| 1. |
- Matthieu, Meryet-Figuiere, et al.
(författare)
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Temporal separation of replication and transcription during S-phase progression.
- 2014
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Ingår i: Cell Cycle. - : Informa UK Limited. - 1538-4101 .- 1551-4005. ; 13:20, s. 3241-3248
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Tidskriftsartikel (refereegranskat)abstract
- Transcriptional events during S-phase are critical for cell cycle progression. Here, by using a nascent RNA capture assay coupled with high-throughput sequencing, we determined the temporal patterns of transcriptional events that occur during S-phase. We show that genes involved in critical S-phase-specific biological processes such as nucleosome assembly and DNA repair have temporal transcription patterns across S-phase that are not evident from total RNA levels. By comparing transcription timing with replication timing in S-phase, we show that early replicating genes show increased transcription late in S-phase whereas late replicating genes are predominantly transcribed early in S-phase. Global anti-correlation between replication and transcription timing was observed only based on nascent RNA but not total RNA. Our data provides a detailed view of ongoing transcriptional events during the S-phase of cell cycle, and supports that transcription and replication are temporally separated.
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| 2. |
- Mitra, Sanhita, et al.
(författare)
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Subcellular distribution of p53 by the p53-responsive lncRNA NBAT1 determines chemotherapeutic response in neuroblastoma.
- 2021
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Ingår i: Cancer research. - 1538-7445. ; 81:6, s. 1457-1471
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Tidskriftsartikel (refereegranskat)abstract
- Neuroblastoma has a low mutation rate for the p53 gene. Alternative ways of p53 inactivation have been proposed in neuroblastoma, such as abnormal cytoplasmic accumulation of wild-type p53. However, mechanisms leading to p53 inactivation via cytoplasmic accumulation are not well investigated. Here we show that the neuroblastoma risk-associated locus 6p22.3-derived tumor suppressor NBAT1 is a p53-responsive lncRNA that regulates p53 subcellular levels. Low expression of NBAT1 provided resistance to genotoxic drugs by promoting p53 accumulation in cytoplasm and loss from mitochondrial and nuclear compartments. Depletion of NBAT1 altered CRM1 function and contributed to the loss of p53-dependent nuclear gene expression during genotoxic drug treatment. CRM1 inhibition rescued p53-dependent nuclear functions and sensitized NBAT1-depleted cells to genotoxic drugs. Combined inhibition of CRM1 and MDM2 was even more effective in sensitizing aggressive neuroblastoma cells with p53 cytoplasmic accumulation. Thus, our mechanistic studies uncover an NBAT1-dependent CRM1/MDM2-based potential combination therapy for high-risk neuroblastoma patients.
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| 3. |
- Mitra, Sanhita
(författare)
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Understanding the role of long non-coding RNAs in neuroblastoma development and progression
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Neuroblastoma (NB), a common cancer of childhood, contributes to 15% of all pediatric cancer deaths. The improper neuronal differentiation of neural crest cells to mature neurons in the sympathetic nervous system leads to NB tumor formation. NB is an extremely heterogeneous disease and high-risk NB is very difficult to treat, with the incidence of relapse in 50% of cases despite of intensive chemotherapeutic treatment. Long non-coding RNAs (lncRNAs) are a class of biological molecules that are transcribed but not translated to any functional protein. The mechanism of functions for these lncRNAs are diverse and context-specific. De-regulation of lncRNAs has been proposed to play a critical role in cancer development and progression. The goal of the current thesis was to identify novel neuroblastoma-specific lncRNAs for better stratification of the disease and characterizing their functional role in greater detail. In the first study, we characterized differentially expressed lncRNAs between low-risk and high-risk NB tumors using transcriptome profiling. Among the differentially expressed lncRNAs, we chose a lncRNA, neuroblastoma associated transcript 1 (NBAT1), that maps to NB hotspot locus, 6p22.3, which has been shown to harbor several NB-specific risk-associated SNPs. We showed that NBAT1 is a tumor suppressor lncRNA and it carries out this tumor suppressor function through regulating cellular proliferation and differentiation. Consistent with its tumor suppressor properties, its higher expression in NB patients predicts a good prognosis. Mechanistically, NBAT1 controls NB cell growth through epigenetically silencing cell proliferating genes, as well as NB cell differentiation by repressing the neuron-restrictive silencer factor NRSF, also known as REST. In the second study, we sought to investigate the functional connection between NBAT1 and its sense partner CASC15 lncRNA in NB development and progression. Like NBAT1, CASC15 harbors NB-specific tumor suppressor properties and its higher expression in NB patients correlates with good clinical outcomes. We show that CASC15/NBAT1 (6p22lncRNAs) promote cell differentiation by the specific regulatory interactions with SOX9 and USP36 located on 17q, which is frequently gained in NB. We could show mechanistically that 6p22lncRNAs dictate SOX9 expression by controlling CHD7 stability via modulating cellular localization of USP36, which is a deubiquitinase. In the third and final study, we found that NBAT1 is a p53 responsive lncRNA and regulates p53 subcellular localization. We observed that a decrease in NBAT1 expression in NB cells results in resistance to genotoxic drugs, which in part occurs due to cytoplasmic p53 accumulation and concomitant loss of p53 dependent gene expression. Higher expression of the p53 exporter CRM1 in NBAT1 depleted cells contributes to p53 cytoplasmic localization, while CRM1 inhibition in these cells restores p53 localization. We observed that combined inhibition of CRM1 and MDM2 sensitized aggressive NB cells with cytoplasmic p53, suggesting that this drug combination could be a potential therapeutic strategy for high-risk NB patients. In summary, these findings highlight the regulatory role of lncRNAs in NB disease development.
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| 4. |
- Mondal, Tanmoy, 1981, et al.
(författare)
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MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells. Using one of the chromatin-interacting lncRNAs, MEG3, we explore the mechanisms by which lncRNAs target chromatin. Here we show that MEG3 and EZH2 share common target genes, including the TGF-β pathway genes. Genome-wide mapping of MEG3 binding sites reveals that MEG3 modulates the activity of TGF-β genes by binding to distal regulatory elements. MEG3 binding sites have GA-rich sequences, which guide MEG3 to the chromatin through RNA–DNA triplex formation. We have found that RNA–DNA triplex structures are widespread and are present over the MEG3 binding sites associated with the TGF-β pathway genes. Our findings suggest that RNA–DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.
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| 5. |
- Mondal, Tanmoy, 1981, et al.
(författare)
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Sense-antisense lncRNA pair encoded by locus 6p22.3 determines neuroblastoma susceptibility via the USP36-CHD7-SOX9 regulatory axis
- 2018
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Ingår i: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 33:3
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Tidskriftsartikel (refereegranskat)abstract
- Trait-associated loci often map to genomic regions encoding long noncoding RNAs (lncRNAs), but the role of these lncRNAs in disease etiology is largely unexplored. We show that a pair of sense/antisense lncRNA (6p22lncRNAs) encoded by CASC15 and NBAT1 located at the neuroblastoma (NB) risk-associated 6p22.3 locus are tumor suppressors and show reduced expression in high-risk NBs. Loss of functional synergy between 6p22lncRNAs results in an undifferentiated state that is maintained by a gene-regulatory network, including SOX9 located on 17q, a region frequently gained in NB. 6p22lncRNAs regulate SOX9 expression by controlling CHD7 stability via modulating the cellular localization of USP36, encoded by another 17q gene. This regulatory nexus between 6p22.3 and 17q regions may lead to potential NB treatment strategies.
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| 6. |
- Oldfors Hedberg, Carola, 1969, et al.
(författare)
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Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia
- 2023
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438.
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Tidskriftsartikel (refereegranskat)abstract
- Ribonuclease inhibitor 1, also known as angiogenin inhibitor 1, encoded by RNH1, is a ubiquitously expressed leucine-rich repeat protein, which is highly conserved in mammalian species. Inactivation of rnh1 in mice causes an embryonically lethal anemia, but the exact biological function of RNH1 in humans remains unknown and no human genetic disease has so far been associated with RNH1. Here, we describe a family with two out of seven siblings affected by a disease characterized by congenital cataract, global developmental delay, myopathy and psychomotor deterioration, seizures and periodic anemia associated with upper respiratory tract infections. A homozygous splice-site variant (c.615-2A > C) in RNH1 segregated with the disease. Sequencing of RNA derived from patient fibroblasts and cDNA analysis of skeletal muscle mRNA showed aberrant splicing with skipping of exon 7. Western blot analysis revealed a total lack of the RNH1 protein. Functional analysis revealed that patient fibroblasts were more sensitive to RNase A exposure, and this phenotype was reversed by transduction with a lentivirus expressing RNH1 to complement patient cells. Our results demonstrate that loss-of-function of RNH1 in humans is associated with a multiorgan developmental disease with recessive inheritance. It may be speculated that the infection-induced deterioration resulted from an increased susceptibility toward extracellular RNases and/or other inflammatory responses normally kept in place by the RNase inhibitor RNH1.
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| 7. |
- Pandey, Gaurav Kumar, et al.
(författare)
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The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation.
- 2014
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Ingår i: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 26:5, s. 722-737
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Tidskriftsartikel (refereegranskat)abstract
- Neuroblastoma is an embryonal tumor of the sympathetic nervous system and the most common extracranial tumor of childhood. By sequencing transcriptomes of low- and high-risk neuroblastomas, we detected differentially expressed annotated and nonannotated long noncoding RNAs (lncRNAs). We identified a lncRNA neuroblastoma associated transcript-1 (NBAT-1) as a biomarker significantly predicting clinical outcome of neuroblastoma. CpG methylation and a high-risk neuroblastoma associated SNP on chromosome 6p22 functionally contribute to NBAT-1 differential expression. Loss of NBAT-1 increases cellular proliferation and invasion. It controls these processes via epigenetic silencing of target genes. NBAT-1 loss affects neuronal differentiation through activation of the neuronal-specific transcription factor NRSF/REST. Thus, loss of NBAT-1 contributes to aggressive neuroblastoma by increasing proliferation and impairing differentiation of neuronal precursors.
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| 8. |
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