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Roy SS, Bagri S, Vinayagamurthy S, Sengupta A, Then CR, Kumar R, Sridharan S, Chowdhury S. Artificially inserted strong promoter containing multiple G-quadruplexes induces long-range chromatin modification. eLife 2024; 13:RP96216. [PMID: 39158543 PMCID: PMC11333042 DOI: 10.7554/elife.96216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
Although the role of G-quadruplex (G4) DNA structures has been suggested in chromosomal looping this was not tested directly. Here, to test causal function, an array of G4s, or control sequence that does not form G4s, were inserted within chromatin in cells. In vivo G4 formation of the inserted G4 sequence array, and not the control sequence, was confirmed using G4-selective antibody. Compared to the control insert, we observed a remarkable increase in the number of 3D chromatin looping interactions from the inserted G4 array. This was evident within the immediate topologically associated domain (TAD) and throughout the genome. Locally, recruitment of enhancer histone marks and the transcriptional coactivator p300/Acetylated-p300 increased in the G4-array, but not in the control insertion. Resulting promoter-enhancer interactions and gene activation were clear up to 5 Mb away from the insertion site. Together, these show the causal role of G4s in enhancer function and long-range chromatin interactions. Mechanisms of 3D topology are primarily based on DNA-bound architectural proteins that induce/stabilize long-range interactions. Involvement of the underlying intrinsic DNA sequence/structure in 3D looping shown here therefore throws new light on how long-range chromosomal interactions might be induced or maintained.
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Affiliation(s)
- Shuvra Shekhar Roy
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Sulochana Bagri
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Soujanya Vinayagamurthy
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Avik Sengupta
- Department of Biotechnology, Indian Institute of Technology HyderabadHyderabadIndia
| | - Claudia Regina Then
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Rahul Kumar
- Department of Biotechnology, Indian Institute of Technology HyderabadHyderabadIndia
| | - Sriram Sridharan
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
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2
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Kumar Halder A, Agarwal A, Jodkowska K, Plewczynski D. A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction. Brief Funct Genomics 2024:elae009. [PMID: 38555493 DOI: 10.1093/bfgp/elae009] [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: 11/28/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
Genomic data analysis has witnessed a surge in complexity and volume, primarily driven by the advent of high-throughput technologies. In particular, studying chromatin loops and structures has become pivotal in understanding gene regulation and genome organization. This systematic investigation explores the realm of specialized bioinformatics pipelines designed specifically for the analysis of chromatin loops and structures. Our investigation incorporates two protein (CTCF and Cohesin) factor-specific loop interaction datasets from six distinct pipelines, amassing a comprehensive collection of 36 diverse datasets. Through a meticulous review of existing literature, we offer a holistic perspective on the methodologies, tools and algorithms underpinning the analysis of this multifaceted genomic feature. We illuminate the vast array of approaches deployed, encompassing pivotal aspects such as data preparation pipeline, preprocessing, statistical features and modelling techniques. Beyond this, we rigorously assess the strengths and limitations inherent in these bioinformatics pipelines, shedding light on the interplay between data quality and the performance of deep learning models, ultimately advancing our comprehension of genomic intricacies.
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Affiliation(s)
- Anup Kumar Halder
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Abhishek Agarwal
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Karolina Jodkowska
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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3
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Severov V, Tsvetkov V, Barinov N, Babenko V, Klinov D, Pozmogova G. Spontaneous DNA Synapsis by Forming Noncanonical Intermolecular Structures. Polymers (Basel) 2022; 14:polym14102118. [PMID: 35632001 PMCID: PMC9144187 DOI: 10.3390/polym14102118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/14/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
We report the spontaneous formation of DNA-DNA junctions in solution in the absence of proteins visualised using atomic force microscopy. The synapsis position fits with potential G-quadruplex (G4) sites. In contrast to the Holliday structure, these conjugates have an affinity for G4 antibodies. Molecular modelling was used to elucidate the possible G4/IM-synaptic complex structures. Our results indicate a new role of the intermolecular noncanonical structures in chromatin architecture and genomic rearrangement.
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Affiliation(s)
- Viacheslav Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Correspondence: (V.S.); (V.T.)
| | - Vladimir Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Institute of Biodesign and Complex System Modeling, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991 Moscow, Russia
- A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky prospect Str. 29, 119991 Moscow, Russia
- Correspondence: (V.S.); (V.T.)
| | - Nikolay Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| | - Vladislav Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| | - Dmitry Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya str.6, 117198 Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
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4
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Jablonski KP, Carron L, Mozziconacci J, Forné T, Hütt MT, Lesne A. Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study. Hum Genomics 2022; 16:2. [PMID: 35016721 PMCID: PMC8753905 DOI: 10.1186/s40246-022-00375-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/02/2022] [Indexed: 01/31/2023] Open
Abstract
Background Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no direct explanation of the mechanisms underlying the association. Based on the recent discovery that changes in three-dimensional genome organization may have functional consequences on gene regulation favoring diseases, we investigated systematically the genome-wide distribution of disease-associated SNPs with respect to a specific feature of 3D genome organization: topologically associating domains (TADs) and their borders. Results For each of 449 diseases, we tested whether the associated SNPs are present in TAD borders more often than observed by chance, where chance (i.e., the null model in statistical terms) corresponds to the same number of pointwise loci drawn at random either in the entire genome, or in the entire set of disease-associated SNPs listed in the GWAS catalog. Our analysis shows that a fraction of diseases displays such a preferential localization of their risk loci. Moreover, cancers are relatively more frequent among these diseases, and this predominance is generally enhanced when considering only intergenic SNPs. The structure of SNP-based diseasome networks confirms that localization of risk loci in TAD borders differs between cancers and non-cancer diseases. Furthermore, different TAD border enrichments are observed in embryonic stem cells and differentiated cells, consistent with changes in topological domains along embryogenesis and delineating their contribution to disease risk. Conclusions Our results suggest that, for certain diseases, part of the genetic risk lies in a local genetic variation affecting the genome partitioning in topologically insulated domains. Investigating this possible contribution to genetic risk is particularly relevant in cancers. This study thus opens a way of interpreting genome-wide association studies, by distinguishing two types of disease-associated SNPs: one with an effect on an individual gene, the other acting in interplay with 3D genome organization. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00375-2.
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Affiliation(s)
- Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Leopold Carron
- Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, CNRS, Sorbonne Université, Paris, France.,Laboratory of Computational and Quantitative Biology, LCQB, Sorbonne Université, Paris, France
| | - Julien Mozziconacci
- Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, CNRS, Sorbonne Université, Paris, France.,Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, Paris, France
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, IGMM, CNRS, Univ. Montpellier, Montpellier, France
| | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany.
| | - Annick Lesne
- Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, CNRS, Sorbonne Université, Paris, France. .,Institut de Génétique Moléculaire de Montpellier, IGMM, CNRS, Univ. Montpellier, Montpellier, France.
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5
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Bystrykh L. Python for gene expression. F1000Res 2021; 10:870. [PMID: 35646329 PMCID: PMC9130758 DOI: 10.12688/f1000research.53842.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 09/05/2024] Open
Abstract
Genome biology shows substantial progress in its analytical and computational part in the last decades. Differential gene expression is one of many computationally intense areas; it is largely developed under R programming language. Here we explain possible reasons for such dominance of R in gene expression data. Next, we discuss the prospects for Python to become competitive in this area of research in coming years. We indicate that Python can be used already in a field of a single cell differential gene expression. We pinpoint still missing parts in Python and possibilities for improvement.
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Affiliation(s)
- Leonid Bystrykh
- ERIBA, University Medical Center Groningen, University of Groningen, Groningen, 9713 AV, The Netherlands
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6
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Bystrykh L. Python for gene expression. F1000Res 2021; 10:870. [PMID: 35646329 PMCID: PMC9130758 DOI: 10.12688/f1000research.53842.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2022] [Indexed: 11/20/2022] Open
Abstract
Genome biology shows substantial progress in its analytical and computational part in the last decades. Differential gene expression is one of many computationally intense areas; it is largely developed under R programming language. Here we explain possible reasons for such dominance of R in gene expression data. Next, we discuss the prospects for Python to become competitive in this area of research in coming years. We indicate that Python can be used already in a field of a single cell differential gene expression. We pinpoint still missing parts in Python and possibilities for improvement.
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Affiliation(s)
- Leonid Bystrykh
- ERIBA, University Medical Center Groningen, University of Groningen, Groningen, 9713 AV, The Netherlands
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7
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Lebedev DV, Egorov VV, Shvetsov AV, Zabrodskaya YA, Isaev-Ivanov VV, Konevega AL. Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521020103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract
The review describes the application of small-angle scattering (SAS) of neutrons and complementary methods to study the structures of biomacromolecules. Here we cover SAS techniques, such as the contrast variation, the neutron spin-echo, and the solution of direct and inverse problems of three-dimensional reconstruction of the structures of macromolecules from SAS spectra by means of molecular modeling. A special section is devoted to specific objects of research, such as supramolecular complexes, influenza virus nucleoprotein, and chromatin.
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8
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Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal AW, Kim Y, Kyle PB, Attipoe E, Johnson AC, Uhl KL, Sirpilla OL, Jahanbakhsh S, Robinson M, Levy S, Valdar W, Garrett MR, Solberg Woods LC. Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model. Sci Rep 2021; 11:2071. [PMID: 33483609 PMCID: PMC7822875 DOI: 10.1038/s41598-021-81550-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023] Open
Abstract
Chronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.
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Affiliation(s)
| | - Jeremy W Prokop
- HudsonAlpha Institute, Huntsville, AL, USA
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Hong He
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Katie Holl
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - John Littrell
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aaron W Deal
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yunjung Kim
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick B Kyle
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Esinam Attipoe
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Ashley C Johnson
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Katie L Uhl
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Olivia L Sirpilla
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Seyedehameneh Jahanbakhsh
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | | | - Shawn Levy
- HudsonAlpha Institute, Huntsville, AL, USA
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael R Garrett
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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9
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Di Giorgio E, Dalla E, Franforte E, Paluvai H, Minisini M, Trevisanut M, Picco R, Brancolini C. Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells. Nucleic Acids Res 2020; 48:646-664. [PMID: 31754707 PMCID: PMC6954409 DOI: 10.1093/nar/gkz1120] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/28/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
Transcriptional networks supervising class IIa HDAC expression are poorly defined. Here we demonstrate that MEF2D is the key factor controlling HDAC9 transcription. This control, which is part of a negative feed-back loop during muscle differentiation, is hijacked in cancer. In leiomyosarcomas the MEF2D/HDAC9 vicious circuit sustains proliferation and cell survival, through the repression of the death receptor FAS. Comprehensive genome-wide studies demonstrate that HDAC4 and HDAC9 control different genetic programs and show both specific and common genomic binding sites. Although the number of MEF2-target genes commonly regulated is similar, only HDAC4 represses many additional genes that are not MEF2D targets. As expected, HDAC4-/- and HDAC9-/- cells increase H3K27ac levels around the TSS of the respective repressed genes. However, these genes rarely show binding of the HDACs at their promoters. Frequently HDAC4 and HDAC9 bind intergenic regions. We demonstrate that these regions, recognized by MEF2D/HDAC4/HDAC9 repressive complexes, show the features of active enhancers. In these regions HDAC4 and HDAC9 can differentially influence H3K27 acetylation. Our studies describe new layers of class IIa HDACs regulation, including a dominant positional effect, and can contribute to explain the pleiotropic actions of MEF2 TFs.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Elisa Franforte
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | | | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Matteo Trevisanut
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Raffaella Picco
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
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10
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Shi T, Guo D, Xu H, Su G, Chen J, Zhao Z, Shi J, Wedemeyer M, Attenello F, Zhang L, Lu W. HOTAIRM1, an enhancer lncRNA, promotes glioma proliferation by regulating long-range chromatin interactions within HOXA cluster genes. Mol Biol Rep 2020; 47:2723-2733. [PMID: 32180085 DOI: 10.1007/s11033-020-05371-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/04/2020] [Indexed: 01/31/2023]
Abstract
The long noncoding RNA HOTAIRM1 reportedly plays important roles in acute myeloid leukemia, gastric cancer and colorectal cancer. Here, we analyzed potential function of HOTAIRM1 in glioma and asked whether it participates in long-range chromatin interactions. We monitored expression of HOTAIRM1 in glioma tissues and correlated levels with patient survival using the TCGA dataset. HOTAIRM1 was highly expressed in glioma tissue, with high levels associated with shortened patient survival time. We then suppressed HOTAIRM1 activity in the human glioblastoma U251 line using CRISPR-cas9 to knock in a truncating polyA fragment. Reporter analysis of these and control cells confirmed that the HOTAIRM1 locus serves as an active enhancer. We then performed Capture-C analysis to identify target genes of that locus and applied RNA antisense purification to assess chromatin interactions between the HOTAIRM1 locus and HOXA cluster genes. HOTAIRM1 knockdown in glioma cells decreased proliferation and reduced expression of HOXA cluster genes. HOTAIRM1 regulates long-range interactions between the HOTAIRM1 locus and HOXA genes. Our work suggests a new mechanism by which HOTAIRM1 regulates glioma progression by regulating high-order chromatin structure and could suggest novel therapeutic targets to treat an intractable cancer.
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Affiliation(s)
- Tengfei Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dianhao Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Heming Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jun Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Michelle Wedemeyer
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Frank Attenello
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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11
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Campbell MJ. Tales from topographic oceans: topologically associated domains and cancer. Endocr Relat Cancer 2019; 26:R611-R626. [PMID: 31505466 PMCID: PMC7664306 DOI: 10.1530/erc-19-0348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 01/03/2023]
Abstract
The 3D organization of the genome within the cell nucleus has come into sharp focus over the last decade. This has largely arisen because of the application of genomic approaches that have revealed numerous levels of genomic and chromatin interactions, including topologically associated domains (TADs). The current review examines how these domains were identified, are organized, how their boundaries arise and are regulated, and how genes within TADs are coordinately regulated. There are many examples of the disruption to TAD structure in cancer and the altered regulation, structure and function of TADs are discussed in the context of hormone responsive cancers, including breast, prostate and ovarian cancer. Finally, some aspects of the statistical insight and computational skills required to interrogate TAD organization are considered and future directions discussed.
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Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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12
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Wang DC, Wang W, Zhang L, Wang X. A tour of 3D genome with a focus on CTCF. Semin Cell Dev Biol 2019; 90:4-11. [PMID: 30031214 DOI: 10.1016/j.semcdb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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Mai S. The three-dimensional cancer nucleus. Genes Chromosomes Cancer 2019; 58:462-473. [PMID: 30536826 DOI: 10.1002/gcc.22720] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
Research into the three-dimensional (3D) organization of the cancer cell genome started over 100 years ago. We follow an exciting avenue of research in this field, from Hansemann's early observations of aberrant mitoses and nuclei in cancer cells in the late 19th century to Boveri's theory of the cancer cell in the early 20th century, to current views of nuclear organization and its changes in cancer. Molecular and imaging methods go hand in hand with providing us with a better understanding of the spatial nature of the cancer cell genome. This has led to the concept that the structural order of the nucleus can be used as cancer cell biomarker.
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Affiliation(s)
- Sabine Mai
- Cell Biology, Research Institute for Oncology and Hematology, CancerCare Manitoba, The University of Manitoba, Winnipeg, Manitoba, Canada
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14
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Blokhina YP, Nguyen AD, Draper BW, Burgess SM. The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio. PLoS Genet 2019; 15:e1007730. [PMID: 30653507 PMCID: PMC6336226 DOI: 10.1371/journal.pgen.1007730] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
Meiosis is a cellular program that generates haploid gametes for sexual reproduction. While chromosome events that contribute to reducing ploidy (homologous chromosome pairing, synapsis, and recombination) are well conserved, their execution varies across species and even between sexes of the same species. The telomere bouquet is a conserved feature of meiosis that was first described nearly a century ago, yet its role is still debated. Here we took advantage of the prominent telomere bouquet in zebrafish, Danio rerio, and super-resolution microscopy to show that axis morphogenesis, synapsis, and the formation of double-strand breaks (DSBs) all take place within the immediate vicinity of telomeres. We established a coherent timeline of events and tested the dependence of each event on the formation of Spo11-induced DSBs. First, we found that the axis protein Sycp3 loads adjacent to telomeres and extends inward, suggesting a specific feature common to all telomeres seeds the development of the axis. Second, we found that newly formed axes near telomeres engage in presynaptic co-alignment by a mechanism that depends on DSBs, even when stable juxtaposition of homologous chromosomes at interstitial regions is not yet evident. Third, we were surprised to discover that ~30% of telomeres in early prophase I engage in associations between two or more chromosome ends and these interactions decrease in later stages. Finally, while pairing and synapsis were disrupted in both spo11 males and females, their reproductive phenotypes were starkly different; spo11 mutant males failed to produce sperm while females produced offspring with severe developmental defects. Our results support zebrafish as an important vertebrate model for meiosis with implications for differences in fertility and genetically derived birth defects in males and females. Inherent to reproduction is the transmission of genetic information from one generation to the next. In sexually reproducing organisms, each parent contributes an equal amount of genetic information, packaged in chromosomes, to the offspring. Diploid organisms, like humans, have two copies of every chromosome, while their haploid gametes (e.g. eggs and sperm) have only one. This reduction in ploidy depends on the segregation of chromosomes during meiosis, resulting in gametes with one copy of each chromosome. Missegregation of the chromosomes in the parents leads to abnormal chromosome numbers in the offspring, which is usually lethal or has detrimental developmental effects. While it has been known for over a century that homologous chromosomes pair and recombine to facilitate proper segregation, how homologs find their partners has remained elusive. A structure that has been central to the discussion of homolog pairing is the bouquet, or the dynamic clustering of telomeres during early stages of meiosis. Here we use zebrafish to show that the telomere bouquet is the site where key events leading to homologous chromosome pairing are coordinated. Furthermore, we show that deletion of spo11, a gene required for proper recombination in most studied organisms, resulted in very different effects in males and females where males were sterile while females produced deformed progeny.
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Affiliation(s)
- Yana P. Blokhina
- Department of Molecular and Cellular Biology, University of California, Davis, CA, United States of America
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, United States of America
| | - An D. Nguyen
- Department of Molecular and Cellular Biology, University of California, Davis, CA, United States of America
| | - Bruce W. Draper
- Department of Molecular and Cellular Biology, University of California, Davis, CA, United States of America
| | - Sean M. Burgess
- Department of Molecular and Cellular Biology, University of California, Davis, CA, United States of America
- * E-mail:
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Kessler H, Jiang K, Jarvis JN. Using Chromatin Architecture to Understand the Genetics and Transcriptomics of Juvenile Idiopathic Arthritis. Front Immunol 2018; 9:2964. [PMID: 30619322 PMCID: PMC6302745 DOI: 10.3389/fimmu.2018.02964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
The presence of abnormal gene expression signatures is a well-described feature of the oligoarticular and polyarticular forms of juvenile idiopathic arthritis. In this review, we discuss how new insights into genetic risk for JIA and the three dimensional architecture of the genome may be used to develop a better understanding of the mechanisms driving these gene expression patterns.
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Affiliation(s)
- Haeja Kessler
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
| | - Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States.,Genetics, Genomics, and Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
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Chromosome positioning and male infertility: it comes with the territory. J Assist Reprod Genet 2018; 35:1929-1938. [PMID: 30229502 DOI: 10.1007/s10815-018-1313-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/11/2018] [Indexed: 01/30/2023] Open
Abstract
The production of functional spermatozoa through spermatogenesis requires a spatially and temporally highly regulated gene expression pattern, which in case of alterations, leads to male infertility. Changes of gene expression by chromosome anomalies, gene variants, and epigenetic alterations have been described as the main genetic causes of male infertility. Recent molecular and cytogenetic approaches have revealed that higher order chromosome positioning is essential for basic genome functions, including gene expression. This review addresses this issue by exposing well-founded evidences which support that alterations on the chromosome topology in spermatogenetic cells leads to defective sperm function and could be considered as an additional genetic cause of male infertility.
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