scholarly journals Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Chan-Wang Lio ◽  
Jiayuan Zhang ◽  
Edahí González-Avalos ◽  
Patrick G Hogan ◽  
Xing Chang ◽  
...  

Ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine, facilitating DNA demethylation and generating new epigenetic marks. Here we show that concomitant loss of Tet2 and Tet3 in mice at early B cell stage blocked the pro- to pre-B cell transition in the bone marrow, decreased Irf4 expression and impaired the germline transcription and rearrangement of the Igκ locus. Tet2/3-deficient pro-B cells showed increased CpG methylation at the Igκ 3’ and distal enhancers that was mimicked by depletion of E2A or PU.1, as well as a global decrease in chromatin accessibility at enhancers. Importantly, re-expression of the Tet2 catalytic domain in Tet2/3-deficient B cells resulted in demethylation of the Igκ enhancers and restored their chromatin accessibility. Our data suggest that TET proteins and lineage-specific transcription factors cooperate to influence chromatin accessibility and Igκ enhancer function by modulating the modification status of DNA.

2015 ◽  
Vol 112 (31) ◽  
pp. E4236-E4245 ◽  
Author(s):  
Jinsuk Kang ◽  
Matthias Lienhard ◽  
William A. Pastor ◽  
Ashu Chawla ◽  
Mark Novotny ◽  
...  

Dioxygenases of the TET (Ten-Eleven Translocation) family produce oxidized methylcytosines, intermediates in DNA demethylation, as well as new epigenetic marks. Here we show data suggesting that TET proteins maintain the consistency of gene transcription. Embryos lacking Tet1 and Tet3 (Tet1/3 DKO) displayed a strong loss of 5-hydroxymethylcytosine (5hmC) and a concurrent increase in 5-methylcytosine (5mC) at the eight-cell stage. Single cells from eight-cell embryos and individual embryonic day 3.5 blastocysts showed unexpectedly variable gene expression compared with controls, and this variability correlated in blastocysts with variably increased 5mC/5hmC in gene bodies and repetitive elements. Despite the variability, genes encoding regulators of cholesterol biosynthesis were reproducibly down-regulated in Tet1/3 DKO blastocysts, resulting in a characteristic phenotype of holoprosencephaly in the few embryos that survived to later stages. Thus, TET enzymes and DNA cytosine modifications could directly or indirectly modulate transcriptional noise, resulting in the selective susceptibility of certain intracellular pathways to regulation by TET proteins.


2018 ◽  
Author(s):  
Chan-Wang J. Lio ◽  
Vipul Shukla ◽  
Daniela Samaniego-Castruita ◽  
Edahi González-Avalos ◽  
Abhijit Chakraborty ◽  
...  

AbstractTET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Here we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, encoding the cytidine deaminase AID essential for CSR. TET enzymes deposit 5hmC, demethylate and maintain chromatin accessibility at two TET-responsive elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Transcriptional profiling identified BATF as the bZIP transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF recruits TET proteins to the Aicda enhancer. Our data emphasize the importance of TET enzymes for bolstering AID expression, and highlight 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.


2020 ◽  
Author(s):  
Vinay S. Mahajan ◽  
Hamid Mattoo ◽  
Na Sun ◽  
Vinayak Viswanadham ◽  
Grace J. Yuen ◽  
...  

AbstractWe show that DNA methylation is a layered process in B lymphocytes. An underlying foundational methylome is stably established during B lineage commitment and overlaid with a DNMT3A-maintained dynamic methylome which is sculpted in distinct ways in B1 and B2 B cells during B cell development. An engineered loss of DNMT3A after commitment to the B lineage unmasks a foundational methylome that is shared in both B1 and B2 sub-lineages. The dynamic methylome is comprised of novel enhancers whose methylation state is maintained by DNMT3A but can be modulated in strikingly different ways in B1 and B2 B cells. During B1 B cell development, the dynamic methylome undergoes a prominent programmed demethylation event that is not observed during B2 B cell development. The methylation pattern of the dynamic methylome is determined by the coincident recruitment of DNMT3A and TET enzymes and it regulates the developmental expression of B1 and B2 lineage-specific genes.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1303-1303
Author(s):  
Esther J.H. Tijchon ◽  
Liesbeth van Emst ◽  
Jørn Havinga ◽  
Jean-Pierre Rouault ◽  
Felice Tirone ◽  
...  

Abstract Abstract 1303 B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common form of cancer in children, characterized by genetic aberrations affecting master regulators of lymphoid differentiation, such as RUNX1, IKZF1, TCF3, and PAX5, as well as tumor suppressor genes that control the cell cycle, including RB1 and CDKN2A. Another gene frequently altered in BCP-ALL is BTG1, which displays highly clustered mono-allelic deletions in childhood BCP-ALL (9%) and adult ALL (6%). The frequency of BTG1 deletions is two- to three-fold higher in ETV6-RUNX1- and BCR-ABL1-positive leukemias. BTG1, and its close homologue BTG2 regulate gene expression, for instance by associating with protein arginine methyltransferase 1 (PRMT1), affecting the activity of a variety of transcription factors, including several nuclear hormone receptors and HoxB9. In addition, BTG1 and BTG2 have been implicated in regulating mRNA stability by interacting with the Ccr4-Not complex. Recent studies have also identified missense point mutations in BTG1 and BTG2 in about 20% of non-Hodgkin lymphomas, arguing that altered function of these genes contributes to B cell malignancies. To investigate a role of BTG1 and BTG2 in B cell development, we studied the phenotype of Btg1 and Btg2 single knockout (KO) and Btg1;Btg2 double KO mice. Animals deficient for either BTG1 or BTG2 displayed a mild B cell phenotype with a moderate reduction of ∼20% in the total amount of B220+ progenitor B cells in bone marrow, while splenic B cells were present at normal frequencies. More detailed analyses revealed that Btg1−/− and Btg2−/− mice both showed a partial block at the pre-pro-B cell stage (Hardy fraction A). Methylcellulose colony assays in the presence of interleukin-7 (IL-7) demonstrated 30% fewer colonies using bone marrow from Btg2−/− mice, whereas 70% fewer colonies were obtained using bone marrow derived from Btg1−/− mice. To assess whether BTG1 and BTG2 fulfill redundant functions during B cell development, we analyzed the phenotype of Btg1−/−;Btg2−/− mice. Hence we observed that the combined loss of BTG1 and BTG2 led to a much stronger block in B cell differentiation, with the majority of progenitor B cells arrested at the pre-pro-B cell stage. In the spleens of these double knockout mice we observed a roughly 50% reduction in B220+ IgM+ B cells, suggesting that these genes act to modify the activity of B lineage transcription factors rather than to fully block their activities. This is consistent with a role for these genes as modifiers of transcriptional activity. Current studies are aimed at defining the molecular targets regulated by BTG1 and BTG2 during early B cell development using RNA sequencing and protein interaction experiments. In conclusion, our data demonstrate that BTG1 and BTG2 act as important regulators of normal B cell differentiation, and that this function might be critical for their role as tumor suppressors in (early) B cell malignancies. Disclosures: No relevant conflicts of interest to declare.


2019 ◽  
Vol 4 (34) ◽  
pp. eaau7523 ◽  
Author(s):  
Chan-Wang J. Lio ◽  
Vipul Shukla ◽  
Daniela Samaniego-Castruita ◽  
Edahi González-Avalos ◽  
Abhijit Chakraborty ◽  
...  

TET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). Here, we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, which encodes the activation-induced cytidine deaminase (AID) enzyme essential for CSR. TET enzymes deposit 5hmC, facilitate DNA demethylation, and maintain chromatin accessibility at two TET-responsive enhancer elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Our data identify the bZIP transcription factor, ATF-like (BATF) as a key transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF facilitates TET recruitment to this Aicda enhancer. Our study emphasizes the importance of TET enzymes for bolstering AID expression and highlights 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1145-1145
Author(s):  
Vipul Shukla ◽  
Daniela Samaniego-Castruita ◽  
Zhen Dong ◽  
Edahi Gonzalez Avalos ◽  
Qingqing Yan ◽  
...  

Abstract The three members of TET family of Fe(II) and alpha-ketoglutarate-dependent dioxygenases mediate DNA demethylation by sequentially oxidizing 5-methylcytosine (5mC) to 5-hydroxymethyl- (5hmC), 5-formyl- (5fC) and 5-carboxyl-cytosine (5caC). TET enzymes are required for normal development, and loss of TET function due to mutations, metabolic perturbations and hypoxia, among other mechanisms, occurs frequently in many hematological malignancies and solid tumors. Recent studies have identified mutations in TET proteins (TET2, most commonly) and metabolic enzymes which regulate TET catalytic activity in a large cohort of patients with Diffuse Large B-cell Lymphoma (DLBCL). However, the clinical significance of these mutations in DLBCL and the molecular mechanisms through which TET proteins suppress development of malignancies in general, are not fully-understood. To investigate the role of TET loss-of-function in the pathogenesis of DLBCL, we generated mice with B-cell-specific deletion of TET2 and TET3, the major TET homologs expressed in mature B cells. TET deficiency in B cells perturbed mature B cell homeostasis resulting in spontaneous development of Germinal Center-derived B cell lymphomas. Moreover, B cells with TET deficiency demonstrated increased genomic instability, a feature previously associated with TET loss-of-function in other hematopoietic lineages. Transcriptional profiling of TET-deficient expanded B cells revealed altered expression of genes and proteins involved in modulating the levels of secondary DNA structures, G-quadruplexes and DNA:RNA hybrids (R-loops) which have been linked to genomic instability and transcriptional perturbations in many different cancers. Using previously described methods and newer approaches, we observed a substantial increase in the levels of G-quadruplex and R-loop structures in TET-deficient B cells compared with control B cells. The increase in G-quadruplex and R-loop structures was evident in naïve, activated and GC B cells following acute TET deletion as well as in TET-deficient myeloid cells and T cells. Genome-wide mapping studies and high-throughput genome-wide translocation sequencing (HTGTS) showed a strong correlation of increased G-quadruplex and R-loop structures with increased DNA DSBs in switch regions of immunoglobulin heavy chain locus in TET-deficient B cells. Deletion of the DNA methyltransferase DNMT1 in TET-deficient B cells prevented the expansion of germinal center B cells, diminished the accumulation of G-quadruplexes and R-loops, and caused a notable delay in lymphoma development, consistent with the opposing functions of DNMT and TET enzymes in DNA methylation and demethylation. CRISPR-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops decreased the viability of TET-deficient B cells. Our studies suggest a molecular mechanism by which TET loss-of-function might predispose to development of B cell-derived and other malignancies, and highlight novel therapeutic avenues that could be further explored. Disclosures Rao: Cambridge Epigenetix: Membership on an entity's Board of Directors or advisory committees.


2005 ◽  
Vol 25 (5) ◽  
pp. 1804-1820 ◽  
Author(s):  
Henrietta Szutorisz ◽  
Claudia Canzonetta ◽  
Andrew Georgiou ◽  
Cheok-Man Chow ◽  
László Tora ◽  
...  

ABSTRACT The differentiation potential of stem cells is determined by the ability of these cells to establish and maintain developmentally regulated gene expression programs that are specific to different lineages. Although transcriptionally potentiated epigenetic states of genes have been described for haematopoietic progenitors, the developmental stage at which the formation of lineage-specific gene expression domains is initiated remains unclear. In this study, we show that an intergenic cis-acting element in the mouse λ5-VpreB1 locus is marked by histone H3 acetylation and histone H3 lysine 4 methylation at a discrete site in embryonic stem (ES) cells. The epigenetic modifications spread from this site toward the VpreB1 and λ5 genes at later stages of B-cell development, and a large, active chromatin domain is established in pre-B cells when the genes are fully expressed. In early B-cell progenitors, the binding of haematopoietic factor PU.1 coincides with the expansion of the marked region, and the region becomes a center for the recruitment of general transcription factors and RNA polymerase II. In pre-B cells, E2A also binds to the locus, and general transcription factors are distributed across the active domain, including the gene promoters and the intergenic region. These results suggest that localized epigenetic marking is important for establishing the transcriptional competence of the λ5 and VpreB1 genes as early as the pluripotent ES cell stage.


2007 ◽  
Vol 204 (4) ◽  
pp. 819-830 ◽  
Author(s):  
Tracy C. Kuo ◽  
Arthur L. Shaffer ◽  
Joseph Haddad ◽  
Yong Sung Choi ◽  
Louis M. Staudt ◽  
...  

Memory B cells provide rapid protection to previously encountered antigens; however, how these cells develop from germinal center B cells is not well understood. A previously described in vitro culture system using human tonsillar germinal center B cells was used to study the transcriptional changes that occur during differentiation of human memory B cells. Kinetic studies monitoring the expression levels of several known late B cell transcription factors revealed that BCL-6 is not expressed in memory B cells generated in vitro, and gene expression profiling studies confirmed that BCL-6 is not expressed in these memory B cells. Furthermore, ectopic expression of BCL-6 in human B cell cultures resulted in formation of fewer memory B cells. In addition, the expression profile of in vitro memory B cells showed a unique pattern that includes expression of genes encoding multiple costimulatory molecules and cytokine receptors, antiapoptotic proteins, T cell chemokines, and transcription factors. These studies establish new molecular criteria for defining the memory B cell stage in human B cells.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1255-1255
Author(s):  
Lai N Chan ◽  
Zhengshan Chen ◽  
Daniel Braas ◽  
Huimin Geng ◽  
Christian Hurtz ◽  
...  

Abstract Oncogenic lesions in hematopoietic progenitor cells give rise to B-cell or myeloid malignancies. While often transformed by the same oncogenes, B-cell and myeloid leukemias markedly differ in biological and clinical characteristics. Our metabolic analyses revealed that B-cell-unlike myeloid-leukemia cells are massively restricted in their glycolytic capacity. Low glycolytic reserves in B cells resulted in a state of chronic energy depletion and engaged the energy sensor LKB1-AMPK. Myeloid cells strongly activated glucose transport through insulin receptor (INSR)-AKT signaling and lacked activity of LKB1-AMPK, reflecting energy abundance. Conversely, B-cells lacked INSR-AKT signaling and were critically dependent on LKB1-AMPK-mediated glucose uptake. Cre-mediated deletion of Lkb1 caused acute glycolytic exhaustion and cell death in B-lineage but increased glycolysis, energy levels and proliferation in myeloid leukemia. C/EBPa-mediated conversion of B-cell into myeloid identity reversed the detrimental effects of Lkb1-deletion and restored glycolysis, energy levels and survival of B→myeloid reprogrammed cells. In >80% of B-lineage leukemia cases, we found genetic lesions of transcription factors (e.g. deletion of PAX5, IKZF1, rearrangement of MLL) that caused a B→myeloid lineage shift. While previously of unknown functional significance, these lesions relieved B-cell-specific transcriptional repression of molecules that mediate glucose uptake and utilization (INSR, GLUT1, HK2, G6PD) and amplified glycolytic energy supply for transforming oncogenes. Likewise, glucocorticoid receptor (NR3C1)-mediated inhibition of glucose uptake and glycolysis was strictly dependent on a B-lymphoid transcriptional program. B→myeloid lineage conversion abolished NR3C1 expression and activity, which provides a mechanistic explanation for the empiric finding that glucocorticoids are highly active in the treatment of B-cell-but not myeloid malignancies. In conclusion, B-cell-specific restriction of glycolytic energy supply represents a previously unrecognized metabolic barrier against malignant transformation and reveals LKB1-AMPK as a novel target for the treatment of human B-lineage leukemia. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 5 (3) ◽  
pp. 745-755
Author(s):  
Andrea Paun ◽  
Estefania Claudio ◽  
Ulrich K. Siebenlist

Abstract There is a considerable body of work exploring the role of NF-κB family of transcription factors in the maturation and functions of later stage B cells; however, their role in the earlier bone marrow stages of development is less well understood despite the demonstration that NF-κB activity is present at all early stages of B-cell development. To explore the consequences of early, B cell–targeted constitutive activation of both NF-κB pathways on B-cell development, we generated mice that have either or both. NF-κB pathways constitutively activated beginning in early pro-B cells. In marked contrast to activating a single pathway, we found mice with both pathways constitutively activated displayed a profound loss of B cells, starting with early pro-B cells and peaking at the late pro-B-cell stage, at least in part as a result of increased apoptosis. This effect was found to be cell autonomous and to have striking phenotypic consequences on the secondary lymphoid organs and circulating antibody levels. This effect was also found to be temporal in nature as similar activation under a Cre expressed later in development did not result in generation of a similar phenotype. Taken together, these findings help to shed further light on the need for tight regulation of the NF-κB family of transcription factors during the various stages of B-cell development in the bone marrow.


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