1
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Tabe-Bordbar S, Sinha S. Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention. BMC Genomics 2023; 24:395. [PMID: 37442953 DOI: 10.1186/s12864-023-09498-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Many long non-coding RNAs, known to be involved in transcriptional regulation, are enriched in the nucleus and interact with chromatin. However, their mechanisms of chromatin interaction and the served cellular functions are poorly understood. We sought to characterize the mechanisms of lncRNA nuclear retention by systematically mapping the sequence and chromatin features that distinguish lncRNA-interacting genomic segments. RESULTS We found DNA 5-mer frequencies to be predictive of chromatin interactions for all lncRNAs, suggesting sequence-specificity as a global theme in the interactome. Sequence features representing protein-DNA and protein-RNA binding motifs revealed potential mechanisms for specific lncRNAs. Complementary to these global themes, transcription-related features and DNA-RNA triplex formation potential were noted to be highly predictive for two mutually exclusive sets of lncRNAs. DNA methylation was also noted to be a significant predictor, but only when combined with other epigenomic features. CONCLUSIONS Taken together, our statistical findings suggest that a group of lncRNAs interacts with transcriptionally inactive chromatin through triplex formation, whereas another group interacts with transcriptionally active regions and is involved in DNA Damage Response (DDR) through formation of R-loops. Curiously, we observed a strong pattern of enrichment of 5-mers in four potentially interacting entities: lncRNA-bound DNA tiles, lncRNAs, miRNA seed sequences, and repeat elements. This finding points to a broad sequence-based network of interactions that may underlie regulation of fundamental cellular functions. Overall, this study reveals diverse sequence and chromatin features related to lncRNA-chromatin interactions, suggesting potential mechanisms of nuclear retention and regulatory function.
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Affiliation(s)
- Shayan Tabe-Bordbar
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Saurabh Sinha
- Department of Biomedical Engineering, Georgia Institute of Technology, UAW 3108, 313 Ferst Drive NW, Atlanta, GA, 30332, USA.
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2
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Lin TC, Liu YL, Liu YT, Liu WH, Liu ZY, Chang KL, Chang CY, Ni HC, Huang JH, Tsai HK. TRIPBASE: a database for identifying the human genomic DNA and lncRNA triplexes. NAR Genom Bioinform 2023; 5:lqad043. [PMID: 37223317 PMCID: PMC10202427 DOI: 10.1093/nargab/lqad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/04/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Long-non-coding RNAs (lncRNAs) are defined as RNA sequences which are >200 nt with no coding capacity. These lncRNAs participate in various biological mechanisms, and are widely abundant in a diversity of species. There is well-documented evidence that lncRNAs can interact with genomic DNAs by forming triple helices (triplexes). Previously, several computational methods have been designed based on the Hoogsteen base-pair rule to find theoretical RNA-DNA:DNA triplexes. While powerful, these methods suffer from a high false-positive rate between the predicted triplexes and the biological experiments. To address this issue, we first collected the experimental data of genomic RNA-DNA triplexes from antisense oligonucleotide (ASO)-mediated capture assays and used Triplexator, the most widely used tool for lncRNA-DNA interaction, to reveal the intrinsic information on true triplex binding potential. Based on the analysis, we proposed six computational attributes as filters to improve the in-silico triplex prediction by removing most false positives. Further, we have built a new database, TRIPBASE, as the first comprehensive collection of genome-wide triplex predictions of human lncRNAs. In TRIPBASE, the user interface allows scientists to apply customized filtering criteria to access the potential triplexes of human lncRNAs in the cis-regulatory regions of the human genome. TRIPBASE can be accessed at https://tripbase.iis.sinica.edu.tw/.
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Affiliation(s)
| | | | | | - Wan-Hsin Liu
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Zong-Yan Liu
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Kai-Li Chang
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Chin-Yao Chang
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Hung Chih Ni
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Jia-Hsin Huang
- Correspondence may also be addressed to Jia-Hsin Huang. Tel: +886 2 2788 3799 (Ext 1475); Fax: +886 2 2651 9574;
| | - Huai-Kuang Tsai
- To whom correspondence should be addressed. Tel: +886 2 2788 3799 (Ext 1718); Fax: +886 2 2782 4814;
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3
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Cicconetti C, Lauria A, Proserpio V, Masera M, Tamburrini A, Maldotti M, Oliviero S, Molineris I. 3plex enables deep computational investigation of triplex forming lncRNAs. Comput Struct Biotechnol J 2023; 21:3091-3102. [PMID: 37273849 PMCID: PMC10236371 DOI: 10.1016/j.csbj.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression through different molecular mechanisms, including DNA binding via the formation of RNA:DNA:DNA triple helices (TPXs). Despite the increasing amount of experimental evidence, TPXs investigation remains challenging. Here we present 3plex, a software able to predict TPX interactions in silico. Given an RNA sequence and a set of DNA sequences, 3plex integrates 1) Hoogsteen pairing rules that describe the biochemical interactions between RNA and DNA nucleotides, 2) RNA secondary structure prediction and 3) determination of the TPX thermal stability derived from a collection of TPX experimental evidences. We systematically collected and uniformly re-analysed published experimental lncRNA binding sites on human and mouse genomes. We used these data to evaluate 3plex performance and showed that its specific features allow a reliable identification of TPX interactions. We compared 3plex with the other available software and obtained comparable or even better accuracy at a fraction of the computation time. Interestingly, by inspecting collected data with 3plex we found that TPXs tend to be shorter and more degenerated than previously expected and that the majority of analysed lncRNAs can directly bind to the genome by TPX formation. Those results suggest that an important fraction of lncRNAs can exert its biological function through this mechanism. The software is available at https://github.com/molinerisLab/3plex.
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Affiliation(s)
- Chiara Cicconetti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Andrea Lauria
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Valentina Proserpio
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Marco Masera
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Annalaura Tamburrini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Ivan Molineris
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
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4
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Kohestani H, Wereszczynski J. The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics. Biophys J 2023; 122:1229-1239. [PMID: 36798026 PMCID: PMC10111275 DOI: 10.1016/j.bpj.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 01/22/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Noncoding RNAs (ncRNAs) are an emerging epigenetic factor and have been recognized as playing a key role in many gene expression pathways. Structurally, binding of ncRNAs to isolated DNA is strongly dependent on sequence complementary and results in the formation of an RNA.DNA-DNA (RDD) triple helix. However, in vivo DNA is not isolated but is rather packed in chromatin fibers, the fundamental unit of which is the nucleosome. Biochemical experiments have shown that ncRNA binding to nucleosomal DNA is elevated at DNA entry and exit sites and is dependent on the presence of the H3 N-terminal tails. However, the structural and dynamical bases for these mechanisms remain unknown. Here, we have examined the mechanisms and effects of RDD formation in the context of the nucleosome using a series of all-atom molecular dynamics simulations. Results highlight the importance of DNA sequence on complex stability, elucidate the effects of the H3 tails on RDD structures, show how RDD formation impacts the structure and dynamics of the H3 tails, and show how RNA alters the local and global DNA double-helical structure. Together, our results suggest ncRNAs can modify nucleosome, and potentially higher-order chromatin, structures and dynamics as a means of exerting epigenetic control.
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Affiliation(s)
- Havva Kohestani
- Department of Biology, Illinois Institute of Technology, Chicago, Illinois
| | - Jeff Wereszczynski
- Departments of Physics & Biology, Illinois Institute of Technology, Chicago, Illinois.
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5
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Abstract
The human genome carries a vast amount of information within its DNA sequences. The chemical bases A, T, C, and G are the basic units of information content, that are arranged into patterns and codes. Expansive areas of the genome contain codes that are not yet well understood. To decipher these, mathematical and computational tools are applied here to study genomic signatures or general designs of sequences. A novel binary components analysis is devised and utilized. This seeks to isolate the physical and chemical properties of DNA bases, which reveals sequence design and function. Here, information theory tools break down the information content within DNA bases, in order to study them in isolation for their genomic signatures and non-random properties. In this way, the RY (purine/pyrimidine), WS (weak/strong), and KM (keto/amino) general designs are observed in the sequences. The results show that RY, KM, and WS components have a similar and stable overall profile across all human chromosomes. It reveals that the RY property of a sequence is most distant from randomness in the human genome with respect to the genomic signatures. This is true across all human chromosomes. It is concluded that there exists a widespread potential RY code, and furthermore, that this is likely a structural code. Ascertaining this feature of general design, and potential RY structural code has far-reaching implications. This is because it aids in the understanding of cell biology, growth, and development, as well as downstream in the study of human disease and potential drug design.
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6
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Bezzecchi E, Pagani G, Forte B, Percio S, Zaffaroni N, Dolfini D, Gandellini P. MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism. Front Cell Dev Biol 2022; 10:909097. [PMID: 35784469 PMCID: PMC9247157 DOI: 10.3389/fcell.2022.909097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/31/2022] [Indexed: 01/11/2023] Open
Abstract
Aside serving as host gene for miR-205, MIR205HG transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as LEADR (Long Epithelial Alu-interacting Differentiation-related RNA). We previously showed the presence of Alu sequences in the promoters of genes modulated upon MIR205HG/LEADR manipulation. Notably, an Alu element also spans the first and second exons of MIR205HG/LEADR, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map MIR205HG/LEADR chromatin occupancy at genome-wide level in prostate basal cells. Our results confirmed preferential binding to regions proximal to gene transcription start site (TSS). Moreover, enrichment of triplex-forming sequences was found upstream of MIR205HG/LEADR-bound genes, peaking at −1,500/−500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within MIR205HG/LEADR sequence, located just upstream of the Alu element. Notably, triplex-forming regions of bound genes were themselves enriched in Alu elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which MIR205HG/LEADR selects and physically interacts with target DNA, from the other that direct or protein-mediated Alu (RNA)/Alu (DNA) interaction may represent a further functional requirement. We also found that triplex-forming regions were enriched in specific histone modifications, including H3K4me1 in the absence of H3K27ac, H3K4me3 and H3K27me3, indicating that in prostate basal cells MIR205HG/LEADR may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep MIR205HG/LEADR target genes repressed but, at the same time, responsive to differentiation cues.
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Affiliation(s)
- Eugenia Bezzecchi
- Department of Biosciences, University of Milan, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Pagani
- Department of Biosciences, University of Milan, Milan, Italy
| | - Barbara Forte
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Percio
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, Milan, Italy
- *Correspondence: Paolo Gandellini,
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7
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Ryabykh GK, Mylarshchikov DE, Kuznetsov SV, Sigorskikh AI, Ponomareva TY, Zharikova AA, Mironov AA. RNA–Chromatin Interactome: What? Where? When? Mol Biol 2022. [DOI: 10.1134/s0026893322020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Ogunleye AJ, Romanova E, Medvedeva YA. Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia. F1000Res 2021; 10:204. [PMID: 34557292 PMCID: PMC8444155 DOI: 10.12688/f1000research.28146.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by genetic and epigenetic aberrations that alter the differentiation capacity of myeloid progenitor cells. The transcription factor
CEBPα is frequently mutated in AML patients leading to an increase in DNA methylation in many genomic locations. Previously, it has been shown that
ecCEBPα (extra coding CEBP
α) - a lncRNA transcribed in the same direction as
CEBPα gene - regulates DNA methylation of
CEBPα promoter in
cis. Here, we hypothesize that
ecCEBPα could participate in the regulation of DNA methylation in
trans. Method: First, we retrieved the methylation profile of AML patients with mutated
CEBPα locus from The Cancer Genome Atlas (TCGA). We then predicted the
ecCEBPα secondary structure in order to check the potential of
ecCEBPα to form triplexes around CpG loci and checked if triplex formation influenced CpG methylation, genome-wide. Results: Using DNA methylation profiles of AML patients with a mutated
CEBPα locus, we show that
ecCEBPα could interact with DNA by forming DNA:RNA triple helices and protect regions near its binding sites from global DNA methylation. Further analysis revealed that triplex-forming oligonucleotides in
ecCEBPα are structurally unpaired supporting the DNA-binding potential of these regions.
ecCEBPα triplexes supported with the RNA-chromatin co-localization data are located in the promoters of leukemia-linked transcriptional factors such as MLF2. Discussion: Overall, these results suggest a novel regulatory mechanism for
ecCEBPα as a genome-wide epigenetic modulator through triple-helix formation which may provide a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.
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Affiliation(s)
- Adewale J Ogunleye
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Ekaterina Romanova
- Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, Russian Federation
| | - Yulia A Medvedeva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russian Federation.,Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, Russian Federation
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9
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RNA:DNA triple helices: from peculiar structures to pervasive chromatin regulators. Essays Biochem 2021; 65:731-740. [PMID: 33835128 DOI: 10.1042/ebc20200089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022]
Abstract
The genomes of complex eukaryotes largely contain non-protein-coding DNA, which is pervasively transcribed into a plethora of non-coding RNAs (ncRNAs). The functional importance of many of these ncRNAs has been investigated in the last two decades, revealing their crucial and multifaceted roles in chromatin regulation. A common mode of action of ncRNAs is the recruitment of chromatin modifiers to specific regions in the genome. Whereas many ncRNA-protein interactions have been characterised in detail, binding of ncRNAs to their DNA target sites is much less understood. Recently developed RNA-centric methods have mapped the genome-wide distribution of ncRNAs, however, how ncRNAs achieve locus-specificity remains mainly unresolved. In terms of direct RNA-DNA interactions, two kinds of triple-stranded structures can be formed: R-loops consisting of an RNA:DNA hybrid and a looped out DNA strand, and RNA:DNA triple helices (triplexes), in which the RNA binds to the major groove of the DNA double helix by sequence-specific Hoogsteen base pairing. In this essay, we will review the current knowledge about RNA:DNA triplexes, summarising triplex formation rules, detection methods, and ncRNAs reported to engage in triplexes. While the functional characterisation of RNA:DNA triplexes is still anecdotal, recent advances in high-throughput and computational analyses indicate their widespread distribution in the genome. Thus, we are witnessing a paradigm shift in the appreciation of RNA:DNA triplexes, away from exotic structures towards a prominent mode of ncRNA-chromatin interactions.
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10
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Ducoli L, Agrawal S, Sibler E, Kouno T, Tacconi C, Hon CC, Berger SD, Müllhaupt D, He Y, Kim J, D'Addio M, Dieterich LC, Carninci P, de Hoon MJL, Shin JW, Detmar M. LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C. Nat Commun 2021; 12:925. [PMID: 33568674 PMCID: PMC7876020 DOI: 10.1038/s41467-021-21217-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. There is ample evidence that distinct types of vasculature undergo tight transcriptional control to preserve their structure, identity, and functions. We determine a comprehensive map of lineage-specific lncRNAs in human dermal lymphatic and blood vascular endothelial cells (LECs and BECs), combining RNA-Seq and CAGE-Seq. Subsequent antisense oligonucleotide-knockdown transcriptomic profiling of two LEC- and two BEC-specific lncRNAs identifies LETR1 as a critical gatekeeper of the global LEC transcriptome. Deep RNA-DNA, RNA-protein interaction studies, and phenotype rescue analyses reveal that LETR1 is a nuclear trans-acting lncRNA modulating, via key epigenetic factors, the expression of essential target genes, including KLF4 and SEMA3C, governing the growth and migratory ability of LECs. Together, our study provides several lines of evidence supporting the intriguing concept that every cell type expresses precise lncRNA signatures to control lineage-specific regulatory programs.
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Affiliation(s)
- Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
- Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Eliane Sibler
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
- Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Carlotta Tacconi
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Chung-Chao Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Simone D Berger
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Daniela Müllhaupt
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Yuliang He
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
- Molecular and Translational Biomedicine PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Jihye Kim
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Marco D'Addio
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Lothar C Dieterich
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
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11
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Amjadi-Moheb F, Paniri A, Akhavan-Niaki H. Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer Therapy. Cancer Res 2021; 81:1925-1936. [PMID: 33472888 DOI: 10.1158/0008-5472.can-20-3613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
MYC is embedded in the transcriptional oasis of the 8q24 gene desert. A plethora of genomic elements has roles in MYC aberrant expression in cancer development by interacting with transcription factors and epigenetics regulators as well as altering the structure of chromatin at the MYC locus and tissue-specific long-range enhancer-promoter contacts. Furthermore, MYC is a master regulator of several human cancers by modulating the transcription of numerous cancer-related genes through epigenetic mechanisms. This review provides a comprehensive overview of the three-dimensional genomic organization around MYC and the role of epigenetic machinery in transcription and function of MYC as well as discusses various epigenetic-targeted therapeutic strategies in MYC-driven cancers.
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Affiliation(s)
- Fatemeh Amjadi-Moheb
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Alireza Paniri
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Haleh Akhavan-Niaki
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
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12
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Bioinformatics Methods in Medical Genetics and Genomics. Int J Mol Sci 2020; 21:ijms21176224. [PMID: 32872128 PMCID: PMC7504073 DOI: 10.3390/ijms21176224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally presented at the “Centenary of Human Population Genetics” Conference-2019, in Moscow. Here we present some recent developments in computational methods tested on actual medical genetics problems dissected through genomics, transcriptomics and proteomics data analysis, gene networks, protein–protein interactions and biomedical literature mining. We have selected materials based on systems biology approaches, database mining. These methods and algorithms were discussed at the Digital Medical Forum-2019, organized by I.M. Sechenov First Moscow State Medical University presenting bioinformatics approaches for the drug targets discovery in cancer, its computational support, and digitalization of medical research, as well as at “Systems Biology and Bioinformatics”-2019 (SBB-2019) Young Scientists School in Novosibirsk, Russia. Selected recent advancements discussed at these events in the medical genomics and genetics areas are based on novel bioinformatics tools.
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