scholarly journals The Distal VH Gene Cluster of the Igh Locus Contains Distinct Regulatory Elements with Pax5 Transcription Factor-Dependent Activity in Pro-B Cells

Immunity ◽  
2011 ◽  
Vol 34 (2) ◽  
pp. 175-187 ◽  
Author(s):  
Anja Ebert ◽  
Shane McManus ◽  
Hiromi Tagoh ◽  
Jasna Medvedovic ◽  
Giorgia Salvagiotto ◽  
...  
Keyword(s):  
Transcription Factor ◽  
B Cells ◽  
Gene Cluster ◽  
Regulatory Elements ◽  
Igh Locus ◽  
Dependent Activity ◽  
Vh Gene

scholarly journals Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary and enhancer elements in B cells

2020 ◽  
Author(s):  
Jessica Cheng ◽  
Joshua S. Clayton ◽  
Rafael D. Acemel ◽  
José L. Gómez-Skarmeta ◽  
Rhonda L. Taylor ◽  
...  
Keyword(s):  
B Cells ◽  
Gene Cluster ◽  
Genetic Disease ◽  
Regulatory Elements ◽  
Innate Immune ◽  
Altered Expression ◽  
Regulatory Architecture ◽  
Gene Enhancer ◽  
Regulators Of Complement Activation ◽  
Genetic Level

ABSTRACTThe Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes which share functions in the innate immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanism underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topological associated domains (TADs). Interestingly, the inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells. We have uncovered novel, long-range mechanisms whereby SLE susceptibility may be influenced by genetic variants, highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.

The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells

2020 ◽  
Vol 5 (51) ◽  
pp. eabb1455 ◽  
Author(s):  
Kazuko Miyazaki ◽  
Hitomi Watanabe ◽  
Genki Yoshikawa ◽  
Kenian Chen ◽  
Reiko Hidaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
T Cell ◽  
B Cells ◽  
Cell Lineage ◽  
Cell Receptor ◽  
Regulatory Elements ◽  
Mouse Strains ◽  
Specific Gene ◽  
T And B Cells

Cell type–specific gene expression is driven by the interplay between lineage-specific transcription factors and cis-regulatory elements to which they bind. Adaptive immunity relies on RAG-mediated assembly of T cell receptor (TCR) and immunoglobulin (Ig) genes. Although Rag1 and Rag2 expression is largely restricted to adaptive lymphoid lineage cells, it remains unclear how Rag gene expression is regulated in a cell lineage–specific manner. Here, we identified three distinct cis-regulatory elements, a T cell lineage–specific enhancer (R-TEn) and the two B cell–specific elements, R1B and R2B. By generating mice lacking either R-TEn or R1B and R2B, we demonstrate that these distinct sets of regulatory elements drive the expression of Rag genes in developing T and B cells. What these elements have in common is their ability to bind the transcription factor E2A. By generating a mouse strain that carries a mutation within the E2A binding site of R-TEn, we demonstrate that recruitment of E2A to this site is essential for orchestrating changes in chromatin conformation that drive expression of Rag genes in T cells. By mapping cis-regulatory elements and generating multiple mouse strains lacking distinct enhancer elements, we demonstrate expression of Rag genes in developing T and B cells to be driven by distinct sets of E2A-dependent cis-regulatory modules.

scholarly journals Chromosomal position of a VH gene segment determines its activation and inactivation as a substrate for V(D)J recombination

2007 ◽  
Vol 204 (13) ◽  
pp. 3247-3256 ◽  
Author(s):  
Jamie Geier Bates ◽  
Dragana Cado ◽  
Hector Nolla ◽  
Mark S. Schlissel
Keyword(s):  
B Cells ◽  
Gene Cluster ◽  
Gene Targeting ◽  
Dna Sequences ◽  
Gene Rearrangement ◽  
Gene Segment ◽  
Allelic Exclusion ◽  
Chromosomal Position ◽  
Lineage Specificity ◽  
Vh Gene

Complete IgHC gene rearrangement occurs only in B cells in a stage-specific and ordered manner. We used gene targeting to reposition a distal VH gene segment to a region just 5′ of the DH gene cluster and found its activation to be highly dependent on the chromosomal domain within which it resides. The targeted VH gene segment rearranged at a higher frequency than its endogenous counterpart, its rearrangement was no longer ordered, and its ability to be silenced by allelic exclusion was lost. Additionally, the targeted VH gene segment lost lineage specificity, as VDJH rearrangement was observed in thymocytes. These data suggest that locus contraction, mimicked by proximal targeting, can override any regulation imposed by DNA sequences immediately surrounding VH gene segments.

scholarly journals VH gene family utilization is regulated by a locus outside of the VH region.

1988 ◽  
Vol 167 (4) ◽  
pp. 1499-1504 ◽  
Author(s):  
G E Wu ◽  
C J Paige
Keyword(s):  
B Cells ◽  
Gene Family ◽  
Recombinant Inbred ◽  
Inbred Strains ◽  
Maternal Influence ◽  
Recombinant Inbred Strains ◽  
Genetic Element ◽  
Cloning Efficiency ◽  
Igh Locus ◽  
Vh Gene

We have used the RNA colony blot method to examine VH usage in colonies derived from primary splenic B cells. We found that there are strain-specific differences in the pattern of VH usage. Using parental F1, congenic, and recombinant inbred strains we demonstrate that the genetic element that causes the observed phenotype is: (a) stably expressed; (b) not due to maternal influence; (c) not due to dominate diffusible factors; (d) not linked to cloning efficiency; and (e) outside the Igh locus.

scholarly journals The E26 Transformation-Specific-family transcription factor Spi-C is dynamically regulated by external signals in B cells

2021 ◽  
Author(s):  
Hannah L. Raczkowski ◽  
Li S. Xu ◽  
Wei Cen Wang ◽  
Rodney P DeKoter
Keyword(s):  
Transcription Factor ◽  
B Cells ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
B Cell Development ◽  
Heme Binding ◽  
Qpcr Analysis ◽  
External Signals ◽  
Insight Into ◽  
Red Pulp

Spi-C is an E26 transformation-specific transcription factor closely related to PU.1 and Spi-B. Spi-C has lineage-instructive functions important in antibody-generating responses, B cell development, and red pulp macrophage generation. Spi-C is inducible by heme- and NF-κB-dependent pathways in macrophages. The present research aimed to examine the regulation of Spi-C expression in B cells. RT-qPCR analysis revealed that Spic expression was reduced in B cells following addition of lipopolysaccharide, anti-IgM antibodies, CD40L, or cytokines BAFF + IL-4 + IL-5. Cytochalasin treatment partially prevented downregulation of Spic. Unstimulated B cells upregulated Spic over time in culture. To determine the mechanism of Spic regulation, we examined the Spic promoter and upstream regulatory elements. The Spic promoter had unidirectional activity, which was reduced by mutation of an NF-κB binding site. Spic was repressed by an upstream regulatory region interacting with the heme-binding regulator Bach2. Taken together, these data indicate that Spi-C is dynamically regulated by external signals in B cells and provide insight into the mechanism of regulation.

Ectopic Fibroblast Growth Factor Receptor 3 (FGFR3) Expression Mediated by Isotype Switch Recombination.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 78-78 ◽  
Author(s):  
Maurizio Affer ◽  
Davide Robbiani ◽  
Marta Chesi ◽  
Peter L. Bergsagel
Keyword(s):  
Multiple Myeloma ◽  
B Cells ◽  
Transgenic Mice ◽  
Tumor Progression ◽  
Plasma Cells ◽  
Growth Parameters ◽  
Ectopic Expression ◽  
Regulatory Elements ◽  
Igh Locus

Abstract FGFR3 is disregulated in approximately 15% of cases of multiple myeloma (MM) occurring by chromosomal translocation in the Igh switch region which results in the juxtaposition of FGFR3 next to the regulatory elements of the IgH locus, causing its ectopic expression in plasma cells. The acquisition of FGFR3 activating mutations in some tumors indicate a role for FGFR3 in tumor progression. In order to study its role in MM progression we developed a strain of transgenic mice in which the expression of the activated form of FGFR3 is mediated by isotype switch recombination by replacing the IgH gamma1 costant region with an FGFR3-IRES-EGFP cassette in a BAC that covers the entire murine IgH locus. We predict that in the transgenic mice B cells that undergo switch recombination to g1 on the productive allele will also undergo switch recombination to g1 at the transgenic locus and express FGFR3 and EGFP. To evaluate FGFR3 expression in vitro, we collected splenocytes from our transgenic mice and induced their proliferation and differentiation to plasma cells (mainly IgG1) using LPS and IL4. After four days of stimulation, the average number of EGFP positive cells went from 0.2% to 80%. We then analyzed FGFR3 expression by RT PCR, Northern and Western blot and detected LPS/IL4 inducible FGFR3 expression in plasma cells mediated mainly by the Igamma1 promoter and in a subset of them by the Vh promoter. We then tested if forced FGFR3 expression in B cells would affect their proliferation rate and ability to differentiate in vitro by MTT assay, cell cycle analysis and PI staining on LPS/IL4 stimulated splenocytes at different time points. With this system, we did not observe any FGFR3 mediated alteration of splenocytes growth parameters when compared to wild type controls. Similarly, in vivo no monoclonal gammopathy has been observed by serum protein electrophoresis and all the transgenic mice remaine tumor free at 1.5 years. Although we have not been able to demonstrate a tumorigenic role for FGFR3 in switched plasmacells we were able to obtaine regulated FGFR3 expression in them. It is possible that FGFR3 expression alone is not sufficient to induce plasma cells transformation and that FGFR3 has a dispensable role in tumor initiation, but that it could still play a role in tumor progression. Consistently, FGFR3 expression is lost in about 25% of multiple myeloma wih a t(4;14). To address this hypotesis we are currently crossing these mice with MMSET (the other gene disregulated in the t(4;14)) transgenic mice to investigate a possible collaborative role between these two genes in the development of MM.

scholarly journals Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hong Wang ◽  
Aiping Duan ◽  
Jing Zhang ◽  
Qi Wang ◽  
Yuexian Xing ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Glucocorticoid Receptor ◽  
Protective Effect ◽  
Histone Modification ◽  
Regulatory Networks ◽  
Target Gene ◽  
Regulatory Elements ◽  
Chromatin Interactions ◽  
Super Enhancer

AbstractElucidating transcription mediated by the glucocorticoid receptor (GR) is crucial for understanding the role of glucocorticoids (GCs) in the treatment of diseases. Podocyte is a useful model for studying GR regulation because GCs are the primary medication for podocytopathy. In this study, we integrated data from transcriptome, transcription factor binding, histone modification, and genome topology. Our data reveals that the GR binds and activates selective regulatory elements in podocyte. The 3D interactome captured by HiChIP facilitates the identification of remote targets of GR. We found that GR in podocyte is enriched at transcriptional interaction hubs and super-enhancers. We further demonstrate that the target gene of the top GR-associated super-enhancer is indispensable to the effective functioning of GC in podocyte. Our findings provided insights into the mechanisms underlying the protective effect of GCs on podocyte, and demonstrate the importance of considering transcriptional interactions in order to fine-map regulatory networks of GR.

scholarly journals Different Mechanisms Participate in the R-dependent Activity of the R2R3 MYB Transcription Factor C1

2004 ◽  
Vol 279 (46) ◽  
pp. 48205-48213 ◽  
Author(s):  
J. Marcela Hernandez ◽  
George F. Heine ◽  
Niloufer G. Irani ◽  
Antje Feller ◽  
Min-Gab Kim ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Myb Transcription Factor ◽  
Dependent Activity ◽  
R2r3 Myb

scholarly journals High-resolution analysis of cis -acting regulatory networks at the α-globin locus

2013 ◽  
Vol 368 (1620) ◽  
pp. 20120361 ◽  
Author(s):  
Jim R. Hughes ◽  
Karen M. Lower ◽  
Ian Dunham ◽  
Stephen Taylor ◽  
Marco De Gobbi ◽  
...  
Keyword(s):  
High Resolution ◽  
Gene Cluster ◽  
Regulatory Networks ◽  
Single Gene ◽  
Regulatory Elements ◽  
Circular Chromosome ◽  
Chromosome Conformation ◽  
Cis Acting ◽  
High Resolution Analysis ◽  
Resolution Analysis

We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis -acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10–1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis -regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the α-globin cluster.

scholarly journals Promoter-Proximal Regulatory Elements Involved in oriP-EBNA1-Independent and -Dependent Activation of the Epstein-Barr Virus C Promoter in B-Lymphoid Cell Lines

2001 ◽  
Vol 75 (13) ◽  
pp. 5796-5811 ◽  
Author(s):  
Tina Nilsson ◽  
Henrik Zetterberg ◽  
Yuyan Camilla Wang ◽  
Lars Rymo
Keyword(s):  
Transcription Factor ◽  
Epstein Barr Virus ◽  
Regulatory Elements ◽  
Negative Regulator ◽  
Regulatory Sequences ◽  
Barr Virus ◽  
Group I ◽  
Epstein Barr ◽  
B Lymphoid ◽  
Virus C

ABSTRACT The identification of the cellular factors that control the transcription regulatory activity of the Epstein-Barr virus C promoter (Cp) is fundamental to the understanding of the molecular mechanisms that control virus latent gene expression. Using transient transfection of reporter plasmids in group I phenotype B-lymphoid cells, we have previously shown that the −248 to −55 region (−248/−55 region) of Cp contains elements that are essential fororiPI-EBNA1-dependent as well asoriPI-EBNA1-independent activation of the promoter. We now establish the importance of this region by a detailed mutational analysis of reporter plasmids carrying Cp regulatory sequences together with or without oriPI. The reporter plasmids were transfected into group I phenotype Rael cells and group III phenotype cbc-Rael cells, and the Cp activity measured was correlated with the binding of candidate transcription factors in electrophoretic mobility shift assays and further assessed in cotransfection experiments. We show that the NF-Y transcription factor interacts with the previously identified CCAAT box in the −71/−63 Cp region (M. T. Puglielli, M. Woisetschlaeger, and S. H. Speck, J. Virol. 70:5758–5768, 1996). We also show that members of the C/EBP transcription factor family interact with a C/EBP consensus sequence in the −119/−112 region of Cp and that this interaction is important for promoter activity. A central finding is the identification of a GC-rich sequence in the −99/−91 Cp region that is essential fororiPI-EBNA1-independent as well asoriPI-EBNA1-dependent activity of the promoter. This region contains overlapping binding sites for Sp1 and Egr-1, and our results suggest that Sp1 is a positive and Egr-1 is a negative regulator of Cp activity. Furthermore, we demonstrate that a reporter plasmid that in addition to oriPI contains only the −111/+76 region of Cp still retains the ability to be activated by EBNA1.

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