Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

Veloso, Artur; Biewen, Benjamin; Paulsen, Michelle T.; Berg, Nathaniel K.; Lima, Leonardo Carmo de Andrade; Prasad, J.K.; Bedi, Karan; Magnuson, Brian; Wilson, Thomas E.; Ljungman, Mats

doi:10.1371/journal.pone.0078190

Cited by 29 publications

(27 citation statements)

References 24 publications

(44 reference statements)

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“…Moreover, our mechanistic findings are not in dispute. Indeed, three other groups came to the same conclusion as us—that topoisomerases preferentially facilitate expression of long genes 1–3 . Our study demonstrates an essential role for topoisomerases in transcriptional elongation of long neuronal genes and suggests a critical role for these enzymes in neurodevelopmental disorders like autism.…”

supporting

confidence: 56%

Zylka et al. reply

Zylka

Philpot

King

2014

Nature

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supporting

confidence: 56%

Zylka et al. reply

Zylka

Philpot

King

2014

Nature

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“…Conversely, if neighboring genes are simultaneously transcribed in a head-to-head fashion, DNA topological barriers could emerge. Indeed, inhibition of DNA topoisomerase I, which relaxes torsional tension induced during the transcription process, has been shown to severely inhibit transcription elongation (Ljungman and Hanawalt 1996;Veloso et al 2013). Interestingly, suppression of the rate of elongation by nearby transcription was independent of the orientation of transcription.…”

Section: Discussionmentioning

confidence: 99%

“…Cell culturing HF1, hTERT immortalized foreskin-derived human fibroblasts, previously called NF (Paulsen et al 2013a,b;Veloso et al 2013), CS-B primary human skin fibroblasts (Coriell, GM00739) and TM, hTERT immortalized human skin fibroblasts (a gift from Dr. Tom Misteli, NCI) were grown in MEM supplemented with 10% FBS, L-glutamine, vitamin mix, and antibiotics. K562 human leukemia cells were grown in IMDM supplemented with 10% FBS and penicillin/streptomycin.…”

Section: Methodsmentioning

confidence: 99%

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

et al. 2014

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The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-b-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 individual genes in human cells. This technique, BruDRB-seq, revealed gene-specific differences in elongation rates with a median rate of around 1.5 kb/min. We found that genes with rapid elongation rates showed higher densities of H3K79me2 and H4K20me1 histone marks compared to slower elongating genes. Furthermore, high elongation rates had a positive correlation with gene length, low complexity DNA sequence, and distance from the nearest active transcription unit. Features that negatively correlated with elongation rate included the density of exons, long terminal repeats, GC content of the gene, and DNA methylation density in the bodies of genes. Our results suggest that some static gene features influence transcription elongation rates and that cells may alter elongation rates by epigenetic regulation. The BruDRB-seq technique offers new opportunities to interrogate mechanisms of regulation of transcription elongation.

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“…Topotecan and related camptothecin analogs inhibit TOP1 by covalently trapping the enzyme on DNA (2). TOP1 inhibitors also reduce the expression of long genes in cancer cell lines (17)(18)(19), revealing a gene length-dependent component to transcription that is common to several mammalian cell types.…”

mentioning

confidence: 99%

Topoisomerase 1 inhibition reversibly impairs synaptic function

Mabb

Kullmann

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Topotecan is a topoisomerase 1 (TOP1) inhibitor that is used to treat various forms of cancer. We recently found that topotecan reduces the expression of multiple long genes, including many neuronal genes linked to synapses and autism. However, whether topotecan alters synaptic protein levels and synapse function is currently unknown. Here we report that in primary cortical neurons, topotecan depleted synaptic proteins that are encoded by extremely long genes, including Neurexin-1, Neuroligin-1, Cntnap2, and GABA A β3. Topotecan also suppressed spontaneous network activity without affecting resting membrane potential, action potential threshold, or neuron health. Topotecan strongly suppressed inhibitory neurotransmission via pre-and postsynaptic mechanisms and reduced excitatory neurotransmission. The effects on synaptic protein levels and inhibitory neurotransmission were fully reversible upon drug washout. Collectively, our findings suggest that TOP1 controls the levels of multiple synaptic proteins and is required for normal excitatory and inhibitory synaptic transmission.synapse | topoisomerase | transcription T opoisomerase inhibitors such as topotecan (Hycamtin) are widely used to treat multiple forms of cancer, including brain metastases, ovarian cancer, and small cell lung cancer (1). Topoisomerases resolve DNA supercoiling during cell division and during gene transcription (2). Type I topoisomerases, encoded by Top1, Top3a, and Top3b in mammals, resolve supercoiling by cleaving a single strand of DNA, whereas type II topoisomerases, encoded by Top2a and Top2b, cleave both DNA strands (2). Recently, both types of topoisomerases were associated with neurodevelopment (3-5). For instance, topoisomerase 1 (TOP1) and topoisomerase 2 (TOP2) inhibitors transcriptionally up-regulate the paternal copy of Ubiquitin-protein ligase E3A (Ube3a) (5), a gene that affects synaptic activity and that is deleted or duplicated in distinct neurodevelopmental disorders (Angelman syndrome and autism, respectively) (6, 7). Moreover, a de novo mutation in Top1 and de novo mutations in genes that interact with Top1 and Top3b were identified recently in patients with autism (8, 9), whereas deletion of Top3b increases the risk for schizophrenia and intellectual disability (10, 11). Top2b is also required for axon outgrowth in different regions of the nervous system and for the survival of postmitotic neurons (12-15).TOP1 is localized primarily in the nucleus of postmitotic neurons and is expressed throughout the developing and adult brain (16), suggesting a nuclear function. Indeed, we recently found that topotecan, a selective TOP1 inhibitor, reduced the expression of extremely long genes (>200 kb) in postmitotic neurons by impairing transcription elongation (17). Topotecan and related camptothecin analogs inhibit TOP1 by covalently trapping the enzyme on DNA (2). TOP1 inhibitors also reduce the expression of long genes in cancer cell lines (17-19), revealing a gene length-dependent component to transcription that is common to sev...

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Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

Cited by 29 publications

References 24 publications

Zylka et al. reply

Zylka et al. reply

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

Topoisomerase 1 inhibition reversibly impairs synaptic function

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