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https://www.readbyqxmd.com/read/29332159/transposable-elements-genome-innovation-chromosome-diversity-and-centromere-conflict
#1
REVIEW
Savannah J Klein, Rachel J O'Neill
Although it was nearly 70 years ago when transposable elements (TEs) were first discovered "jumping" from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive...
January 13, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29329524/uncovering-the-evolutionary-history-of-neo-xy-sex-chromosomes-in-the-grasshopper-ronderosia-bergii-orthoptera-melanoplinae-through-satellite-dna-analysis
#2
Octavio M Palacios-Gimenez, Diogo Milani, Bernardo Lemos, Elio R Castillo, Dardo A Martí, Erica Ramos, Cesar Martins, Diogo C Cabral-de-Mello
BACKGROUND: Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS: The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes...
January 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29328419/screening-and-clinical-evaluation-of-dominant-peptides-of-centromere-protein-f-antigen-for-early-diagnosis-of-hepatocellular-carcinoma
#3
Siwen Li, Xiaojin Li, Anjian Xu, Bei Zhang, Xiaomin He, Hongda Chen, Jian Huang
Tumor-associated antigens, such as centromere protein F (CENP‑F), have been recognized as potential serological biomarkers for early diagnosis of hepatocellular carcinoma (HCC); however, the exact regions corresponding to the dominant peptides of CENP‑F antigen remain to be explored. We aimed to screen and evaluate potential dominant peptides of CENP‑F for early diagnosis of HCC. Dominant peptides of CENP‑F were predicted by BioSun version 3.0, and the corresponding recombinant proteins were prepared...
January 4, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29305387/simple-and-complex-centromeric-satellites-in-drosophila-sibling-species
#4
Paul Talbert, Sivakanthan Kasinathan, Steven Henikoff
Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appear to be present at all centromeres, and none of which are found only at centromeres...
January 5, 2018: Genetics
https://www.readbyqxmd.com/read/29301188/a-boy-with-46-x-mar-presenting-gynecomastia-and-short-stature
#5
Ki Eun Kim, Ye Jin Kim, Mo Kyoung Jung, Hyun-Wook Chae, Ah Reum Kwon, Woo Jung Lee, Duk-Hee Kim, Ho-Seong Kim
A 15-year-old boy was referred due to gynecomastia and short stature. He was overweight and showed the knuckle-dimple sign on the left hand, a short fourth toe on the left foot, and male external genitalia with a small phallus. His levels of estradiol and follicle-stimulating hormone were increased, and his testosterone concentration was normal. Other hormonal tests were within the normal range. Radiographs showed short fourth and fifth metacarpals and fourth metatarsal bones. The karyotype was reported as 46,X,+mar, and the marker chromosome was shown to originate from the Y chromosome, which was identified by fluorescence in situ hybridization...
December 2017: Annals of Pediatric Endocrinology & Metabolism
https://www.readbyqxmd.com/read/29298360/chromosome-passenger-complex-is-required-for-the-survival-of-cells-with-ring-chromosomes-in-fission-yeast
#6
Ahmed G K Habib, Kanako Sugiura, Masaru Ueno
Ring chromosomes are circular chromosomal abnormalities that have been reported in association with some genetic disorders and cancers. In Schizosaccharomyces pombe, lack of function of protection of telomere 1 (Pot1) or telomerase catalytic subunit (Trt1) results in survivors with circular chromosomes. Hitherto, it is poorly understood how cells with circular chromosomes survive and how circular chromosomes are maintained. Fission yeast Cut17/Bir1, Ark1, Pic1, and Nbl1 is a conserved chromosome passenger complex (CPC) functioning mainly throughout mitosis...
2018: PloS One
https://www.readbyqxmd.com/read/29296952/mosaic-chromosome-20q-deletions-are-more-frequent-in-the-aging-population
#7
Mitchell J Machiela, Weiyin Zhou, Neil Caporaso, Michael Dean, Susan M Gapstur, Lynn Goldin, Nathaniel Rothman, Victoria L Stevens, Meredith Yeager, Stephen J Chanock
Deletions on the long-arm of chromosome 20, del(20q), are common karyotypic abnormalities in myeloid disorders. Bioinformatic analyses of the B-allele frequency and log R ratio values from genome-wide association data have identified individuals who are mosaic for large structural abnormalities (>2 Mb). We investigated the most common autosomal event, namely mosaic del(20q), in 46 254 nonhematologic cancer cases and 36 229 cancer-free controls. We detected 91 mosaic del(20q) in leukocytes (80%) and buccal material (20%)...
February 14, 2017: Blood Advances
https://www.readbyqxmd.com/read/29295563/structural-analysis-and-epitope-prediction-of-mhc-class-1-chain-related-protein-a-for-cancer-vaccine-development
#8
Tayo Alex Adekiya, Raphael Taiwo Aruleba, Sbonelo Khanyile, Priscilla Masamba, Babatunji Emmanuel Oyinloye, Abidemi Paul Kappo
Major histocompatibility complex class 1 chain-related gene sequence A is a polymorphic gene found at about 46.6 kb centromeric to HLA-B. It encodes a transmembrane protein, which is a non-classical human leukocyte antigen whose expression is normally induced by stress conditions like cancer and viral infections. The expression of MIC-A leads to the activation of NKG2D receptors of natural killer and T cells, leading to the generation of innate immune response that can easily eliminate/cleanse tumour cells and other cells that express the protein...
December 25, 2017: Vaccines
https://www.readbyqxmd.com/read/29285197/correlation-of-telomere-length-to-malignancy-potential-in-non-melanoma-skin-cancers
#9
Hanae Yamada-Hishida, Yoshimasa Nobeyama, Hidemi Nakagawa
Telomeres are associated with cell fate and aging through their role in the cellular response to stress and growth stimulation resulting from previous cell divisions and DNA damage. Telomere shortening has been observed in most human cancers, and is known to be a feature of malignancy. The aim of this study is to clarify whether telomere length is related to the malignant potential of non-melanoma skin cancers. Telomere length was analyzed using tissue quantitative fluorescence in situ hybridization in 36 non-melanoma skin cancers including basal cell carcinoma (BCC), squamous cell carcinoma (SCC), Bowen's disease (BD) and actinic keratosis (AK), and also in 26 samples of normal-appearing epidermal tissue surrounding or located close to each tumor...
January 2018: Oncology Letters
https://www.readbyqxmd.com/read/29284742/the-long-intergenic-non-coding-rna-lincrna-landscape-of-the-soybean-genome
#10
Agnieszka Golicz, Mohan B Singh, Prem L Bhalla
Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with Rhizobium bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities...
December 28, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29282022/chromosomal-instability-induced-by-increased-birc5-survivin-levels-affects-tumorigenicity-of-glioma-cells
#11
Marina Conde, Susanne Michen, Ralf Wiedemuth, Barbara Klink, Evelin Schröck, Gabriele Schackert, Achim Temme
BACKGROUND: Survivin, belonging to the inhibitor of apoptosis (IAP) gene family, is abundantly expressed in tumors. It has been hypothesized that Survivin facilitates carcinogenesis by inhibition of apoptosis resulting in improved survival of tumorigenic progeny. Additionally, Survivin plays an essential role during mitosis. Together with its molecular partners Aurora B, Borealin and inner centromere protein it secures bipolar chromosome segregation. However, whether increased Survivin levels contribute to progression of tumors by inducing chromosomal instability remains unclear...
December 28, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29280735/decoding-the-centromeric-nucleosome-through-cenp-n
#12
Satyakrishna Pentakota, Keda Zhou, Charlotte Smith, Stefano Maffini, Arsen Petrovic, Garry P Morgan, John R Weir, Ingrid R Vetter, Andrea Musacchio, Karolin Luger
Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis. Two kinetochore proteins, CENP-C and CENP-N, recognize CENP-A in the context of a rare CENP-A nucleosome. Here, we reveal the structural basis for the exquisite selectivity of CENP-N for centromeres. CENP-N uses charge and space complementarity to decode the L1 loop that is unique to CENP-A...
December 27, 2017: ELife
https://www.readbyqxmd.com/read/29279323/the-hidden-genomic-and-transcriptomic-plasticity-of-giant-marker-chromosomes-in-cancer
#13
Gemma Macchia, Marco Severgnini, Stefania Purgato, Doron Tolomeo, Hilen Casciaro, Ingrid Cifola, Alberto L'Abbate, Anna Loverro, Orazio Palumbo, Massimo Carella, Laurence Bianchini, Giovanni Perini, Gianluca De Bellis, Fredrik Mertens, Mariano Rocchi, Clelia T Storlazzi
Genome amplification in the form of rings or giant rod-shaped marker chromosomes is a common genetic alteration in soft tissue tumours. The mitotic stability of these structures is often rescued by perfectly functioning analphoid neocentromeres, which therefore significantly contribute to cancer progression. Here, we disentangled the genomic architecture of many neocentromeres stabilizing marker chromosomes in well-differentiated liposarcoma and lung sarcomatoid carcinoma samples. In cells carrying heavily rearranged RGMs, these structures were assembled as patchworks of multiple short amplified sequences, disclosing an extremely high level of complexity and definitely ruling out the existence of regions prone to the neocentromere seeding...
December 26, 2017: Genetics
https://www.readbyqxmd.com/read/29277426/centromere-size-and-its-relationship-to-haploid-formation-in-plants
#14
REVIEW
Na Wang, R Kelly Dawe
Wide species crosses often result in uniparental genome elimination and visible failures in centromere function. Crosses involving lines with mutated forms of the CENH3 histone variant that organizes the centromere/kinetochore interface have been shown to have similar effects, inducing haploids at high frequencies. Here we propose a simple centromere size model that endeavors to explain both observations. It is based on the idea of a quantitative centromere architecture where each centromere in an individual is the same size, and the average size is dictated by a natural equilibrium between bound and unbound CENH3 (and its chaperones or binding proteins)...
December 19, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29273679/the-hoxd-cluster-is-a-dynamic-and-resilient-tad-boundary-controlling-the-segregation-of-antagonistic-regulatory-landscapes
#15
Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre J Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hanh Nguyen Huynh, Hakan Ozadam, Job Dekker, Denis Duboule
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed...
December 22, 2017: Genes & Development
https://www.readbyqxmd.com/read/29273057/cenp-b-protects-centromere-chromatin-integrity-by-facilitating-histone-deposition-via-the-h3-3-specific-chaperone-daxx
#16
Viacheslav M Morozov, Serena Giovinazzi, Alexander M Ishov
BACKGROUND: The main chromatin unit, the nucleosome, can be modulated by the incorporation of histone variants that, in combination with posttranslational histones modifications, determine epigenetics properties of chromatin. Understanding the mechanism that creates a histone variants landscape at different genomic elements is expected to elevate our comprehension of chromatin assembly and function. The Daxx chaperone deposits transcription-associated histone H3.3 at centromeres, but mechanism of centromere-specific Daxx targeting remains unclear...
December 22, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29259092/effects-of-temperature-on-the-meiotic-recombination-landscape-of-the-yeast-saccharomyces-cerevisiae
#17
Ke Zhang, Xue-Chang Wu, Dao-Qiong Zheng, Thomas D Petes
Although meiosis in warm-blooded organisms takes place in a narrow temperature range, meiosis in many organisms occurs over a wide variety of temperatures. We analyzed the properties of meiosis in the yeast Saccharomyces cerevisiae in cells sporulated at 14°C, 30°C, or 37°C. Using comparative-genomic-hybridization microarrays, we examined the distribution of Spo11-generated meiosis-specific double-stranded DNA breaks throughout the genome. Although there were between 300 and 400 regions of the genome with high levels of recombination (hot spots) observed at each temperature, only about 20% of these hot spots were found to have occurred independently of the temperature...
December 19, 2017: MBio
https://www.readbyqxmd.com/read/29259000/genes-important-for-schizosaccharomyces-pombe-meiosis-identified-through-a-functional-genomics-screen
#18
Julie Blyth, Vasso Makrantoni, Rachael E Barton, Christos Spanos, Juri Rappsilber, Adele L Marston
Meiosis is a specialized cell division that generates gametes, such as eggs and sperm. Errors in meiosis result in miscarriages and are the leading cause of birth defects, however the molecular origins of these defects remain unknown. Studies in model organisms are beginning to identify the genes and pathways important for meiosis, but the parts list is still poorly defined. Here we present a comprehensive catalog of genes important for meiosis in the fission yeast, Schizosaccharomyces pombe Our genome-wide functional screen surveyed all non-essential genes for roles in chromosome segregation and spore formation...
December 19, 2017: Genetics
https://www.readbyqxmd.com/read/29251022/impact-of-double-positive-for-anti-centromere-and-anti-ss-a-ro-antibodies-on-clinicopathological-characteristics-of-primary-sj%C3%A3-gren-s-syndrome-a-retrospective-cohort-study
#19
Yasunori Suzuki, Hiroshi Fujii, Hideki Nomura, Ichiro Mizushima, Kazunori Yamada, Masakazu Yamagishi, Mitsuhiro Kawano
OBJECTIVES: The purpose of our study was to define the clinical characteristics of anti-centromere antibody and anti-SS-A/Ro antibody (ACA/SS-A) double positive Sjögren's syndrome (SS) and to clarify the clinical impact of these antibodies. METHODS: We examined 108 patients (6 males, mean age 57.9 years) with SS who underwent labial salivary gland biopsy. The patients were divided into 4 groups by ACA and anti-SS-A/Ro antibody positivity. Symptoms, laboratory and pathological data, and scleroderma-related data were compared among the groups...
December 18, 2017: Modern Rheumatology
https://www.readbyqxmd.com/read/29250165/evaluating-the-associations-between-human-circadian-rhythms-and-dysregulated-genes-in-liver-cancer-cells
#20
Andrea Polo, Sakshi Singh, Anna Crispo, Marilina Russo, Aldo Giudice, Maurizio Montella, Giovanni Colonna, Susan Costantini
Network analysis is a useful approach in cancer biology as it provides information regarding the genes and proteins. In our previous study, a network analysis was performed on dysregulated genes in HepG2 cells, a hepatoblastoma cell line that lacks the viral infection, compared with normal hepatocytes, identifying the presence of 26 HUB genes. The present study aimed to identify whether these previously identified HUB genes participate in the network that controls the human circadian rhythms. The results of the present study demonstrated that 20/26 HUB genes were associated with the metabolic processes that control human circadian rhythms, which supports the hypothesis that a number of cancer types are dependent from circadian cycles...
December 2017: Oncology Letters
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