scholarly journals EcDNA hubs drive cooperative intermolecular oncogene expression

2020 ◽  
Author(s):  
King L. Hung ◽  
Kathryn E. Yost ◽  
Liangqi Xie ◽  
Sihan Wu ◽  
Joshua T. Lange ◽  
...  
Keyword(s):  
Single Molecule ◽  
Nuclear Bodies ◽  
Distal Enhancer ◽  
Single Molecule Sequencing ◽  
Bet Inhibitor ◽  
Cooperative Evolution ◽  
Oncogene Expression ◽  
Dna Elements ◽  
Altered Gene ◽  
Bet Protein

ABSTRACTExtrachromosomal DNAs (ecDNAs) are prevalent in human cancers and mediate high oncogene expression through elevated copy number and altered gene regulation1. Gene expression typically involves distal enhancer DNA elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs, comprised of ~10-100 ecDNAs clustered in the nucleus of interphase cells, drive intermolecular enhancer input for amplified oncogene expression. Single-molecule sequencing, single-cell multiome, and 3D enhancer connectome reveal subspecies of MYC-PVT1 ecDNAs lacking enhancers that access intermolecular and ectopic enhancer-promoter interactions in ecDNA hubs. ecDNA hubs persist without transcription and are tethered by BET protein BRD4. BET inhibitor JQ1 disperses ecDNA hubs, preferentially inhibits ecDNA oncogene transcription, and kills ecDNA+ cancer cells. Two amplified oncogenes MYC and FGFR2 intermix in ecDNA hubs, engage in intermolecular enhancer-promoter interactions, and transcription is uniformly sensitive to JQ1. Thus, ecDNA hubs are nuclear bodies of many ecDNAs tethered by proteins and platforms for cooperative transcription, leveraging the power of oncogene diversification and combinatorial DNA interactions. We suggest ecDNA hubs, rather than individual ecDNAs, as units of oncogene function, cooperative evolution, and new targets for cancer therapy.

scholarly journals The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation

2015 ◽  
Vol 112 (27) ◽  
pp. 8326-8331 ◽  
Author(s):  
Chiara Pastori ◽  
Philipp Kapranov ◽  
Clara Penas ◽  
Veronica Peschansky ◽  
Claude-Henry Volmar ◽  
...  
Keyword(s):  
Single Molecule ◽  
Noncoding Rna ◽  
Single Molecule Sequencing ◽  
Antiproliferative Effects ◽  
Protein Inhibition ◽  
Control Tumor Growth ◽  
Cancer Initiation ◽  
Bromodomain Proteins ◽  
Control Tumor ◽  
Bet Protein

Bromodomain and extraterminal (BET) domain proteins have emerged as promising therapeutic targets in glioblastoma and many other cancers. Small molecule inhibitors of BET bromodomain proteins reduce expression of several oncogenes required for Glioblastoma Multiforme (GBM) progression. However, the mechanism through which BET protein inhibition reduces GBM growth is not completely understood. Long noncoding RNAs (lncRNAs) are important epigenetic regulators with critical roles in cancer initiation and malignant progression, but mechanistic insight into their expression and regulation by BET bromodomain inhibitors remains elusive. In this study, we used Helicos single molecule sequencing to comprehensively profile lncRNAs differentially expressed in GBM, and we identified a subset of GBM-specific lncRNAs whose expression is regulated by BET proteins. Treatment of GBM cells with the BET bromdomain inhibitor I-BET151 reduced levels of the tumor-promoting lncRNA HOX transcript antisense RNA (HOTAIR) and restored the expression of several other GBM down-regulated lncRNAs. Conversely, overexpression of HOTAIR in conjunction with I-BET151 treatment abrogates the antiproliferative activity of the BET bromodomain inhibitor. Moreover, chromatin immunoprecipitation analysis demonstrated binding of Bromodomain Containing 4 (BRD4) to the HOTAIR promoter, suggesting that BET proteins can directly regulate lncRNA expression. Our data unravel a previously unappreciated mechanism through which BET proteins control tumor growth of glioblastoma cells and suggest that modulation of lncRNA networks may, in part, mediate the antiproliferative effects of many epigenetic inhibitors currently in clinical trials for cancer and other diseases.

scholarly journals Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

2021 ◽  
Author(s):  
Fei Ge ◽  
Jingtao Qu ◽  
Peng Liu ◽  
Lang Pan ◽  
Chaoying Zou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Inbred Line ◽  
Genome Mapping ◽  
Maize Inbred Line ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Maize Genetic ◽  
Induction Ratio ◽  
Phenotypic Variations

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

2. How to read the book of life

2018 ◽  
pp. 12-27
Author(s):  
John Archibald
Keyword(s):  
Dna Sequencing ◽  
Human Genome ◽  
Single Molecule ◽  
Human Genome Project ◽  
Genome Project ◽  
Chain Termination ◽  
Single Molecule Sequencing ◽  
Semiconductor Sequencing ◽  
The Cost ◽  
The Human Genome Project

For all its biological importance, DNA is a fragile molecule so extracting it is a difficult process. ‘How to read the book of life’ explains the techniques required to sequence DNA. It begins by explaining the techniques developed for protein and RNA sequencing by Frederick Sanger, Robert Holley, and Carl Woese that were then developed further for DNA sequencing. Following the success of the Human Genome Project, the next generation of DNA sequencing was developed in the mid-2000s. Pyrosequencing was capable of generating orders of magnitude more data at a fraction of the cost, but was superceded within a decade by semiconductor sequencing, reversible chain-termination sequencing, and single-molecule sequencing.

scholarly journals SDS-assisted protein transport through solid-state nanopores

Nanoscale ◽  
2017 ◽  
Vol 9 (32) ◽  
pp. 11685-11693 ◽  
Author(s):  
Laura Restrepo-Pérez ◽  
Shalini John ◽  
Aleksei Aksimentiev ◽  
Chirlmin Joo ◽  
Cees Dekker
Keyword(s):  
Solid State ◽  
Sodium Dodecyl Sulfate ◽  
Single Molecule ◽  
Protein Transport ◽  
Sodium Dodecyl ◽  
Single Molecule Sequencing ◽  
Dodecyl Sulfate ◽  
Multiple Challenges

Using nanopores for single-molecule sequencing of proteins faces multiple challenges. Here, we investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore traslocations.

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