Role of Tet proteins in enhancer activity and telomere elongation

Abstract Background Signal fidelity depends on protein–protein interaction–‘hubs’ integrating cues from large interactomes. Recently, and based on a common secondary structure motif, the αα-hubs were defined, which are small α-helical domains of large, modular proteins binding intrinsically disordered transcriptional regulators. Methods Comparative structural biology. Results We assign the harmonin-homology-domain (HHD, also named the harmonin N-terminal domain, NTD) present in large proteins such as harmonin, whirlin, cerebral cavernous malformation 2, and regulator of telomere elongation 1 to the αα-hubs. The new member of the αα-hubs expands functionality to include scaffolding of supra-modular complexes mediating sensory perception, neurovascular integrity and telomere regulation, and reveal novel features of the αα-hubs. As a common trait, the αα-hubs bind intrinsically disordered ligands of similar properties integrating similar cellular cues, but without cross-talk. Conclusion The inclusion of the HHD in the αα-hubs has uncovered new features, exemplifying the utility of identifying groups of hub domains, whereby discoveries in one member may cross-fertilize discoveries in others. These features make the αα-hubs unique models for decomposing signal specificity and fidelity. Using these as models, together with other suitable hub domain, we may advance the functional understanding of hub proteins and their role in cellular communication and signaling, as well as the role of intrinsically disordered proteins in signaling networks.

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Ascorbic acid improves parthenogenetic embryo development through TET proteins in mice

Bioscience Reports ◽

10.1042/bsr20181730 ◽

2019 ◽

Vol 39 (1) ◽

Cited By ~ 5

Author(s):

Wei Gao ◽

Xianfeng Yu ◽

Jindong Hao ◽

Ling Wang ◽

Minghui Qi ◽

...

Keyword(s):

Ascorbic Acid ◽

Vitamin C ◽

Embryonic Development ◽

Real Time Pcr ◽

Quantitative Real Time Pcr ◽

Qrt Pcr ◽

Tet Proteins ◽

Parthenogenetic Embryo ◽

Blastocyst Rate

Abstract The TET (Ten-Eleven Translocation) proteins catalyze the oxidation of 5mC (5-methylcytosine) to 5hmC (5-hydroxymethylcytosine) and play crucial roles in embryonic development. Ascorbic acid (Vc, Vitamin C) stimulates the expression of TET proteins, whereas DMOG (dimethyloxallyl glycine) inhibits TET expression. To investigate the role of TET1, TET2, and TET3 in PA (parthenogenetic) embryonic development, Vc and DMOG treatments were administered during early embryonic development. The results showed that Vc treatment increased the blastocyst rate (20.73 ± 0.46 compared with 26.57 ± 0.53%). By contrast, DMOG reduced the blastocyst rate (20.73 ± 0.46 compared with 11.18 ± 0.13%) in PA embryos. qRT-PCR (quantitative real-time PCR) and IF (immunofluorescence) staining results revealed that TET1, TET2, and TET3 expressions were significantly lower in PA embryos compared with normal fertilized (Con) embryos. Our results revealed that Vc stimulated the expression of TET proteins in PA embryos. However, treatment with DMOG significantly inhibited the expression of TET proteins. In addition, 5hmC was increased following treatment with Vc and suppressed by DMOG in PA embryos. Taken together, these results indicate that the expression of TET proteins plays crucial roles mediated by 5hmC in PA embryonic development.

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The Role of Transcription Factor PU.I in the Activity of the Intronic Enhancer of the Eosinophil-Derived Neurotoxin (RNS2) Gene

Blood ◽

10.1182/blood.v91.6.2126.2126_2126_2132 ◽

1998 ◽

Vol 91 (6) ◽

pp. 2126-2132 ◽

Cited By ~ 1

Author(s):

Thamar B. van Dijk ◽

Eric Caldenhoven ◽

Jan A.M. Raaijmakers ◽

Jan-Willem J. Lammers ◽

Leo Koenderman ◽

...

Keyword(s):

Transcription Factor ◽

Point Mutations ◽

Proximal Promoter ◽

Multiple Forms ◽

Enhancer Activity ◽

Promoter Sequences ◽

Intronic Enhancer ◽

First Intron ◽

Shift Analysis

Eosinophil-derived neurotoxin (EDN) found in the granules of human eosinophils is a cationic ribonuclease toxin. Expression of the EDN gene (RNS2) in eosinophils is dependent on proximal promoter sequences in combination with an enhancer located in the first intron. We further define here the active region of the intron using transfections in differentiated eosinophilic HL60 cells. We show that a region containing a tandem PU.I binding site is important for intronic enhancer activity. This region binds multiple forms of transcription factor PU.I as judged by gel-shift analysis and DNA affinity precipitation. Importantly, introducing point mutations in the PU.I site drastically reduces the intronic enhancer activity, showing the importance of PU.I for expression of EDN in cells of the eosinophilic lineage.

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Effects of the maternal factor Zelda on zygotic enhancer activity in the Drosophila embryo

10.1101/385070 ◽

2018 ◽

Author(s):

Xiao-Yong Li ◽

Michael B. Eisen

Keyword(s):

Binding Sites ◽

Expression Patterns ◽

Drosophila Embryo ◽

Temporal Expression ◽

Reporter Construct ◽

Limited Effect ◽

Enhancer Activity ◽

Maternal Factor ◽

Anterior Posterior

AbstractThe maternal factor Zelda is broadly bound to zygotic enhancers during early fly embryogenesis, and has been shown to be important for the expression of a large number of genes. However, its function remains poorly understood. Here, we carried out detailed analysis of the functional role of Zelda on the activities of a group of enhancers that drive patterned gene expression along the anterior -posterior axis. We found that among these enhancers, only one lost its activity entirely when all its Zelda bind sites were mutated. For all others, mutations of all of their Zelda binding sites only had limited effect, which varied temporally and spatially. These results suggest that Zld may exert a quantitative effect on a broad range of enhancers, which presumably is critical to generate highly diverse spatial and temporal expression patterns for different genes in the developmental gene network in fly embryo. Lastly, we found that the observed effect of Zelda site mutations was much stronger when a mutant enhancer was tested using a BAC based reporter construct than a simple reporter construct, suggesting that the effect of Zld is dependent on chromatin environment.

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MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming

10.21203/rs.3.rs-384560/v1 ◽

2021 ◽

Author(s):

Alexandre Gaspar-Maia ◽

Wazim Mohammed Ismail ◽

Amelia Mazzone ◽

Jagneet Kaur ◽

Stephanie Safgren ◽

...

Keyword(s):

Regulatory Elements ◽

Histone Variants ◽

Cellular Reprogramming ◽

Negative Regulator ◽

Cellular Heterogeneity ◽

Enhancer Activity ◽

Active Enhancer ◽

A Cell ◽

Cell Type Specific

Abstract Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27 acetylation (H3K27ac). However, apart from poised enhancers that are observed in early stages of development and putative silencers, the functional significance of cis-regulatory elements lacking H3K27ac is poorly understood. Here we show that macroH2A histone variants mark a subset of enhancers in normal and cancer cells, which we coined ‘macroH2A-Bound Enhancers’, that negatively modulate enhancer activity. We find macroH2A variants enriched at enhancer elements that are devoid of H3K27ac in a cell type-specific manner, indicating a role for macroH2A at inactive enhancers to maintain cell identity. In following, reactivation of macro-bound enhancers is associated with oncogenic programs in breast cancer and its repressive role is correlated with the activity of macroH2A2 as a negative regulator of BRD4 chromatin occupancy. Finally, through single cell epigenomic profiling, we show that the loss of macroH2A2 leads to increased cellular heterogeneity that may help to explain the role of macroH2A variants in defining oncogenic transcriptional dependencies.

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Immunoglobulin heavy-chain enhancer is required to maintain transfected gamma 2A gene expression in a pre-B-cell line

Molecular and Cellular Biology ◽

10.1128/mcb.10.3.1076-1083.1990 ◽

1990 ◽

Vol 10 (3) ◽

pp. 1076-1083

Author(s):

B Porton ◽

D M Zaller ◽

R Lieberson ◽

L A Eckhardt

Keyword(s):

B Cell ◽

Cell Lines ◽

Heavy Chain ◽

Gene Activation ◽

Immunoglobulin Heavy Chain ◽

Transcription Unit ◽

Enhancer Activity ◽

Igh Genes ◽

High Level

The immunoglobulin heavy-chain (IgH) enhancer serves to activate efficient and accurate transcription of cloned IgH genes when introduced into B lymphomas or myelomas. The role of this enhancer after gene activation, however, is unclear. The endogenous IgH genes in several cell lines, for example, have lost the IgH enhancer by deletion and yet continue to be expressed. This might be explained if the role of the enhancer were to establish high-level gene transcription but not to maintain it. Alternatively, other enhancers might lie adjacent to endogenous IgH genes, substituting their activity for that of the lost IgH enhancer. To address both of these alternatives, we searched for enhancer activity within the flanking regions of one of these IgH enhancer-independent genes and designed an experiment that allowed us to consider separately the establishment and maintenance of expression of a transfected gene. For the latter experiment we generated numerous pre-B cell lines stably transformed with a gamma 2a gene. In this gene, the IgH enhancer lay at a site outside the heavy-chain transcription unit, between DH and JH gene segments. After expression of the transfected gene was established, selective conditions were chosen for the outgrowth of subclones that had undergone D-J joining and thus IgH enhancer deletion. Measurements of gamma 2a expression before and after enhancer deletion revealed that the enhancer was required for maintenance of expression of the transfected gene. The implication of this finding for models of enhancer function in endogenous genes is discussed.

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Inflammation increases cells expressing ZSCAN4 and progenitor cell markers in the adult pancreas

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00299.2012 ◽

2013 ◽

Vol 304 (12) ◽

pp. G1103-G1116 ◽

Cited By ~ 7

Author(s):

Shigeru B. H. Ko ◽

Sakiko Azuma ◽

Yukihiro Yokoyama ◽

Akiko Yamamoto ◽

Kazuhiro Kyokane ◽

...

Keyword(s):

Autoimmune Pancreatitis ◽

Genome Stability ◽

Progenitor Cell ◽

Es Cells ◽

Embryonic Stem ◽

Corticosteroid Treatment ◽

Human Pancreas ◽

Cell Markers ◽

Telomere Elongation

We have recently identified the zinc finger and SCAN domain containing 4 (Zscan4), which is transiently expressed and regulates telomere elongation and genome stability in mouse embryonic stem (ES) cells. The aim of this study was to examine the expression of ZSCAN4 in the adult pancreas and elucidate the role of ZSCAN4 in tissue inflammation and subsequent regeneration. The expression of ZSCAN4 and other progenitor or differentiated cell markers in the human pancreas was immunohistochemically examined. Pancreas sections of alcoholic or autoimmune pancreatitis patients before and under maintenance corticosteroid treatment were used in this study. In the adult human pancreas a small number of ZSCAN4-positive (ZSCAN4+) cells are present among cells located in the islets of Langerhans, acini, ducts, and oval-shaped cells. These cells not only express differentiated cell markers for each compartment of the pancreas but also express other tissue stem/progenitor cell markers. Furthermore, the number of ZSCAN4+cells dramatically increased in patients with chronic pancreatitis, especially in the pancreatic tissues of autoimmune pancreatitis actively regenerating under corticosteroid treatment. Interestingly, a number of ZSCAN4+cells in the pancreas of autoimmune pancreatitis returned to the basal level after 1 yr of maintenance corticosteroid treatment. In conclusion, coexpression of progenitor cell markers and differentiated cell markers with ZSCAN4 in each compartment of the pancreas may indicate the presence of facultative progenitors for both exocrine and endocrine cells in the adult pancreas.

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Role for the Related Poly(ADP-Ribose) Polymerases Tankyrase 1 and 2 at Human Telomeres

Molecular and Cellular Biology ◽

10.1128/mcb.22.1.332-342.2002 ◽

2002 ◽

Vol 22 (1) ◽

pp. 332-342 ◽

Cited By ~ 197

Author(s):

Brandoch D. Cook ◽

Jasmin N. Dynek ◽

William Chang ◽

Grigoriy Shostak ◽

Susan Smith

Keyword(s):

Potential Role ◽

Telomere Maintenance ◽

Telomeric Dna ◽

Continuous Growth ◽

Telomere Elongation ◽

Bona Fide ◽

Tankyrase 1 ◽

Growth Of Tumor

ABSTRACT Telomere maintenance is essential for the continuous growth of tumor cells. In most human tumors telomeres are maintained by telomerase, a specialized reverse transcriptase. Tankyrase 1, a human telomeric poly(ADP-ribose) polymerase (PARP), positively regulates telomere length through its interaction with TRF1, a telomeric DNA-binding protein. Tankyrase 1 ADP-ribosylates TRF1, inhibiting its binding to telomeric DNA. Overexpression of tankyrase 1 in the nucleus promotes telomere elongation, suggesting that tankyrase 1 regulates access of telomerase to the telomeric complex. The recent identification of a closely related homolog of tankyrase 1, tankyrase 2, opens the possibility for a second PARP at telomeres. We therefore sought to establish the role of tankyrase 1 at telomeres and to determine if tankyrase 2 might have a telomeric function. We show that endogenous tankyrase 1 is a component of the human telomeric complex. We demonstrate that telomere elongation by tankyrase 1 requires the catalytic activity of the PARP domain and does not occur in telomerase-negative primary human cells. To investigate a potential role for tankyrase 2 at telomeres, recombinant tankyrase 2 was subjected to an in vitro PARP assay. Tankyrase 2 poly(ADP-ribosyl)ated itself and TRF1. Overexpression of tankyrase 2 in the nucleus released endogenous TRF1 from telomeres. These findings establish tankyrase 2 as a bona fide PARP, with itself and TRF1 as acceptors of ADP-ribosylation, and suggest the possibility of a role for tankyrase 2 at telomeres.

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Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1900343116 ◽

2019 ◽

Vol 116 (20) ◽

pp. 9893-9902 ◽

Cited By ~ 14

Author(s):

Christopher M. Uyehara ◽

Daniel J. McKay

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Nuclear Receptor ◽

Binding Sites ◽

Transcriptional Responses ◽

Enhancer Activity ◽

Developmental Transitions ◽

Experimental Systems ◽

The Impact

The ecdysone pathway was among the first experimental systems employed to study the impact of steroid hormones on the genome. In Drosophila and other insects, ecdysone coordinates developmental transitions, including wholesale transformation of the larva into the adult during metamorphosis. Like other hormones, ecdysone controls gene expression through a nuclear receptor, which functions as a ligand-dependent transcription factor. Although it is clear that ecdysone elicits distinct transcriptional responses within its different target tissues, the role of its receptor, EcR, in regulating target gene expression is incompletely understood. In particular, EcR initiates a cascade of transcription factor expression in response to ecdysone, making it unclear which ecdysone-responsive genes are direct EcR targets. Here, we use the larval-to-prepupal transition of developing wings to examine the role of EcR in gene regulation. Genome-wide DNA binding profiles reveal that EcR exhibits widespread binding across the genome, including at many canonical ecdysone response genes. However, the majority of its binding sites reside at genes with wing-specific functions. We also find that EcR binding is temporally dynamic, with thousands of binding sites changing over time. RNA-seq reveals that EcR acts as both a temporal gate to block precocious entry to the next developmental stage as well as a temporal trigger to promote the subsequent program. Finally, transgenic reporter analysis indicates that EcR regulates not only temporal changes in target enhancer activity but also spatial patterns. Together, these studies define EcR as a multipurpose, direct regulator of gene expression, greatly expanding its role in coordinating developmental transitions.

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Alternative Lengthening of Telomeres and Chromatin Status

Genes ◽

10.3390/genes11010045 ◽

2019 ◽

Vol 11 (1) ◽

pp. 45 ◽

Cited By ~ 1

Author(s):

Ion Udroiu ◽

Antonella Sgura

Keyword(s):

Homologous Recombination ◽

Reverse Transcriptase ◽

Spatial Heterogeneity ◽

Telomere Length ◽

Epigenetic Modifications ◽

Alternative Lengthening Of Telomeres ◽

Telomere Elongation ◽

Alternative Lengthening ◽

Alt Activity

Telomere length is maintained by either telomerase, a reverse transcriptase, or alternative lengthening of telomeres (ALT), a mechanism that utilizes homologous recombination (HR) proteins. Since access to DNA for HR enzymes is regulated by the chromatin status, it is expected that telomere elongation is linked to epigenetic modifications. The aim of this review is to elucidate the epigenetic features of ALT-positive cells. In order to do this, it is first necessary to understand the telomeric chromatin peculiarities. So far, the epigenetic nature of telomeres is still controversial: some authors describe them as heterochromatic, while for others, they are euchromatic. Similarly, ALT activity should be characterized by the loss (according to most researchers) or formation (as claimed by a minority) of heterochromatin in telomeres. Besides reviewing the main works in this field and the most recent findings, some hypotheses involving the role of telomere non-canonical sequences and the possible spatial heterogeneity of telomeres are given.

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