| 1. |
- Mondal, Tanmoy, 1981, et al.
(author)
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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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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Journal article (peer-reviewed)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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| 2. |
- Ali, Mohamad Moustafa, et al.
(author)
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PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
- 2018
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1
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Journal article (peer-reviewed)abstract
- Despite improvement in our understanding of long noncoding RNAs (lncRNAs) role in cancer, efforts to find clinically relevant cancer-associated lncRNAs are still lacking. Here, using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets. Systematic clinical investigation of 14 Pan-Cancer data sets identified 633 independent prognostic markers. Silencing of the top differentially expressed and clinically relevant S-phase-enriched lncRNAs in several cancer models affects crucial cancer cell hallmarks. Mechanistic investigations on SCAT7 in multiple cancer types reveal that it interacts with hnRNPK/YBX1 complex and affects cancer cell hallmarks through the regulation of FGF/FGFR and its downstream PI3K/AKT and MAPK pathways. We also implement a LNA-antisense oligo-based strategy to treat cancer cell line and patient-derived tumor (PDX) xenografts. Thus, this study provides a comprehensive list of lncRNA-based oncogenic drivers with potential prognostic value.
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| 3. |
- Ma, Haixia, et al.
(author)
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The transcription factor Foxp1 regulates aerobic glycolysis in adipocytes and myocytes
- 2023
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In: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 299:6
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Journal article (peer-reviewed)abstract
- In recent years, lactate has been recognized as an important circulating energy substrate rather than only a dead-end metabolic waste product generated during glucose oxidation at low levels of oxygen. The term "aerobic glycolysis" has been coined to denote increased glucose uptake and lactate pro-duction despite normal oxygen levels and functional mito-chondria. Hence, in "aerobic glycolysis," lactate production is a metabolic choice, whereas in "anaerobic glycolysis," it is a metabolic necessity based on inadequate levels of oxygen. Interestingly, lactate can be taken up by cells and oxidized to pyruvate and thus constitutes a source of pyruvate that is in-dependent of insulin. Here, we show that the transcription factor Foxp1 regulates glucose uptake and lactate production in adipocytes and myocytes. Overexpression of Foxp1 leads to increased glucose uptake and lactate production. In addition, protein levels of several enzymes in the glycolytic pathway are upregulated, such as hexokinase 2, phosphofructokinase, aldolase, and lactate dehydrogenase. Using chromatin immu-noprecipitation and real-time quantitative PCR assays, we demonstrate that Foxp1 directly interacts with promoter consensus cis-elements that regulate expression of several of these target genes. Conversely, knockdown of Foxp1 suppresses these enzyme levels and lowers glucose uptake and lactate production. Moreover, mice with a targeted deletion of Foxp1 in muscle display systemic glucose intolerance with decreased muscle glucose uptake. In primary human adipocytes with induced expression of Foxp1, we find increased glycolysis and glycolytic capacity. Our results indicate Foxp1 may play an important role as a regulator of aerobic glycolysis in adipose tissue and muscle.
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| 4. |
- Mahale, Sagar, et al.
(author)
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HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells.
- 2022
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other's transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.
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| 5. |
- Matthieu, Meryet-Figuiere, et al.
(author)
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Temporal separation of replication and transcription during S-phase progression.
- 2014
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In: Cell Cycle. - : Informa UK Limited. - 1538-4101 .- 1551-4005. ; 13:20, s. 3241-3248
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Journal article (peer-reviewed)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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| 6. |
- Mitra, Sanhita, et al.
(author)
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Subcellular distribution of p53 by the p53-responsive lncRNA NBAT1 determines chemotherapeutic response in neuroblastoma.
- 2021
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In: Cancer research. - 1538-7445. ; 81:6, s. 1457-1471
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Journal article (peer-reviewed)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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| 7. |
- Mondal, Tanmoy, 1981, et al.
(author)
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Chromatin RNA Immunoprecipitation (ChRIP).
- 2017
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In: Methods in molecular biology. - New York, NY : Humana Press. - 1940-6029. - 9781493973798 ; , s. 65-76
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Book chapter (peer-reviewed)abstract
- Researchers have recently had a growing interest in understanding the functional role of long noncoding RNAs (lncRNAs) in chromatin organization. Accumulated evidence suggests lncRNAs could act as interphase molecules between chromatin and chromatin remodelers to define the epigenetic code. However, it is not clear how lncRNAs target chromatin remodelers to specific chromosomal regions in order to establish a functionally distinct epigenetic state of chromatin. We developed and optimized chromatin RNA immunoprecipitation (ChRIP) technology to characterize the lncRNAs associated with active and inactive chromatin compartments. Use of ChRIP to identify chromatin-bound lncRNA will further improve our knowledge regarding the functional role of lncRNAs in establishing epigenetic modifications of chromatin.
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| 8. |
- Mondal, Tanmoy, 1981, et al.
(author)
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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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In: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 33:3, s. 417-434.e7
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Journal article (peer-reviewed)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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| 9. |
- Pandey, Gaurav Kumar, et al.
(author)
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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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In: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 26:5, s. 722-737
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Journal article (peer-reviewed)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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| 10. |
- Subhash, Santhilal, 1987
(author)
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Chromatin and transcriptome-based integrative approaches to profile functional long noncoding RNAs - A computational approach
- 2020
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Doctoral thesis (other academic/artistic)abstract
- One of the major hallmarks of cancer is aberrant or uncontrollable cell division, which occurs due to a defective cell cycle process. During the synthesis phase (S-phase) of the cell cycle, before cell division or mitosis phase, the DNA in the cell makes a new copy to pass on genetic information to the daughter cells. Therefore, S-phase is one of the crucial steps for a successful cell division to occur. The DNA in the nucleus is wrapped around a set of proteins called histones, forming nucleosomes, and multiple nucleosomes give rise to the higher-order chromatin structure. This well-established chromatin structure determines which portion of DNA or gene gets activated or suppressed by switching between open or closed chromatin states. Tri- or di-methylation of lysine 4 from histone 3 (H3K4me2/3) leads to open chromatin, which in turn promotes active gene transcription. The product of gene transcription is either protein-coding mRNA that translates into protein for its function or noncoding RNA, which do not code for any protein and function as RNA. However, the human genome project has identified that protein-coding genes only constitute 2% of the genome, and the vast majority of it is noncoding. Unlike protein-coding genes, the significance of RNAs transcribed from the noncoding genome is not well-established. Apart from housekeeping noncoding RNAs (rRNA, tRNA, snRNA, and snoRNA) and microRNAs (miRNAs), most functional noncoding RNAs fall into the long noncoding RNA (lncRNA) category. In this thesis, we implemented comprehensive computational approaches to identify functionally relevant lncRNAs by analyzing chromatin and transcriptome-based sequencing datasets. In the first study (paper I), using a transcriptome approach, we profiled lncRNAs associated with the S-phase stage of the cell cycle. We demonstrated the oncogenic properties of various S-phase associated lncRNAs in multiple cancers. Earlier, studies proposed that chromatin-associated RNAs, with the help of chromatin-modifying enzymes, determines the active/open or close chromatin status to promote or suppress gene transcription. Hence, in the second study (paper II), we used chromatin-based approaches to propose a possible mechanism through which the active chromatin- associated lncRNAs may function. We show that active chromatin-associated lncRNAs regulate their partner genes in-cis by recruiting the WDR5 chromatin modifier to establish an open chromatin structure at the partner protein-coding gene promoters. In our third study (paper III), we integrated both transcriptome and chromatin-based approaches to find early development-associated lncRNAs. Here, we focused on tracing the molecular footprints of sperm lncRNAs throughout the stages of organismal development. For this purpose, we integrated datasets from gametes, preimplantation and post-implantation stages of an embryo. Interestingly, we observed distinct chromatin structures in the sperm. Also, sperm lncRNAs were active during the onset of zygotic genome activation in the preimplantation stages and in cancers. In summary, this study reveals a unique set of sperm-specific lncRNAs that are temporally activated during preimplantation stages and also aberrantly expressed in multiple cancers. Overall, the present thesis provides an extensive catalogue of functionally relevant lncRNAs that can take part in cell cycle regulation, cancer, chromatin modulation, and organism development. Our studies can serve as a comprehensive resource for future investigations on lncRNAs.
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