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Beknazarov N, Jin S, Poptsova M. Deep learning approach for predicting functional Z-DNA regions using omics data. Sci Rep 2020; 10:19134. [PMID: 33154517 PMCID: PMC7644757 DOI: 10.1038/s41598-020-76203-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Computational methods to predict Z-DNA regions are in high demand to understand the functional role of Z-DNA. The previous state-of-the-art method Z-Hunt is based on statistical mechanical and energy considerations about B- to Z-DNA transition using sequence information. Z-DNA CHiP-seq experiment results showed little overlap with Z-Hunt predictions implying that sequence information only is not sufficient to explain emergence of Z-DNA at different genomic locations. Adding epigenetic and other functional genomic mark-ups to DNA sequence level can help revealing the functional Z-DNA sites. Here we take advantage of the deep learning approach that can analyze and extract information from large volumes of molecular biology data. We developed a machine learning approach DeepZ that aggregates information from genome-wide maps of epigenetic markers, transcription factor and RNA polymerase binding sites, and chromosome accessibility maps. With the developed model we not only verify the experimental Z-DNA predictions, but also generate the whole-genome annotation, introducing new possible Z-DNA regions, which have not yet been found in experiments and can be of interest to the researchers from various fields.
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Affiliation(s)
- Nazar Beknazarov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky boulvar, Moscow, Russia, 101000
| | - Seungmin Jin
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky boulvar, Moscow, Russia, 101000
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky boulvar, Moscow, Russia, 101000.
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Quevedo R, Spreafico A, Bruce J, Danesh A, El Ghamrasni S, Giesler A, Hanna Y, Have C, Li T, Yang SYC, Zhang T, Asa SL, Haibe-Kains B, Krzyzanowska M, Smith AC, Singh S, Siu LL, Pugh TJ. Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor. Genome Med 2020; 12:38. [PMID: 32345369 PMCID: PMC7189550 DOI: 10.1186/s13073-020-00730-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/10/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Pancreatic neuroendocrine tumors (PANETs) are rare, slow growing cancers that often present with local and distant metastasis upon detection. PANETS contain distinct karyotypes, epigenetic dysregulation, and recurrent mutations in MEN1, ATRX, and DAXX (MAD+); however, the molecular basis of disease progression remains uncharacterized. METHODS We evaluated associations between aneuploidy and the MAD+ mutational state of 532 PANETs from 11 published genomic studies and 19 new cases using a combination of exome, targeted panel, shallow WGS, or RNA-seq. We mapped the molecular timing of MAD+ PANET progression using cellular fractions corrected for inferred tumor content. RESULTS In 287 PANETs with mutational data, MAD+ tumors always exhibited a highly recurrent signature of loss of heterozygosity (LOH) and copy-number alterations affecting 11 chromosomes, typically followed by genome doubling upon metastasis. These LOH chromosomes substantially overlap with those that undergo non-random mis-segregation due to ectopic CENP-A localization to flanking centromeric regions in DAXX-depleted cell lines. Using expression data from 122 PANETs, we found decreased gene expression in the regions immediately adjacent to the centromere in MAD+ PANETs. Using 43 PANETs from AACR GENIE, we inferred this signature to be preceded by mutations in MEN1, ATRX, and DAXX. We conducted a meta-analysis on 226 PANETs from 8 CGH studies to show an association of this signature with metastatic incidence. Our study shows that MAD+ tumors are a genetically diverse and aggressive subtype of PANETs that display extensive chromosomal loss after MAD+ mutation, which is followed by genome doubling. CONCLUSIONS We propose an evolutionary model for a subset of aggressive PANETs that is initiated by mutation of MEN1, ATRX, and DAXX, resulting in defects in centromere cohesion from ectopic CENP-A deposition that leads to selective loss of chromosomes and the LOH phenotype seen in late-stage metastatic PANETs. These insights aid in disease risk stratification and nominate potential therapeutic vulnerabilities to treat this disease.
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Affiliation(s)
- Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Division of Medical Oncology and Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Jeff Bruce
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Amanda Giesler
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Cherry Have
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tong Zhang
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Sylvia L Asa
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Monika Krzyzanowska
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada
| | - Adam C Smith
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Simron Singh
- Susan Leslie Clinic for Neuroendocrine Cancer, Sunnybrook Odette Cancer Center, Toronto, Ontario, Canada
| | - Lillian L Siu
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Suite 5-718, Toronto, Ontario, M5G 2M9, Canada. .,Division of Medical Oncology and Hematology, University of Toronto, Toronto, Ontario, Canada.
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 9-305, Toronto, Ontario, M5G 1L7, Canada.
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Ling YH, Lin Z, Yuen KWY. Genetic and epigenetic effects on centromere establishment. Chromosoma 2019; 129:1-24. [PMID: 31781852 DOI: 10.1007/s00412-019-00727-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/24/2019] [Accepted: 10/10/2019] [Indexed: 01/19/2023]
Abstract
Endogenous chromosomes contain centromeres to direct equal chromosomal segregation in mitosis and meiosis. The location and function of existing centromeres is usually maintained through cell cycles and generations. Recent studies have investigated how the centromere-specific histone H3 variant CENP-A is assembled and replenished after DNA replication to epigenetically propagate the centromere identity. However, existing centromeres occasionally become inactivated, with or without change in underlying DNA sequences, or lost after chromosomal rearrangements, resulting in acentric chromosomes. New centromeres, known as neocentromeres, may form on ectopic, non-centromeric chromosomal regions to rescue acentric chromosomes from being lost, or form dicentric chromosomes if the original centromere is still active. In addition, de novo centromeres can form after chromatinization of purified DNA that is exogenously introduced into cells. Here, we review the phenomena of naturally occurring and experimentally induced new centromeres and summarize the genetic (DNA sequence) and epigenetic features of these new centromeres. We compare the characteristics of new and native centromeres to understand whether there are different requirements for centromere establishment and propagation. Based on our understanding of the mechanisms of new centromere formation, we discuss the perspectives of developing more stably segregating human artificial chromosomes to facilitate gene delivery in therapeutics and research.
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Affiliation(s)
- Yick Hin Ling
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Zhongyang Lin
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong.
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Uittenbogaard M, Chiaramello A. Novel subcellular localization of the DNA helicase Twinkle at the kinetochore complex during mitosis in neuronal-like progenitor cells. Histochem Cell Biol 2015; 145:275-86. [PMID: 26678504 DOI: 10.1007/s00418-015-1388-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2015] [Indexed: 11/28/2022]
Abstract
During mitosis, the kinetochore, a multi-protein structure located on the centromeric DNA, is responsible for proper segregation of the replicated genome. More specifically, the outer kinetochore complex component Ndc80/Hec1 plays a critical role in regulating microtubule attachment to the spindle for accurate sister chromatid segregation. In addition, DNA helicases play a key contribution for precise and complete disjunction of sister chromatids held together through double-stranded DNA catenations until anaphase. In this study, we focused our attention on the nuclear-encoded DNA helicase Twinkle, which functions as an essential helicase for replication of mitochondrial DNA. It regulates the copy number of the mitochondrial genome, while maintaining its integrity, two processes essential for mitochondrial biogenesis and bioenergetic functions. Although the majority of the Twinkle protein is imported into mitochondria, a small fraction remains cytosolic with an unknown function. In this study, we report a novel expression pattern of Twinkle during chromosomal segregation at distinct mitotic phases. By immunofluorescence microscopy, we found that Twinkle protein colocalizes with the outer kinetochore protein HEC1 as early as prophase until late anaphase in neuronal-like progenitor cells. Thus, our collective results have revealed an unexpected cell cycle-regulated expression pattern of the DNA helicase Twinkle, known for its role in mtDNA replication. Therefore, its recruitment to the kinetochore suggests an evolutionary conserved function for both mitochondrial and nuclear genomic inheritance.
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Affiliation(s)
- Martine Uittenbogaard
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, 2300 I Street N.W., Washington, DC, 20037, USA
| | - Anne Chiaramello
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, 2300 I Street N.W., Washington, DC, 20037, USA.
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Nic-Can G, Hernández-Castellano S, Kú-González A, Loyola-Vargas VM, De-la-Peña C. An efficient immunodetection method for histone modifications in plants. PLANT METHODS 2013; 9:47. [PMID: 24341414 PMCID: PMC3868413 DOI: 10.1186/1746-4811-9-47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/02/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND Epigenetic mechanisms can be highly dynamic, but the cross-talk among them and with the genome is still poorly understood. Many of these mechanisms work at different places in the cell and at different times of organism development. Covalent histone modifications are one of the most complex and studied epigenetic mechanisms involved in cellular reprogramming and development in plants. Therefore, the knowledge of the spatial distribution of histone methylation in different tissues is important to understand their behavior on specific cells. RESULTS Based on the importance of epigenetic marks for biology, we present a simplified, inexpensive and efficient protocol for in situ immunolocalization on different tissues such as flowers, buds, callus, somatic embryo and meristematic tissue from several plants of agronomical and biological importance. Here, we fully describe all the steps to perform the localization of histone modifications. Using this method, we were able to visualize the distribution of H3K4me3 and H3K9me2 without loss of histological integrity of tissues from several plants, including Agave tequilana, Capsicum chinense, Coffea canephora and Cedrela odorata, as well as Arabidopsis thaliana. CONCLUSIONS There are many protocols to study chromatin modifications; however, most of them are expensive, difficult and require sophisticated equipment. Here, we provide an efficient protocol for in situ localization of histone methylation that dispenses with the use of expensive and sensitive enzymes. The present method can be used to investigate the cellular distribution and localization of a wide array of proteins, which could help to clarify the biological role that they play at specific times and places in different tissues of various plant species.
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Affiliation(s)
- Geovanny Nic-Can
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Sara Hernández-Castellano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Angela Kú-González
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
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Du J, Tian Z, Sui Y, Zhao M, Song Q, Cannon SB, Cregan P, Ma J. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean. THE PLANT CELL 2012; 24:21-32. [PMID: 22227891 PMCID: PMC3289580 DOI: 10.1105/tpc.111.092759] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/07/2011] [Accepted: 12/20/2011] [Indexed: 05/18/2023]
Abstract
The evolutionary forces that govern the divergence and retention of duplicated genes in polyploids are poorly understood. In this study, we first investigated the rates of nonsynonymous substitution (Ka) and the rates of synonymous substitution (Ks) for a nearly complete set of genes in the paleopolyploid soybean (Glycine max) by comparing the orthologs between soybean and its progenitor species Glycine soja and then compared the patterns of gene divergence and expression between pericentromeric regions and chromosomal arms in different gene categories. Our results reveal strong associations between duplication status and Ka and gene expression levels and overall low Ks and low levels of gene expression in pericentromeric regions. It is theorized that deleterious mutations can easily accumulate in recombination-suppressed regions, because of Hill-Robertson effects. Intriguingly, the genes in pericentromeric regions-the cold spots for meiotic recombination in soybean-showed significantly lower Ka and higher levels of expression than their homoeologs in chromosomal arms. This asymmetric evolution of two members of individual whole genome duplication (WGD)-derived gene pairs, echoing the biased accumulation of singletons in pericentromeric regions, suggests that distinct genomic features between the two distinct chromatin types are important determinants shaping the patterns of divergence and retention of WGD-derived genes.
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Affiliation(s)
- Jianchang Du
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhixi Tian
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Yi Sui
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
- Institute of Oil Crops, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qijian Song
- U.S. Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center-West, Beltsville, Maryland 20705
| | - Steven B. Cannon
- U.S. Department of Agriculture, Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Ames, Iowa 50011
| | - Perry Cregan
- U.S. Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center-West, Beltsville, Maryland 20705
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
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