of genomic regions associated with both broadly and specifically expressed genes. These locations serve as beacons for additional factors, exemplified by liver X receptors, which drive both cell-specific gene expression and signal-dependent responses. Together with analyses of transcription factor binding and H3K4me1 patterns in other cell types, these studies suggest that simple combinations of lineage-determining transcription factors can specify the genomic sites ultimately responsible for both cell identity and cell type-specific responses to diverse signaling inputs.
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Affiliation(s)
- Sven Heinz
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Christopher Benner
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Nathanael Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Eric Bertolino
- Molecular Genetics and Cell Biology, The University of Chicago, 929 E. 57th St. GCIS W522, Chicago IL 60637
| | - Yin C. Lin
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Peter Laslo
- Section of Experimental Haematology, University of Leeds, Leeds, UK LS9 7TF
| | - Jason X. Cheng
- Molecular Genetics and Cell Biology, The University of Chicago, 929 E. 57th St. GCIS W522, Chicago IL 60637
| | - Cornelis Murre
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- To whom correspondence should be addressed: Office: 858-534-6011,
| | - Harinder Singh
- Molecular Genetics and Cell Biology, The University of Chicago, 929 E. 57th St. GCIS W522, Chicago IL 60637
- Department of Discovery Immunology, Genentech, San Francisco, California 94080
- To whom correspondence should be addressed: Office: 858-534-6011,
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- To whom correspondence should be addressed: Office: 858-534-6011,
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