scholarly journals Transcriptional activity of TRF2 is telomere length dependent

2016 ◽  
Author(s):  
Ananda Kishore Mukherjee ◽  
Shalu Sharma ◽  
Parashar Dhapola ◽  
Dhurjhoti Saha ◽  
Tabish Hussain ◽  
...  
Keyword(s):  
Telomere Length ◽  
Genome Stability ◽  
Telomere Maintenance ◽  
Regulatory Control ◽  
Gene Promoters ◽  
Multiple Gene ◽  
Telomere Repeat ◽  
Genome Wide ◽  
Binding Factor

AbstractTRF2 is a telomere repeat binding factor crucial for telomere maintenance and genome stability. An emerging non-conventional role of TRF2 is as a transcriptional regulator through extra-telomeric bindings. Herein we report that increase in telomere length leads to sequestration of TRF2 at the telomeres leading to reduced extra-telomeric TRF2 occupancy genome wide. Decrease in TRF2 occupancy was found on multiple gene promoters in cells with elongated telomeres, including the cell cycle regulator kinase-p21. We found that TRF2 is a transcriptional repressor of p21, and, interestingly, TRF2-mediated regulatory control of p21 is telomere length dependent.

scholarly journals The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation

2011 ◽  
Vol 22 (10) ◽  
pp. 1753-1765 ◽  
Author(s):  
Hui-Yong Lian ◽  
E. Douglas Robertson ◽  
Shin-ichiro Hiraga ◽  
Gina M. Alvino ◽  
David Collingwood ◽  
...  
Keyword(s):  
Telomere Length ◽  
Replication Timing ◽  
Repeat Length ◽  
Genome Integrity ◽  
Histone Tail ◽  
Telomere Repeat ◽  
Replication Time ◽  
Genome Wide ◽  
Telomere Replication

DNA replication in Saccharomyces cerevisiae proceeds according to a temporal program. We have investigated the role of the telomere-binding Ku complex in specifying late replication of telomere-proximal sequences. Genome-wide analysis shows that regions extending up to 80 kb from telomeres replicate abnormally early in a yku70 mutant. We find that Ku does not appear to regulate replication time by binding replication origins directly, nor is its effect on telomere replication timing mediated by histone tail acetylation. We show that Ku instead regulates replication timing through its effect on telomere length, because deletion of the telomerase regulator Pif1 largely reverses the short telomere defect of a yku70 mutant and simultaneously rescues its replication timing defect. Consistent with this conclusion, deleting the genome integrity component Elg1 partially rescued both length and replication timing of yku70 telomeres. Telomere length–mediated control of replication timing requires the TG1–3 repeat-counting component Rif1, because a rif1 mutant replicates telomeric regions early, despite having extended TG1–3 tracts. Overall, our results suggest that the effect of Ku on telomere replication timing results from its impact on TG1–3 repeat length and support a model in which Rif1 measures telomere repeat length to ensure that telomere replication timing is correctly programmed.

scholarly journals RAD50 and RAD51 Define Two Pathways That Collaborate to Maintain Telomeres in the Absence of Telomerase

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 143-152 ◽  
Author(s):  
Siyuan Le ◽  
J Kent Moore ◽  
James E Haber ◽  
Carol W Greider
Keyword(s):  
Cell Death ◽  
Telomere Length ◽  
Gene Conversion ◽  
De Novo ◽  
Dna Recombination ◽  
Telomere Maintenance ◽  
Triple Mutant ◽  
Yeast Telomerase ◽  
Telomere Lengthening

Abstract Telomere length is maintained by the de novo addition of telomere repeats by telomerase, yet recombination can elongate telomeres in the absence of telomerase. When the yeast telomerase RNA component, TLC1, is deleted, telomeres shorten and most cells die. However, gene conversion mediated by the RAD52 pathway allows telomere lengthening in rare survivor cells. To further investigate the role of recombination in telomere maintenance, we assayed telomere length and the ability to generate survivors in several isogenic DNA recombination mutants, including rad50, rad51, rad52, rad54, rad57, xrs2, and mre11. The rad51, rad52, rad54, and rad57 mutations increased the rate of cell death in the absence of TLC1. In contrast, although the rad50, xrs2, and mre11 strains initially had short telomeres, double mutants with tlc1 did not affect the rate of cell death, and survivors were generated at later times than tlc1 alone. While none of the double mutants of recombination genes and tlc1 (except rad52 tlc1) blocked the ability to generate survivors, a rad50 rad51 tlc1 triple mutant did not allow the generation of survivors. Thus RAD50 and RAD51 define two separate pathways that collaborate to allow cells to survive in the absence of telomerase.

scholarly journals The Intra- and Extra-Telomeric Role of TRF2 in the DNA Damage Response

2021 ◽  
Vol 22 (18) ◽  
pp. 9900
Author(s):  
Siti A. M. Imran ◽  
Muhammad Dain Yazid ◽  
Wei Cui ◽  
Yogeswaran Lokanathan
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Response Factors ◽  
Telomere Repeat ◽  
Protection Mechanism ◽  
Dna Instability ◽  
Binding Factor ◽  
Damage Response ◽  
Dna Break

Telomere repeat binding factor 2 (TRF2) has a well-known function at the telomeres, which acts to protect the telomere end from being recognized as a DNA break or from unwanted recombination. This protection mechanism prevents DNA instability from mutation and subsequent severe diseases caused by the changes in DNA, such as cancer. Since TRF2 actively inhibits the DNA damage response factors from recognizing the telomere end as a DNA break, many more studies have also shown its interactions outside of the telomeres. However, very little has been discovered on the mechanisms involved in these interactions. This review aims to discuss the known function of TRF2 and its interaction with the DNA damage response (DDR) factors at both telomeric and non-telomeric regions. In this review, we will summarize recent progress and findings on the interactions between TRF2 and DDR factors at telomeres and outside of telomeres.

scholarly journals Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

2022 ◽  
Vol 12 ◽  
Author(s):  
Inge Holm ◽  
Luisa Nardini ◽  
Adrien Pain ◽  
Emmanuel Bischoff ◽  
Cameron E. Anderson ◽  
...  
Keyword(s):  
Malaria Vector ◽  
Regulatory Elements ◽  
Specific Cell ◽  
Insect Vector ◽  
Anopheles Coluzzii ◽  
Gene Promoters ◽  
Transcriptional Enhancers ◽  
Genome Wide ◽  
A Genome

Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences.Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.

scholarly journals BisMapR: a strand-specific, nuclease-based method for genome-wide R-loop detection

2021 ◽  
Author(s):  
Phillip Wulfridge ◽  
Kavitha Sarma
Keyword(s):  
Genome Stability ◽  
Antisense Transcription ◽  
Gene Promoters ◽  
Normal Cells ◽  
Disease States ◽  
Detection Strategy ◽  
Genome Wide ◽  
Loop Detection ◽  
Nucleic Acid Structures ◽  
Nuclear Processes

AbstractR-loops are three stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation as seen in some neurodevelopmental diseases and cancers and is associated with compromised genome stability. Genome-wide profiling of R-loops in normal cells and their comparison in disease states can help identify precise locations of pathogenic R-loops and advance efforts to attenuate deviant R-loops while preserving biologically important ones. Toward this, we have developed an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce high-resolution, genome-wide R-loop profiles that retain strand information. Furthermore, BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. We applied BisMapR to reveal discrete R-loop behavior at gene promoters and enhancers. We show that gene promoters exhibiting antisense transcription form R-loops in both directions. and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. Thus, BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.

scholarly journals Telomere repeat–binding factor 2 binds extensively to extra-telomeric G-quadruplexes and regulates the epigenetic status of several gene promoters

2019 ◽  
Vol 294 (47) ◽  
pp. 17709-17722 ◽  
Author(s):  
Ananda Kishore Mukherjee ◽  
Shalu Sharma ◽  
Sulochana Bagri ◽  
Rintu Kutum ◽  
Pankaj Kumar ◽  
...  
Keyword(s):  
Gene Promoters ◽  
Telomere Repeat ◽  
Binding Factor

The Fluctuation of Telomere Repeat Binding Factor 1 during Cell Cycle and Its Localization in Telomerase-Positive and Negative Cells.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4326-4326
Author(s):  
Jianping Lan ◽  
He Huang ◽  
Yuanyuan Zhu ◽  
Jie Sun
Keyword(s):  
Cell Cycle ◽  
Telomere Length ◽  
Hela Cells ◽  
Cell Cycle Progression ◽  
Promyelocytic Leukemia ◽  
Final Concentration ◽  
Cycle Progression ◽  
Telomere Repeat ◽  
Binding Factor ◽  
M Phase

Abstract Telomere is a nucleoprotein complex which caps the extreme ends of eukaryotic chromosomes. In human, telomere is composed of a tandem repeat array of TTAGGG hexanucleotide and bound to a set of specific proteins. These proteins function to maintain the integrity of chromosomes and genomic stability. Among these proteins, telomere repeat binding factor 1(TRF1) is the first telomere binding protein which was isolated by DNA affinity chromatography in 1995. TRF1 serves as a negative regulator of telomere length since TRF1 overexpression would elicit the shortening of telomere length in telomerase-positive cells. Meanwhile, overexpression of TRF1 would also induce the entry into mitosis and increase mitotic cells. These observation indicated TRF1 might participate in cell cycle regulation. However, the underlying mechanism in which TRF1 regulates the cell cycle and the endogenous level of TRF1 were not well-documented during cell cycle progression. To address these questions, we arrested HeLa cells at different phases by a combination of thymidine(5mM at final concentration) and nocodazole(20mM at final concentration) and detected the TRF1 levels by semi-quantitive Western Blotting assay. Cell cycle was verified by flow cytometry. Our results showed TRF1 level fluctuated coincided with cell cycle progression which reached the zenith at the M phase and went down to the nadir at G1/S point. Densitometry analysis demonstrated that the level of TRF1 at M phase was 3.9 times more than that at G1/S point(n=3, p<0.01). These results suggested that TRF1 might be essential for proper cell cycle progression and it was likely to take part in regulation of cell cycle chechpoint. TRF1 is also expressed in telomerase-negative cells. To further discriminate the different functions of TRF1 and decipher its protein-protein interaction network in telomerase-positive and negative cells, full-length TRF1 cDNA was amplified by PCR and subsequently subcloned into pEGFP-C2 vector to express TRF1 tagged by enhanced green fluorescent protein. This construct was then transiently transfected into telomerase-negative cells(WI38-2RA) and telomerase-positive cells(HeLa). Immunoflourescent staining was employed to check the localization of TRF1 in these two kinds of cells. Although in both cells, TRF1 was distributed in a speckled pattern in the nuclei, TRF1 did exclusively colocalize with promyelocytic leukemia(PML) nuclear body in WI38-2RA cells but not in HeLa cells. PML fused with RARα due to chromosome15,17 translocation which led to disassembly of PML nucleur body in acute promyelocytic leukemia. These preliminary results suggested that TRF1 might have the different regulating mechanism and interacting network.

scholarly journals Role of Ndt80p in Sterol Metabolism Regulation and Azole Resistance in Candida albicans

2009 ◽  
Vol 8 (8) ◽  
pp. 1174-1183 ◽  
Author(s):  
Adnane Sellam ◽  
Faïza Tebbji ◽  
André Nantel
Keyword(s):  
Candida Albicans ◽  
Stress Responses ◽  
Efflux Pump ◽  
Transcriptional Profiling ◽  
Ergosterol Biosynthesis ◽  
Gene Promoters ◽  
Sterol Metabolism ◽  
Metabolism Regulation ◽  
Genome Wide

ABSTRACT The Ndt80p transcription factor modulates azole tolerance in Candida albicans by controlling the expression of the gene for the drug efflux pump Cdr1p. To date, the contribution of this transcriptional modulator to drug tolerance is not yet well understood. Here, we investigate the role of Ndt80p in mediating fluconazole tolerance by determining its genome-wide occupancy using chromatin immunoprecipitation coupled to high-density tiling arrays. Ndt80p was found to bind a large number of gene promoters with diverse biological functions. Gene ontology analysis of these Ndt80p targets revealed a significant enrichment in gene products related to the cell wall, carbohydrate metabolism, stress responses, hyphal development, multidrug transport, and the cell cycle. Ndt80p was found on the promoters of ergosterol biosynthesis genes, including on the azole target Erg11p. Additionally, expression profiling was used to identify fluconazole-responsive genes that require Ndt80p for their proper expression. We found that Ndt80p is crucial for the expression of numerous fluconazole-responsive genes, especially genes involved in ergosterol metabolism. Therefore, by combining genome-wide location and transcriptional profiling, we have characterized the Ndt80p fluconazole-dependent regulon and demonstrated the key role of this global transcriptional regulator in modulating sterol metabolism and drug resistance in C. albicans.

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