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Journal articles on the topic 'Eukaryotic gene; Genes; Chromosomal domain'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Nützmann, Hans-Wilhelm, Daniel Doerr, América Ramírez-Colmenero, et al. "Active and repressed biosynthetic gene clusters have spatially distinct chromosome states." Proceedings of the National Academy of Sciences 117, no. 24 (2020): 13800–13809. http://dx.doi.org/10.1073/pnas.1920474117.

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While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution micros

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2

Shopland, Lindsay S., Carol V. Johnson, Meg Byron, John McNeil, and Jeanne B. Lawrence. "Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains." Journal of Cell Biology 162, no. 6 (2003): 981–90. http://dx.doi.org/10.1083/jcb.200303131.

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Typically, eukaryotic nuclei contain 10–30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain “choice” appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3–4 subregions of the chromosome periphery that contact a domain.

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LaSalle, Janine M., and Marc Lalande. "Domain organization of allele-specific DNA replication within the GABAA receptor gene cluster." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 766–67. http://dx.doi.org/10.1017/s0424820100140208.

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Parental imprinting is a gamete-specific modification that distinguishes the paternal and maternal chromosomes in higher eukaryotes, resulting in allele-specific changes in chromatin organization, transcription and replication. One example of parental imprinting in humans is revealed by two distinct genetic diseases, Prader-Willi syndrome (PWS) and Angelman syndrome (AS) which both map to chromosome 15q11-13. PWS is caused by the absence of a paternal contribution to 15q11-13, while AS results from the lack of a maternal copy of the region. Within this chromosomal subregion lies a cluster of G

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4

Orlov, Y. L., O. Thierry, A. G. Bogomolov, et al. "Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data." Biomeditsinskaya Khimiya 63, no. 5 (2017): 418–22. http://dx.doi.org/10.18097/pbmc20176305418.

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The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental

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Schiklenk, Christoph, Boryana Petrova, Marc Kschonsak, et al. "Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1." Journal of Cell Biology 217, no. 7 (2018): 2383–401. http://dx.doi.org/10.1083/jcb.201711097.

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Although the formation of rod-shaped chromosomes is vital for the correct segregation of eukaryotic genomes during cell divisions, the molecular mechanisms that control the chromosome condensation process have remained largely unknown. Here, we identify the C2H2 zinc-finger transcription factor Zas1 as a key regulator of mitotic condensation dynamics in a quantitative live-cell microscopy screen of the fission yeast Schizosaccharomyces pombe. By binding to specific DNA target sequences in their promoter regions, Zas1 controls expression of the Cnd1 subunit of the condensin protein complex and

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Landis, G., and J. Tower. "The Drosophila chiffon gene is required for chorion gene amplification, and is related to the yeast Dbf4 regulator of DNA replication and cell cycle." Development 126, no. 19 (1999): 4281–93. http://dx.doi.org/10.1242/dev.126.19.4281.

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The Drosophila chorion genes encode the major protein components of the chorion (eggshell) and are arranged in two clusters in the genome. To meet the demand for rapid chorion synthesis, Drosophila ovary follicle cells amplify the chorion gene clusters approximately 80-fold. Amplification proceeds through repeated firing of one or more DNA replication origins located near the center of each gene cluster. Hypomorphic mutant alleles of the chiffon gene cause thin, fragile chorions and female sterility, and were found to eliminate chorion gene amplification. Null alleles of chiffon had the additi

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Kellum, R., and P. Schedl. "A group of scs elements function as domain boundaries in an enhancer-blocking assay." Molecular and Cellular Biology 12, no. 5 (1992): 2424–31. http://dx.doi.org/10.1128/mcb.12.5.2424.

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Chromosomes of higher eukaryotes are thought to be organized into a series of discrete and topologically independent higher-order domains. In addition to providing a mechanism for chromatin compaction, these higher-order domains are thought to define independent units of gene activity. Implicit in most models for the folding of the chromatin fiber are special nucleoprotein structures, the domain boundaries, which serve to delimit each higher-order chromosomal domain. We have used an "enhancer-blocking assay" to test putative domain boundaries for boundary function in vivo. This assay is based

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Kellum, R., and P. Schedl. "A group of scs elements function as domain boundaries in an enhancer-blocking assay." Molecular and Cellular Biology 12, no. 5 (1992): 2424–31. http://dx.doi.org/10.1128/mcb.12.5.2424-2431.1992.

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Chromosomes of higher eukaryotes are thought to be organized into a series of discrete and topologically independent higher-order domains. In addition to providing a mechanism for chromatin compaction, these higher-order domains are thought to define independent units of gene activity. Implicit in most models for the folding of the chromatin fiber are special nucleoprotein structures, the domain boundaries, which serve to delimit each higher-order chromosomal domain. We have used an "enhancer-blocking assay" to test putative domain boundaries for boundary function in vivo. This assay is based

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9

Shazadee, Hamna, Nadeem Khan, Jingjing Wang, et al. "Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L." International Journal of Molecular Sciences 20, no. 6 (2019): 1395. http://dx.doi.org/10.3390/ijms20061395.

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The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C ge

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10

Howe, Kerstin, Philipp H. Schiffer, Julia Zielinski, et al. "Structure and evolutionary history of a large family of NLR proteins in the zebrafish." Open Biology 6, no. 4 (2016): 160009. http://dx.doi.org/10.1098/rsob.160009.

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Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided in

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11

Wiese, Oliver, Davide Marenduzzo, and Chris A. Brackley. "Nucleosome positions alone can be used to predict domains in yeast chromosomes." Proceedings of the National Academy of Sciences 116, no. 35 (2019): 17307–15. http://dx.doi.org/10.1073/pnas.1817829116.

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We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the formation of chromosomal interaction domains, chromosome regions of around 0.5 to 10 kbp which show enriched self-interactions, which were experimentally observed in recent MicroC experiments (importantly these are at a different length scale from the 100- to 1,000-kbp–sized domains observed in higher eukaryotes). We show that the sole input of n

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Kuhn, Emily J., Craig M. Hart, and Pamela K. Geyer. "Studies of the Role of the Drosophila scs and scs′ Insulators in Defining Boundaries of a Chromosome Puff." Molecular and Cellular Biology 24, no. 4 (2004): 1470–80. http://dx.doi.org/10.1128/mcb.24.4.1470-1480.2004.

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ABSTRACT Insulators are DNA elements that establish independent transcriptional domains within eukaryotic genomes. The Drosophila scs and scs′ insulators localize near the borders of a structural domain in the polytene chromosomes, known as a puff, produced by transcription of the 87A heat shock protein (hsp) genes. It has been suggested that scs and scs′ are boundary elements that delimit this decondensed chromatin domain, reflecting the mechanism by which these sequences act to constrain regulatory interactions. This model was tested using transposons that carried a yellow gene to assess enh

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Weber, V., M. Harata, H. Hauser, and U. Wintersberger. "The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus." Molecular Biology of the Cell 6, no. 10 (1995): 1263–70. http://dx.doi.org/10.1091/mbc.6.10.1263.

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Actin-related proteins, a group of protein families that exhibit about 50% sequence identity among each other and to conventional actin, have been found in a variety of eukaryotic organisms. In the budding yeast Saccharomyces cerevisiae, genes for one conventional actin (ACT1) and for three actin-related proteins (ACT2, ACT3, and ACT5) are known. ACT3, which we recently discovered, is an essential gene coding for a polypeptide of 489 amino acids (Act3p), with a calculated molecular mass of 54.8 kDa. Besides its homology to conventional actin, Act3p possesses a domain exhibiting weak similarity

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14

Li, Chaoqiong, Xiaoli Li, Hongzhan Liu, et al. "Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly." Plant and Cell Physiology 61, no. 5 (2020): 978–87. http://dx.doi.org/10.1093/pcp/pcaa026.

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Abstract Eukaryotic chromatin is tightly packed into hierarchical structures, allowing appropriate gene transcription in response to environmental and developmental cues. Here, we provide a chromosome-scale de novo genome assembly of sesame with a total length of 292.3 Mb and a scaffold N50 of 20.5 Mb, containing estimated 28,406 coding genes using Pacific Biosciences long reads combined with a genome-wide chromosome conformation capture (Hi-C) approach. Based on this high-quality reference genome, we detected changes in chromatin architectures between normal growth and dark-treated sesame see

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15

Formaggioni, Alessandro, Andrea Luchetti, and Federico Plazzi. "Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence." Life 11, no. 7 (2021): 663. http://dx.doi.org/10.3390/life11070663.

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Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is

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16

PEÑA-DÍAZ, Javier, Andrea MONTALVETTI, Ana CAMACHO, Claribel GALLEGO, Luis M. RUIZ-PEREZ, and Dolores GONZALEZ-PACANOWSKA. "A soluble 3-hydroxy-3-methylglutaryl-CoA reductase in the protozoan Trypanosoma cruzi." Biochemical Journal 324, no. 2 (1997): 619–26. http://dx.doi.org/10.1042/bj3240619.

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We report the isolation and characterization of a genomic clone containing the open reading frame sequence for 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase from Trypanosoma cruzi, the causative agent of Chagas' disease. The protozoan gene encoded for a smaller polypeptide than the rest of the genes described from eukaryotic organisms and the deduced amino acid sequence could be aligned with the C-terminal half of animal and plant reductases exhibiting pronounced similarity to other eukaryotic counterparts. Further examination of the 5′ flanking region by cDNA analysis and establishment o

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Naito, Mizue, Joseph B. Morton, and Teresa E. Pawlowska. "Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota." Proceedings of the National Academy of Sciences 112, no. 25 (2015): 7791–96. http://dx.doi.org/10.1073/pnas.1501676112.

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Arbuscular mycorrhizal fungi (AMF, Glomeromycota) colonize roots of the majority of terrestrial plants. They provide essential minerals to their plant hosts and receive photosynthates in return. All major lineages of AMF harbor endobacteria classified as Mollicutes, and known as mycoplasma-related endobacteria (MRE). Except for their substantial intrahost genetic diversity and ability to transmit vertically, virtually nothing is known about the life history of these endobacteria. To understand MRE biology, we sequenced metagenomes of three MRE populations, each associated with divergent AMF ho

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18

Shi, Liang, and Weiwen Zhang. "Comparative analysis of eukaryotic-type protein phosphatases in two streptomycete genomes." Microbiology 150, no. 7 (2004): 2247–56. http://dx.doi.org/10.1099/mic.0.27057-0.

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Inspection of the genomes of Streptomyces coelicolor A3(2) and Streptomyces avermitilis reveals that each contains 55 putative eukaryotic-type protein phosphatases (PPs), the largest number ever identified from any single prokaryotic organism. Unlike most other prokaryotic genomes that have only one or two superfamilies of eukaryotic-type PPs, the streptomycete genomes possess the eukaryotic-type PPs that belong to four superfamilies: 2 phosphoprotein phosphatases and 2 low-molecular-mass protein tyrosine phosphatases in each species, 49 Mg2+- or Mn2+-dependent protein phosphatases (PPMs) and

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19

Masson, J. Y., and D. Ramotar. "The Saccharomyces cerevisiae IMP2 gene encodes a transcriptional activator that mediates protection against DNA damage caused by bleomycin and other oxidants." Molecular and Cellular Biology 16, no. 5 (1996): 2091–100. http://dx.doi.org/10.1128/mcb.16.5.2091.

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Bleomycin belongs to a class of antitumor drugs that damage cellular DNA through the production of free radicals. The molecular basis by which eukaryotic cells provide resistance to the lethal effects of bleomycin is not clear. Using the yeast Saccharomyces cerevisiae as a model with which to study the effect of bleomycin damage on cellular DNA, we isolated several mutants that display hypersensitivity to bleomycin. A DNA clone containing the IMP2 gene that complemented the most sensitive bleomycin mutant was identified. A role for IMP2 in defense against the toxic effects of bleomycin has not

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20

MacQueen, Alice, Dacheng Tian, Wenhan Chang, Eric Holub, Martin Kreitman, and Joy Bergelson. "Population Genetics of the Highly Polymorphic RPP8 Gene Family." Genes 10, no. 9 (2019): 691. http://dx.doi.org/10.3390/genes10090691.

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Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb

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Fort, Rafael Sebastián, and María Ana Duhagon. "Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology." F1000Research 10 (June 9, 2021): 182. http://dx.doi.org/10.12688/f1000research.28510.2.

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Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (

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Fort, Rafael Sebastián, and María Ana Duhagon. "Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology." F1000Research 10 (March 5, 2021): 182. http://dx.doi.org/10.12688/f1000research.28510.1.

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Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (

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Aparicio, Jennifer G., Christopher J. Viggiani, Daniel G. Gibson, and Oscar M. Aparicio. "The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae." Molecular and Cellular Biology 24, no. 11 (2004): 4769–80. http://dx.doi.org/10.1128/mcb.24.11.4769-4780.2004.

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ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins

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Kalendar, Ruslan, Olga Raskina, Alexander Belyayev, and Alan H. Schulman. "Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants." International Journal of Molecular Sciences 21, no. 8 (2020): 2931. http://dx.doi.org/10.3390/ijms21082931.

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Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-

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Baiamonte, Elena, Rosalia Di Stefano, Melania Lo Iacono, et al. "The Sea Urchin sns5 Chromatin Insulator Improves the Likelihood of Lentiviral Vectors in Erythroid Milieu By Organizing an Independent Chromatin Domain at the Integration Site." Blood 126, no. 23 (2015): 4414. http://dx.doi.org/10.1182/blood.v126.23.4414.4414.

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Abstract Retroviral vectors are currently the most suitable vehicles for therapeutic gene transfer in hematopoietic stem cells. However, these vectors are known to integrate rather randomly throughout the genome, suffering the so called chromosomal position effects (PE). Such a critical occurrence most probably depends upon the ability of heterochromatin to spread in the inserted vector sequences. Moreover, the use of transgenes imply genotoxicity effects, since the cis-regulatory sequences harbored by the vector can disturb the proper transcription of the resident genes neighboring the integr

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26

Yang, Qing, ShengNan Wang, ChuanBao Wu, et al. "Malus domestica ADF1 severs actin filaments in growing pollen tubes." Functional Plant Biology 44, no. 4 (2017): 455. http://dx.doi.org/10.1071/fp16360.

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A dynamic actin cytoskeleton is essential for pollen tube growth and germination. However, the molecular mechanism that determines the organisation of the actin cytoskeleton in pollen remains poorly understood. ADF modulates the structure and dynamics of actin filaments and influences the higher-order organisation of the actin cytoskeleton in eukaryotic cells. Members of the ADF family have been shown to have important functions in pollen tube growth. However, the role of this gene family remains largely unknown in apple (Malus domestica Borkh.). In this study, we identified seven ADFs in the

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27

Yokoyama, Akihiko, and Hiroshi Okuda. "The Molecular Mechanism of Transcriptional Activation By MLL-AEP Fusion Proteins." Blood 126, no. 23 (2015): 2435. http://dx.doi.org/10.1182/blood.v126.23.2435.2435.

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Abstract Chromosomal translocations generate a variety of mixed lineage leukemia (MLL) fusion genes, which cause aggressive leukemia. Although >70 different fusion partners have been identified, the majority of the cases are caused by the chimeric genes of MLL and a component of the AEP co-activator complex (hereafter referred to as AEP), which comprises of AF4 family proteins (e.g. AF4, AF5Q31), ENL family proteins (e.g. ENL, AF9), and the P-TEFb elongation factor. MLL-AEP fusion proteins constitutively activate their target genes by recruiting AEP components to their target chromatin, whe

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28

Li, Huiyu, Xiaomei Chen, Wei Xiong, Fang Liu, and Shiang Huang. "The Regulation of Zinc Finger Proteins by Mirnas Enriched in ALL-Microvesicles." Blood 120, no. 21 (2012): 1448. http://dx.doi.org/10.1182/blood.v120.21.1448.1448.

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Abstract Abstract 1448 Microvesicles (MVs) are submicrometric membrane fragments and they can “hijack” membrane components and engulf cytoplasmic contents from their cellular origin. MVs are enriched in various bioactive molecules of their parental cells, such as proteins, DNA, mRNA and miRNAs. Microvesicles (MVs) released by leukemia cells constitute an important part of the leukemia microenvironment. As a cell-to-cell communication tool, MVs transfer microRNA (miRNA) between cells. MVs miRNAs may also provide an insight in the role of miRNAs playing in the underlying of pathophysiologic proc

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Dong, Chongmei, Ryan Whitford, and Peter Langridge. "A DNA mismatch repair gene links to the Ph2 locus in wheat." Genome 45, no. 1 (2002): 116–24. http://dx.doi.org/10.1139/g01-126.

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DNA mismatch repair is an essential system for maintaining genetic stability in bacteria and higher eukaryotes. Based on the conserved regions of the bacterial MutS gene and its homologues in yeast and human, a wheat cDNA homologue of MSH6, designated TaMSH7, was isolated by RTPCR. The deduced amino acid sequence of TaMSH7 shows conserved domains characteristic of other MSH6 genes, with highest similarity to maize MSH7 and Arabidopsis MSH7. TaMSH7 is expressed in meristem tissue associated with a high level of mitotic and meiotic activity, with maximum expression in the reproductive organs of

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Hennig, Wolfgang, Reindert C. Brand, Johannes Hackstein, et al. "Y chromosomal fertility genes of Drosophila: a new type of eukaryotic genes." Genome 31, no. 2 (1989): 561–71. http://dx.doi.org/10.1139/g89-105.

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The Y chromosomal fertility genes of Drosophila are required for sperm differentiation. They are active only in primary spermatocytes where they form giant lampbrush loops. The molecular structure of these genes was investigated and revealed an unusual composition of DNA. Short, tandemly repeated sequence clusters are interrupted by longer and more heterogeneous sequences, which probably all represent transposable elements. No indication of the presence of protein-coding regions has been found within the fertility genes. However, the lampbrush loops bind site-specific proteins recognized by im

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Ross, Benjamin D., Leah Rosin, Andreas W. Thomae, et al. "Stepwise Evolution of Essential Centromere Function in a Drosophila Neogene." Science 340, no. 6137 (2013): 1211–14. http://dx.doi.org/10.1126/science.1234393.

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Evolutionarily young genes that serve essential functions represent a paradox; they must perform a function that either was not required until after their birth or was redundant with another gene. How young genes rapidly acquire essential function is largely unknown. We traced the evolutionary steps by which the Drosophila gene Umbrea acquired an essential role in chromosome segregation in D. melanogaster since the gene's origin less than 15 million years ago. Umbrea neofunctionalization occurred via loss of an ancestral heterochromatin-localizing domain, followed by alterations that rewired i

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Yang, Yan-Qing, and Yun-Hai Lu. "Genome-wide survey, characterization, and expression analysis of RING finger protein genes in Brassica oleracea and their syntenic comparison to Brassica rapa and Arabidopsis thaliana." Genome 61, no. 9 (2018): 685–97. http://dx.doi.org/10.1139/gen-2018-0046.

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The ubiquitin-mediated post-translational regulatory pathway regulates a broad range of cell functions in all eukaryotes. It requires the involvement of a large number of E3 ligases, of which more than one third belongs to the RING protein family as in Arabidopsis thaliana. In this study, a total of 756 RING domains in 734 predicted proteins were identified in Brassica oleracea. Their encoding genes were characterized by RING domain type, additional domain, and expression pattern, and mapped on the nine chromosomes of B. oleracea. Comparison of these results with B. rapa and A. thaliana reveal

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Shi, Wei, Therese Vu, Glen Boyle, et al. "SSB1/NABP2 and SSB2/NABP1 Have Essential and Overlapping Roles in Maintaining Hematopoietic Stem and Progenitor Cells." Blood 126, no. 23 (2015): 2405. http://dx.doi.org/10.1182/blood.v126.23.2405.2405.

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Abstract Single-stranded DNA binding (SSB) proteins are essential for a variety of DNA metabolic processes and the maintenance of genomic stability. SSB1 and its homolog SSB2, share greater sequence and domain homology to the archaeal and bacterial SSBs than eukaryotic RPA. They form complexes with two other proteins, C9Orf80 and INTS3, and play roles in mediating transcription and DNA repair. SSB1 (also known as OBFC2B or NABP2) is recurrently mutated in various cancers, however the precise function in normal development is incompletely understood. We have previously shown that Ssb1 is requir

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Runyen-Janecky, L. J., and S. M. Payne. "Identification of Chromosomal Shigella flexneri Genes Induced by the Eukaryotic Intracellular Environment." Infection and Immunity 70, no. 8 (2002): 4379–88. http://dx.doi.org/10.1128/iai.70.8.4379-4388.2002.

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ABSTRACT Upon entry into the eukaryotic cytosol, the facultative intracellular bacterium Shigella flexneri is exposed to an environment that may necessitate the expression of particular genes for it to survive and grow intracellularly. To identify genes that are induced in response to the intracellular environment, we screened a library containing fragments of the S. flexneri chromosome fused to a promoterless green fluorescent protein gene (gfp). Bacteria containing promoter fusions that had a higher level of gfp expression when S. flexneri was intracellular (in Henle cells) than when S. flex

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Calestagne-Morelli, Alison, and Juan Ausió. "Long-range histone acetylation: biological significance, structural implications, and mechanismsThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 84, no. 4 (2006): 518–27. http://dx.doi.org/10.1139/o06-067.

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Genomic characterization of various euchromatic regions in higher eukaryotes has revealed that domain-wide hyperacetylation (over several kb) occurs at a range of loci, including individual genes, gene family clusters, compound clusters, and more general clusters of unrelated genes. Patterns of long-range histone hyperacetylation are strictly conserved within each unique cellular system studied and they reflect biological variability in gene regulation. Domain-wide histone acetylation consists generally of nonuniform peaks of enriched hyperacetylation of specific core histones, histone isoform

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Tejera Nevado, Paloma, Eugenia Bifeld, Katharina Höhn, and Joachim Clos. "A Telomeric Cluster of Antimony Resistance Genes on Chromosome 34 of Leishmania infantum." Antimicrobial Agents and Chemotherapy 60, no. 9 (2016): 5262–75. http://dx.doi.org/10.1128/aac.00544-16.

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ABSTRACTThe mechanisms underlying the drug resistance ofLeishmaniaspp. are manifold and not completely identified. Apart from the highly conserved multidrug resistance gene family known from higher eukaryotes,Leishmaniaspp. also possess genus-specific resistance marker genes. One of them, ARM58, was first identified inLeishmania braziliensisusing a functional cloning approach, and its domain structure was characterized inL. infantum. Here we report thatL. infantumARM58 is part of a gene cluster at the telomeric end of chromosome 34 also comprising the neighboring genes ARM56 and HSP23. We show

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ZHENG, Jiarui, Yongling LIAO, Feng XU, et al. "Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 49, no. 2 (2021): 12086. http://dx.doi.org/10.15835/nbha49212086.

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The WD40 transcription factor family is a superfamily found in eukaryotes and implicated in regulating growth and development. In this study, 167 WD40 family genes are identified in the Ginkgo biloba genome. They are divided into 5 clusters and 16 subfamilies based on the difference analysis of a phylogenetic tree and domain structures. The distribution of WD40 genes in chromosomes, gene structures, and motifs is analyzed. Promoter analysis shows that five GbWD40 gene promoters contain the MYB binding site participating in the regulation of flavonoid metabolism, suggesting that these five gene

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Shoja, Valia, T. M. Murali, and Liqing Zhang. "Expression Divergence of Tandemly Arrayed Genes in Human and Mouse." Comparative and Functional Genomics 2007 (2007): 1–8. http://dx.doi.org/10.1155/2007/60964.

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Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members a

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Dundr, Miroslav, Jason K. Ospina, Myong-Hee Sung, et al. "Actin-dependent intranuclear repositioning of an active gene locus in vivo." Journal of Cell Biology 179, no. 6 (2007): 1095–103. http://dx.doi.org/10.1083/jcb.200710058.

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Although bulk chromatin is thought to have limited mobility within the interphase eukaryotic nucleus, directed long-distance chromosome movements are not unknown. Cajal bodies (CBs) are nuclear suborganelles that nonrandomly associate with small nuclear RNA (snRNA) and histone gene loci in human cells during interphase. However, the mechanism responsible for this association is uncertain. In this study, we present an experimental system to probe the dynamic interplay of CBs with a U2 snRNA target gene locus during transcriptional activation in living cells. Simultaneous four-dimensional tracki

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Heusipp, Gerhard, Glenn M. Young, and Virginia L. Miller. "HreP, an In Vivo-Expressed Protease of Yersinia enterocolitica, Is a New Member of the Family of Subtilisin/Kexin-Like Proteases." Journal of Bacteriology 183, no. 12 (2001): 3556–63. http://dx.doi.org/10.1128/jb.183.12.3556-3563.2001.

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ABSTRACT The role of proteases in pathogenesis is well established for several microorganisms but has not been described for Yersinia enterocolitica. Previously, we identified a gene,hreP, which showed significant similarity to proteases in a screen for chromosomal genes of Y. enterocoliticathat were exclusively expressed during an infection of mice. We cloned this gene by chromosome capture and subsequently determined its nucleotide sequence. Like inv, the gene encoding the invasin protein of Y. enterocolitica,hreP is located in a cluster of flagellum biosynthesis and chemotaxis genes. The ge

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Harris, P. V., O. M. Mazina, E. A. Leonhardt, R. B. Case, J. B. Boyd, and K. C. Burtis. "Molecular cloning of Drosophila mus308, a gene involved in DNA cross-link repair with homology to prokaryotic DNA polymerase I genes." Molecular and Cellular Biology 16, no. 10 (1996): 5764–71. http://dx.doi.org/10.1128/mcb.16.10.5764.

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Mutations in the Drosophila mus308 gene confer specific hypersensitivity to DNA-cross-linking agents as a consequence of defects in DNA repair. The mus308 gene is shown here to encode a 229-kDa protein in which the amino-terminal domain contains the seven conserved motifs characteristic of DNA and RNA helicases and the carboxy-terminal domain shares over 55% sequence similarity with the polymerase domains of prokaryotic DNA polymerase I-like enzymes. This is the first reported member of this family of DNA polymerases in a eukaryotic organism, as well as the first example of a single polypeptid

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Huang, Y. J., R. Stoffel, H. Tobler, and F. Mueller. "A newly formed telomere in Ascaris suum does not exert a telomere position effect on a nearby gene." Molecular and Cellular Biology 16, no. 1 (1996): 130–34. http://dx.doi.org/10.1128/mcb.16.1.130.

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During the process of chromatin diminution in Ascaris suum (formerly named Ascaris lumbricoides var. suum), developmentally regulated chromosomal fragmentation and new telomere addition occur within specific chromosomal breakage regions (CBRs). The DNA sequences flanking one of these CBRs (CBR-1) were analyzed, and two protein-encoding genes were found on either side. The noneliminated gene, agp-1, whose AUG start codon is located within approximately 2 kb of the boundary of CBR-1, encodes a putative GTP-binding protein which is structurally related to eukaryotic and prokaryotic elongation fac

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Richards, Thomas A., Joel B. Dacks, Samantha A. Campbell, et al. "Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements." Eukaryotic Cell 5, no. 9 (2006): 1517–31. http://dx.doi.org/10.1128/ec.00106-06.

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ABSTRACT Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient or

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Li, Bin, Shin Kurihara, Sok Ho Kim, Jue Liang, and Anthony J. Michael. "A polyamine-independent role for S-adenosylmethionine decarboxylase." Biochemical Journal 476, no. 18 (2019): 2579–94. http://dx.doi.org/10.1042/bcj20190561.

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Abstract The only known function of S-adenosylmethionine decarboxylase (AdoMetDC) is to supply, with its partner aminopropyltransferase enzymes such as spermidine synthase (SpdSyn), the aminopropyl donor for polyamine biosynthesis. Polyamine spermidine is probably essential for the growth of all eukaryotes, most archaea and many bacteria. Two classes of AdoMetDC exist, the prokaryotic class 1a and 1b forms, and the eukaryotic class 2 enzyme, which is derived from an ancient fusion of two prokaryotic class 1b genes. Herein, we show that ‘eukaryotic' class 2 AdoMetDCs are found in bacteria and a

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Lawrence, Jeanne B., and Christine M. Clemson. "Gene associations: true romance or chance meeting in a nuclear neighborhood?" Journal of Cell Biology 182, no. 6 (2008): 1035–38. http://dx.doi.org/10.1083/jcb.200808121.

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Many recent studies have raised interest in the nuclear associations of coregulated genes from different chromosomes, often evoking interpretations of gene–gene interactions, communication, and even “romance.” However, in some cases, the associations may be indirect and infrequent and may reflect the segregation of active and inactive genes into different nuclear compartments. The study by Brown et al. (see p. 1083 of this issue) reports that the apparent association of erythroid genes is not a direct interaction nor colocalization to one tiny transcription factory but arises as a result of th

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Glover, D. M. "New doors to open…and so many!" Journal of Cell Science 113, no. 3 (2000): 359–60. http://dx.doi.org/10.1242/jcs.113.3.359.

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The pursuit of science is a wonderful journey of discovery along which there are a myriad of avenues to be explored. There have always been so many objects of fascination, so many questions to ask along the way, so many possibilities to understand new principles, that making the decision about which problem to address and then having the self-discipline to explore it in depth challenge all who practice the art. How then are we, as cell biologists, to cope with the mountain of information that is accumulating as we enter the twenty-first century? We now have the potential to decipher the primar

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Subramaniam, Chandra, Paul Veazey, Seth Redmond, et al. "Chromosome-Wide Analysis of Gene Function by RNA Interference in the African Trypanosome." Eukaryotic Cell 5, no. 9 (2006): 1539–49. http://dx.doi.org/10.1128/ec.00141-06.

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ABSTRACT Trypanosomatids of the order Kinetoplastida are major contributors to global disease and morbidity, and understanding their basic biology coupled with the development of new drug targets represents a critical need. Additionally, trypanosomes are among the more accessible divergent eukaryote experimental systems. The genome of Trypanosoma brucei contains 8,131 predicted open reading frames (ORFs), of which over half have no known homologues beyond the Kinetoplastida and a substantial number of others are poorly defined by in silico analysis. Thus, a major challenge following completion

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Bi, Xin. "Domains of Gene Silencing Near the Left End of Chromosome III inSaccharomyces cerevisiae." Genetics 160, no. 4 (2002): 1401–7. http://dx.doi.org/10.1093/genetics/160.4.1401.

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AbstractIn Saccharomyces cerevisiae the HM loci and regions adjacent to the telomeres are transcriptionally silent. HML is situated 11 kb from the left telomere of chromosome III. I have systematically examined gene silencing along this 11-kb chromosomal region. I found that silencing extends at least 1.1 kb beyond HML, indicating that the HML E silencer acts on both sides. Moreover, I obtained evidence indicating that a 0.71-kb sequence near the E silencer acts as a barrier to the spread of silencing and coincides with the left boundary of the silent HML domain. I also showed that silencing a

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Meijer, Harold J. G., and Francine Govers. "Genomewide Analysis of Phospholipid Signaling Genes in Phytophthora spp.: Novelties and a Missing Link." Molecular Plant-Microbe Interactions® 19, no. 12 (2006): 1337–47. http://dx.doi.org/10.1094/mpmi-19-1337.

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Phospholipids are cellular membrane components in eukaryotic cells that execute many important roles in signaling. Genes encoding enzymes required for phospholipid signaling and metabolism have been characterized in several organisms, but only a few have been described for oomycetes. In this study, the genome sequences of Phytophthora sojae and P. ramorum were explored to construct a comprehensive genomewide inventory of genes involved in the most universal phospholipid signaling pathways. Several genes and gene families were annotated, including those encoding phosphatidylinositol synthase (P

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Brickner, Jason. "Genetic and epigenetic control of the spatial organization of the genome." Molecular Biology of the Cell 28, no. 3 (2017): 364–69. http://dx.doi.org/10.1091/mbc.e16-03-0149.

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Eukaryotic genomes are spatially organized within the nucleus by chromosome folding, interchromosomal contacts, and interaction with nuclear structures. This spatial organization is observed in diverse organisms and both reflects and contributes to gene expression and differentiation. This leads to the notion that the arrangement of the genome within the nucleus has been shaped and conserved through evolutionary processes and likely plays an adaptive function. Both DNA-binding proteins and changes in chromatin structure influence the positioning of genes and larger domains within the nucleus.

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