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Journal articles on the topic 'Genome conformation'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Wang, Yanbo, John Mallon, Haobo Wang, et al. "Real-time observation of Cas9 postcatalytic domain motions." Proceedings of the National Academy of Sciences 118, no. 2 (2020): e2010650118. http://dx.doi.org/10.1073/pnas.2010650118.

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CRISPR-Cas9 fromStreptococcus pyogenesis an RNA-guided DNA endonuclease, which has become the most popular genome editing tool. Coordinated domain motions of Cas9 prior to DNA cleavage have been extensively characterized but our understanding of Cas9 conformations postcatalysis is limited. Because Cas9 can remain stably bound to the cleaved DNA for hours, its postcatalytic conformation may influence genome editing mechanisms. Here, we use single-molecule fluorescence resonance energy transfer to characterize the HNH domain motions of Cas9 that are coupled with cleavage activity of the target s

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Sanford, Thomas J., Harriet V. Mears, Teodoro Fajardo, Nicolas Locker, and Trevor R. Sweeney. "Circularization of flavivirus genomic RNA inhibits de novo translation initiation." Nucleic Acids Research 47, no. 18 (2019): 9789–802. http://dx.doi.org/10.1093/nar/gkz686.

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Abstract Members of the Flaviviridae family, including dengue virus (DENV) and yellow fever virus, cause serious disease in humans, whilst maternal infection with Zika virus (ZIKV) can induce microcephaly in newborns. Following infection, flaviviral RNA genomes are translated to produce the viral replication machinery but must then serve as a template for the transcription of new genomes. However, the ribosome and viral polymerase proceed in opposite directions along the RNA, risking collisions and abortive replication. Whilst generally linear, flavivirus genomes can adopt a circular conformat

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Shepherd, Jeremiah J., Lingxi Zhou, William Arndt, Yan Zhang, W. Jim Zheng, and Jijun Tang. "Exploring genomes with a game engine." Faraday Discuss. 169 (2014): 443–53. http://dx.doi.org/10.1039/c3fd00152k.

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More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualizat

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Brigham, Benjamin S., Jonathan P. Kitzrow, Joshua-Paolo C. Reyes, Karin Musier-Forsyth, and James B. Munro. "Intrinsic conformational dynamics of the HIV-1 genomic RNA 5′UTR." Proceedings of the National Academy of Sciences 116, no. 21 (2019): 10372–81. http://dx.doi.org/10.1073/pnas.1902271116.

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The highly conserved 5′ untranslated region (5′UTR) of the HIV-1 RNA genome is central to the regulation of virus replication. NMR and biochemical experiments support a model in which the 5′UTR can transition between at least two conformational states. In one state the genome remains a monomer, as the palindromic dimerization initiation site (DIS) is sequestered via base pairing to upstream sequences. In the second state, the DIS is exposed, and the genome is competent for kissing loop dimerization and packaging into assembling virions where an extended dimer is formed. According to this model

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Fujishiro, Shin, Naoko Tokuda, and Masaki Sasai. "2P267 Computational chromosome conformation sampling of human diploid genome(21B. Genome biology:Genome structure,Poster)." Seibutsu Butsuri 54, supplement1-2 (2014): S239. http://dx.doi.org/10.2142/biophys.54.s239_3.

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You, Chuihuai, Tianzhen Cui, Chang Zhang, Shoujian Zang, Yachun Su, and Youxiong Que. "Assembly of the Complete Mitochondrial Genome of Gelsemium elegans Revealed the Existence of Homologous Conformations Generated by a Repeat Mediated Recombination." International Journal of Molecular Sciences 24, no. 1 (2022): 527. http://dx.doi.org/10.3390/ijms24010527.

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Gelsemium elegans (G. elegans) is a Chinese medicinal plant with substantial economic and feeding values. There is a lack of detailed studies on the mitochondrial genome of G. elegans. In this study, the mitochondrial genome of G. elegans was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of G. elegans is represented by two circular chromosomes of 406,009 bp in length with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected 145 pairs of repeats and found that four pairs of repeats could mediate the homologous recombinati

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Bentley, Kirsten, Jonathan P. Cook, Andrew K. Tuplin, and David J. Evans. "Structural and functional analysis of the roles of the HCV 5′ NCR miR122-dependent long-range association and SLVI in genome translation and replication." PeerJ 6 (November 6, 2018): e5870. http://dx.doi.org/10.7717/peerj.5870.

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The hepatitis C virus RNA genome possesses a variety of conserved structural elements, in both coding and non-coding regions, that are important for viral replication. These elements are known or predicted to modulate key life cycle events, such as translation and genome replication, some involving conformational changes induced by long-range RNA–RNA interactions. One such element is SLVI, a stem-loop (SL) structure located towards the 5′ end of the core protein-coding region. This element forms an alternative RNA–RNA interaction with complementary sequences in the 5′ untranslated regions that

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Gu, Bowen, Ruifan Sun, Xingqiang Fang, et al. "Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats." Animals 12, no. 5 (2022): 548. http://dx.doi.org/10.3390/ani12050548.

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Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In

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Bolovan-Fritts, Cynthia A., Edward S. Mocarski, and Jean A. Wiedeman. "Peripheral Blood CD14+ Cells From Healthy Subjects Carry a Circular Conformation of Latent Cytomegalovirus Genome." Blood 93, no. 1 (1999): 394–98. http://dx.doi.org/10.1182/blood.v93.1.394.

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Abstract The majority of the human population harbors latent cytomegalovirus. Although CD14+ peripheral blood mononuclear cells have been implicated as sites of latency, the conformation of the latent viral genome in these cells is unknown. In this study, the conformation of viral genomic DNA was assessed in CD14+ cells from healthy virus seropositive carriers using an electrophoretic separation on native agarose gels in combination with polymerase chain reaction detection. Here we show that the viral genome migrates as a circular plasmid with a mobility equivalent to a circular 230-kb Shigell

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Bolovan-Fritts, Cynthia A., Edward S. Mocarski, and Jean A. Wiedeman. "Peripheral Blood CD14+ Cells From Healthy Subjects Carry a Circular Conformation of Latent Cytomegalovirus Genome." Blood 93, no. 1 (1999): 394–98. http://dx.doi.org/10.1182/blood.v93.1.394.401k44_394_398.

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The majority of the human population harbors latent cytomegalovirus. Although CD14+ peripheral blood mononuclear cells have been implicated as sites of latency, the conformation of the latent viral genome in these cells is unknown. In this study, the conformation of viral genomic DNA was assessed in CD14+ cells from healthy virus seropositive carriers using an electrophoretic separation on native agarose gels in combination with polymerase chain reaction detection. Here we show that the viral genome migrates as a circular plasmid with a mobility equivalent to a circular 230-kb Shigella flexner

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Tjong, Harianto, Wenyuan Li, Reza Kalhor, et al. "Population-based 3D genome structure analysis reveals driving forces in spatial genome organization." Proceedings of the National Academy of Sciences 113, no. 12 (2016): E1663—E1672. http://dx.doi.org/10.1073/pnas.1512577113.

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Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Our approach incorporates the stochastic natu

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Hrebík, Dominik, Tibor Füzik, Mária Gondová, et al. "ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating." Proceedings of the National Academy of Sciences 118, no. 19 (2021): e2024251118. http://dx.doi.org/10.1073/pnas.2024251118.

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Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The

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Cao, Pei, Yuan Huang, Mei Zong, and Zilong Xu. "De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers." Genes 14, no. 2 (2023): 526. http://dx.doi.org/10.3390/genes14020526.

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As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformat

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Haque, Md Azizul, Mohammad Zahangir Alam, Asif Iqbal, Yun-Mi Lee, Chang-Gwon Dang, and Jong-Joo Kim. "Genome-Wide Association Studies for Body Conformation Traits in Korean Holstein Population." Animals 13, no. 18 (2023): 2964. http://dx.doi.org/10.3390/ani13182964.

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The objective of this study was to identify quantitative trait loci (QTL) and nearby candidate genes that influence body conformation traits. Phenotypic data for 24 body conformation traits were collected from a population of 2329 Korean Holstein cattle, and all animals were genotyped using the 50 K Illumina bovine SNP chip. A total of 24 genome-wide significant SNPs associated with 24 body conformation traits were identified by genome-wide association analysis. The selection of the most promising candidate genes was based on gene ontology (GO) terms and the previously identified functions tha

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Keown, Jeremy R., Loïc Carrique, Benjamin E. Nilsson-Payant, Ervin Fodor, and Jonathan M. Grimes. "Structural characterization of the full-length Hantaan virus polymerase." PLOS Pathogens 20, no. 12 (2024): e1012781. https://doi.org/10.1371/journal.ppat.1012781.

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Hantaviridae are a family of segmented negative-sense RNA viruses that contains important human and animal pathogens. Hantaviridae contain a viral RNA-dependent RNA polymerase that replicates and transcribes the viral genome. Here we establish the expression and purification polymerase from the Old World Hantaan virus and characterise the structure using Cryo-EM. We determine a series of structures at resolutions between 2.7 and 3.3 Å of RNA free polymerase comprising the core, core and endonuclease, and a full-length polymerase. The full-length polymerase structure depicts the location of the

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Wlasnowolski, Michal, Michal Sadowski, Tymon Czarnota, et al. "3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome." Nucleic Acids Research 48, W1 (2020): W170—W176. http://dx.doi.org/10.1093/nar/gkaa388.

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Abstract Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue o

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Homma, Kengo, Hiromitsu Takahashi, Naomi Tsuburaya, Isao Naguro, Takao Fujisawa, and Hidenori Ichijo. "Genome-wide siRNA screening reveals that DCAF4-mediated ubiquitination of optineurin stimulates autophagic degradation of Cu,Zn-superoxide dismutase." Journal of Biological Chemistry 295, no. 10 (2020): 3148–58. http://dx.doi.org/10.1074/jbc.ra119.010239.

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Cu, Zn superoxide dismutase (SOD1) is one of the genes implicated in the devastating neurodegenerative disorder amyotrophic lateral sclerosis (ALS). Although the precise mechanisms of SOD1 mutant (SOD1mut)-induced motoneuron toxicity are still unclear, defects in SOD1 proteostasis are known to have a critical role in ALS pathogenesis. We previously reported that the SOD1mut adopts a conformation that exposes a Derlin-1–binding region (DBR) and that DBR-exposed SOD1 interacts with Derlin-1, leading to motoneuron death. We also found that an environmental change, i.e. zinc depletion, induces a c

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Xiao, Ke, Dan Xiong, Gong Chen, et al. "RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription." Science Advances 7, no. 26 (2021): eabf8962. http://dx.doi.org/10.1126/sciadv.abf8962.

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Like most DNA viruses, herpesviruses precisely deliver their genomes into the sophisticatedly organized nuclei of the infected host cells to initiate subsequent transcription and replication. However, it remains elusive how the viral genome specifically interacts with the host genome and hijacks host transcription machinery. Using pseudorabies virus (PRV) as model virus, we performed chromosome conformation capture assays to demonstrate a genome-wide specific trans-species chromatin interaction between the virus and host. Our data show that the PRV genome is delivered by the host DNA binding p

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Totikov, Azamat, Andrey Tomarovsky, Lorena Derezanin, et al. "Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research." Proceedings 76, no. 1 (2020): 10. http://dx.doi.org/10.3390/iecge-07149.

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Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seve

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Nayak, Vinod, Moshe Dessau, Kaury Kucera, Karen Anthony, Michel Ledizet, and Yorgo Modis. "Crystal Structure of Dengue Virus Type 1 Envelope Protein in the Postfusion Conformation and Its Implications for Membrane Fusion." Journal of Virology 83, no. 9 (2009): 4338–44. http://dx.doi.org/10.1128/jvi.02574-08.

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ABSTRACT Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conse

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Zirkel, Anne, and Argyris Papantonis. "Transcription as a force partitioning the eukaryotic genome." Biological Chemistry 395, no. 11 (2014): 1301–5. http://dx.doi.org/10.1515/hsz-2014-0196.

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Abstract Eukaryotic genomes – until recently dealt with as if they were a cohort of linear DNA molecules – are perplexed three-dimensional structures, the exact conformation of which profoundly affects genome function. Recent advances in molecular biology and DNA sequencing technologies have led to a new understanding of the folding of chromatin in the nucleus. Changes in chromatin structure underlie deployment of new gene expression programs during development, differentiation, or disease. In this review, we revisit data pointing to, arguably, the major force that shapes genomes: transcriptio

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Rajarajan, Prashanth, Tyler Borrman, Will Liao, et al. "Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk." Science 362, no. 6420 (2018): eaat4311. http://dx.doi.org/10.1126/science.aat4311.

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To explore the developmental reorganization of the three-dimensional genome of the brain in the context of neuropsychiatric disease, we monitored chromosomal conformations in differentiating neural progenitor cells. Neuronal and glial differentiation was associated with widespread developmental remodeling of the chromosomal contact map and included interactions anchored in common variant sequences that confer heritable risk for schizophrenia. We describe cell type–specific chromosomal connectomes composed of schizophrenia risk variants and their distal targets, which altogether show enrichment

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MacKay, Kimberly, and Anthony Kusalik. "Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data." Briefings in Functional Genomics 19, no. 4 (2020): 292–308. http://dx.doi.org/10.1093/bfgp/elaa004.

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Abstract The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure–function relationship of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assays to predict 3D genome organization (the 3D genome reconstruction problem). Many computational tools have been developed that answer this need, but a comprehensive comparison of their underlying algorithmic approaches has not been conducted.

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Xu, Zhichao, and Jesse R. Dixon. "Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies." Briefings in Functional Genomics 19, no. 2 (2019): 139–50. http://dx.doi.org/10.1093/bfgp/elz026.

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Abstract Genomic analysis of individuals or organisms is predicated on the availability of high-quality reference and genotype information. With the rapidly dropping costs of high-throughput DNA sequencing, this is becoming readily available for diverse organisms and for increasingly large populations of individuals. Despite these advances, there are still aspects of genome sequencing that remain challenging for existing sequencing methods. This includes the generation of long-range contiguity during genome assembly, identification of structural variants in both germline and somatic tissues, t

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Bleker, Svenja, Michael Pawlita, and Jürgen A. Kleinschmidt. "Impact of Capsid Conformation and Rep-Capsid Interactions on Adeno-Associated Virus Type 2 Genome Packaging." Journal of Virology 80, no. 2 (2006): 810–20. http://dx.doi.org/10.1128/jvi.80.2.810-820.2006.

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ABSTRACT Single-stranded genomes of adeno-associated virus (AAV) are packaged into preformed capsids. It has been proposed that packaging is initiated by interaction of genome-bound Rep proteins to the capsid, thereby targeting the genome to the portal of encapsidation. Here we describe a panel of mutants with amino acid exchanges in the pores at the fivefold axes of symmetry on AAV2 capsids with reduced packaging and reduced Rep-capsid interaction. Mutation of two threonines at the rim of the fivefold pore nearly completely abolished Rep-capsid interaction and packaging. This suggests a Rep-b

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Su, Ying-Hsiu, Xianchao Zhang, Xiaohe Wang, Nigel W. Fraser, and Timothy M. Block. "Evidence that the Immediate-Early Gene Product ICP4 Is Necessary for the Genome of the Herpes Simplex Virus Type 1 ICP4 Deletion Mutant Strain d120 To Circularize in Infected Cells." Journal of Virology 80, no. 23 (2006): 11589–97. http://dx.doi.org/10.1128/jvi.01869-06.

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ABSTRACT Following infection, the physical state of linear herpes simplex virus (HSV) genomes may change into an “endless” or circular form. In this study, using Southern blot analysis of the HSV genome, we provide evidence that immediate-early protein ICP4 is involved in the process of converting the linear HSV-1 ICP4-deleted mutant strain d120 genome into its endless form. Under conditions where de novo viral DNA synthesis was inhibited, the genome of the ICP4 deletion mutant d120 failed to assume an endless conformation following infection of Vero cells (compared with the ability of wild-ty

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Laflamme, Mark, and Robert W. Lee. "MITOCHONDRIAL GENOME CONFORMATION AMONG CW-GROUP CHLOROPHYCEAN ALGAE1." Journal of Phycology 39, no. 1 (2003): 213–20. http://dx.doi.org/10.1046/j.1529-8817.2003.02045.x.

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Laflamme, Mark, and Robert W. Lee. "MITOCHONDRIAL GENOME CONFORMATION AMONG CW-GROUP CHLOROPHYCEAN ALGAE." Journal of Phycology 39, no. 2 (2003): 462. http://dx.doi.org/10.1046/j.1529-8817.2003.392031.x.

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Yan, A. P., P. A. Salnikov, M. M. Gridina, P. S. Belokopytova, and V. S. Fishman. "Towards development of the 4c-based method detecting interactions of plasmid dna with host genome." Biohimiâ 89, no. 4 (2024): 612–22. http://dx.doi.org/10.31857/s0320972524040051.

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Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and

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Yost, Kathryn E., Yanding Zhao, King L. Hung, et al. "Three-dimensional genome landscape of primary human cancers." Nature Genetics 57, no. 5 (2025): 1189–200. https://doi.org/10.1038/s41588-025-02188-0.

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Abstract Genome conformation underlies transcriptional regulation by distal enhancers, and genomic rearrangements in cancer can alter critical regulatory interactions. Here we profiled the three-dimensional genome architecture and enhancer connectome of 69 tumor samples spanning 15 primary human cancer types from The Cancer Genome Atlas. We discovered the following three archetypes of enhancer usage for over 100 oncogenes across human cancers: static, selective gain or dynamic rewiring. Integrative analyses revealed the enhancer landscape of noncancer cells in the tumor microenvironment for ge

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Ren, Zhongqing, Constantin N. Takacs, Hugo B. Brandão, Christine Jacobs-Wagner, and Xindan Wang. "Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi." PLOS Genetics 19, no. 7 (2023): e1010857. http://dx.doi.org/10.1371/journal.pgen.1010857.

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Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involv

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Deschepper, Pablo, Sam Vanbergen, Lore Esselens, et al. "A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae)." F1000Research 13 (December 6, 2024): 1492. https://doi.org/10.12688/f1000research.157946.1.

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Here, we present novel high quality genome assemblies for five invasive tephritid species of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (read depths between 65 and 78x). Three assemblies (C. capitata, C. quilicii and Z. cucurbitae) were scaffolded with chromosome conformation data and annotated using RNAseq reads. For some species this is the first reference genome available (B. zonata, C. quilicii and C. rosa), for others we have published improved annotated genomes (C. capitata and Z. cucurbitae). Together, the new references p

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Herbert, Alan. "Training your genome." Open Access Government 46, no. 1 (2025): 110–11. https://doi.org/10.56367/oag-046-11483.

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Training your genome Founder and President of InsideOutBio, Alan Herbert, explores the evolving understanding of genome information storage, and the significance of repetitive sequences called flipons in genome training. These flipons can alter their shape without breaking DNA and are vital in cell biology, especially in responding to environmental stress. Our view of how genomes store information has rapidly changed. In the classical view, codons contain the important content. Each codon consists of three DNA bases uniquely mapped to an amino acid. The order of codons gives the position of am

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Long, Mingxue, Bo Wang, Zhangping Yang, and Xubin Lu. "Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle." Animals 14, no. 15 (2024): 2181. http://dx.doi.org/10.3390/ani14152181.

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Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be con

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Deng, Shaoxiong, Yibin Qiu, Zhanwei Zhuang, et al. "Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population." Animals 13, no. 15 (2023): 2414. http://dx.doi.org/10.3390/ani13152414.

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Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the

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Silva, Emanueli F. P., Rita C. Gaia, Henrique A. Mulim, et al. "Genome-Wide Association Study of Conformation Traits in Brazilian Holstein Cattle." Animals 14, no. 17 (2024): 2472. http://dx.doi.org/10.3390/ani14172472.

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The linear conformation of animals exerts an influence on health, reproduction, production, and welfare, in addition to longevity, which directly affects the profitability of milk-producing farms. The objectives of this study were (1) to perform genome-wide association studies (GWASs) of conformation traits, namely the Rump, Feet and Legs, Mammary System, Dairy Strength, and Final Classification traits, and (2) to identify genes and related pathways involved in physiological processes associated with conformation traits in Brazilian Holstein cattle. Phenotypic and genotypic data from 2339 Hols

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Mitter, Michael, Catherina Gasser, Zsuzsanna Takacs, et al. "Conformation of sister chromatids in the replicated human genome." Nature 586, no. 7827 (2020): 139–44. http://dx.doi.org/10.1038/s41586-020-2744-4.

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Nazarov, Leonid I., Mikhail V. Tamm, Vladik A. Avetisov, and Sergei K. Nechaev. "A statistical model of intra-chromosome contact maps." Soft Matter 11, no. 5 (2015): 1019–25. http://dx.doi.org/10.1039/c4sm02519a.

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Zhang, Rong, Jian-Jun Jin, Michael J. Moore, and Ting-Shuang Yi. "Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)." Australian Systematic Botany, 2019. http://dx.doi.org/10.1071/sb19014.

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Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. &amp; C.Fraser, an important medicinal and ornamental species in the Aldinoid clade of Papilionoideae. By mapping paired-end reads, seven hypothetical subgenomic conformations were rejected and two hypothetical complete isometric mitochondrial genome conformations that differed by a 64-kb inver

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Organtini, Lindsey J., Kristin L. Shingler, Robert E. Ashley, et al. "Honey Bee Deformed Wing Virus Structures Reveal that Conformational Changes Accompany Genome Release." Journal of Virology 91, no. 2 (2016). http://dx.doi.org/10.1128/jvi.01795-16.

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ABSTRACT The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and structural details. Here we report the three-dimensional (3-D) structures of DWV capsids isolated from infected honey bees, including the immature procapsid, the genome-filled virion, the putative entry intermediate (A-particle), and the empty capsid that remains after genome release. The capsids are decorated by large spikes around the 5-fold vertices. The 5-fold spikes had an open flower-li

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Qiu, Yueqi, Delong Feng, Wenjuan Jiang, Tingting Zhang, Qianjin Lu, and Ming Zhao. "3D genome organization and epigenetic regulation in autoimmune diseases." Frontiers in Immunology 14 (June 6, 2023). http://dx.doi.org/10.3389/fimmu.2023.1196123.

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Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the r

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Yang, Xin, Yong Liu, Wen Cui, Mengmeng Liu, and Wei Wang. "Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection." RNA, November 16, 2022, rna.079347.122. http://dx.doi.org/10.1261/rna.079347.122.

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During HIV-1 assembly, two copies of viral genomic RNAs (gRNA) are selectively packaged into new viral particles. This process is mediated by specific interactions between HIV-1 Gag and the packaging signals at 5′ RNA leader (5′L). 5′L is able to adopt different conformations, which promotes either gRNA dimerization and packaging or Gag translation. Dimerization and packaging are coupled. Whether the selective packaging of gRNA dimer is due to favorable interactions between Gag and 5′L in packaging conformation is not known. Here, using RNAs mimicking the two 5′L conformers, we show that 5′L c

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Kozlovskii, Igor, and Petr Popov. "Spatiotemporal identification of druggable binding sites using deep learning." Communications Biology 3, no. 1 (2020). http://dx.doi.org/10.1038/s42003-020-01350-0.

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Abstract Identification of novel protein binding sites expands druggable genome and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site identification resemble the object detection problem in computer vision. Here we introduce a computational approach for the large-scale detection of protein binding sites, that considers protein conformations as 3D-images, binding sites as objects on these images to detect, and conformational ensembles of proteins as 3D-videos to analyze. Bi

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Chen, Mengjie, Xingyu Liu, Qingyou Liu, Deshun Shi, and Hui Li. "3D genomics and its applications in precision medicine." Cellular & Molecular Biology Letters 28, no. 1 (2023). http://dx.doi.org/10.1186/s11658-023-00428-x.

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AbstractThree-dimensional (3D) genomics is an emerging discipline that studies the three-dimensional structure of chromatin and the three-dimensional and functions of genomes. It mainly studies the three-dimensional conformation and functional regulation of intranuclear genomes, such as DNA replication, DNA recombination, genome folding, gene expression regulation, transcription factor regulation mechanism, and the maintenance of three-dimensional conformation of genomes. Self-chromosomal conformation capture (3C) technology has been developed, and 3D genomics and related fields have developed

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Qin, Nannan, Shanjie Yang, Yunan Wang, et al. "The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination." Frontiers in Plant Science 15 (August 12, 2024). http://dx.doi.org/10.3389/fpls.2024.1416913.

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IntroductionBottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding.MethodsA hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes.ResultsThe length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes ha

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Li, Tianhao, Mingdong Liu, Zhanxi Gu, et al. "Structures of the mumps virus polymerase complex via cryo-electron microscopy." Nature Communications 15, no. 1 (2024). http://dx.doi.org/10.1038/s41467-024-48389-9.

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AbstractThe viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L–P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has th

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Li, Bingbing, Dan Lin, Xiaoqiao Zhai, et al. "Conformational changes in three-dimensional chromatin structure in Paulownia fortunei after phytoplasma infection." Phytopathology®, June 14, 2021. http://dx.doi.org/10.1094/phyto-01-21-0030-r.

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Abstract Higher-order chromatin structures play important roles in regulating multiple biological processes, growth and development, biotic and abiotic stress response. However, little is known about three-dimensional chromatin structures in Paulownia, or about whole-genome chromatin conformational changes that occur in response to Paulownia witches’ broom (PaWB) disease. We used high-throughput chromosome conformation capture (Hi-C) to obtain genome-wide profiles of chromatin conformation in healthy and phytoplasma-infected Paulownia fortunei genome. The heatmap results indicated that the str

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Bista, Basanta, Laura González-Rodelas, Lucía Álvarez-González, et al. "De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes." Genome Research, October 16, 2024. http://dx.doi.org/10.1101/gr.279443.124.

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Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq:Apalone sp

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Markowski, Julia, Rieke Kempfer, Alexander Kukalev, et al. "GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data." Bioinformatics, April 8, 2021. http://dx.doi.org/10.1093/bioinformatics/btab238.

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Abstract Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of

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Zhang, Xinxin, and Tianzuo Wang. "Plant 3-D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years." Plant and Cell Physiology, September 6, 2021. http://dx.doi.org/10.1093/pcp/pcab134.

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Abstract Over the past few decades, eukaryotic linear genomes and epigenomes have been widely and extensively studied for understanding gene expression regulation. More recently, the three-dimensional (3-D) chromatin organization was found to be important for determining genome functionality, finely tuning physiological processes for appropriate cellular responses. With the development of visualization techniques and chromatin conformation capture (3C)-based techniques, increasing evidence indicates that chromosomal architecture characteristics and chromatin domains with different epigenetic m

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