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Chromosome homology search

James E Haber
The repair of chromosomal double-strand breaks (DSBs) by homologous recombination is essential to maintain genome integrity. The key step in DSB repair is the RecA/Rad51-mediated process to match sequences at the broken end to homologous donor sequences that can be used as a template to repair the lesion. Here, in reviewing research about DSB repair, I consider the many factors that appear to play important roles in the successful search for homology by several homologous recombination mechanisms. See also the video abstract here: https://youtu...
March 30, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
William Douglass Wright, Shanaya Shital Shah, Wolf-Dietrich Heyer
Homologous recombination enables the cell to access and copy intact DNA sequence information in trans, particularly to repair DNA damage affecting both strands of the double helix. Here, we discuss the DNA transactions and enzymatic activities required for this elegantly orchestrated process in the context of the repair of DNA double-strand breaks in somatic cells. This include homology search, DNA strand invasion, repair DNA synthesis, and restoration of intact chromosomes. Aspects of DNA topology affecting individual steps are highlighted...
March 29, 2018: Journal of Biological Chemistry
Eitaro Sawayama, Daiki Noguchi, Kei Nakayama, Motohiro Takagi
We previously reported a body color deformity in juvenile red sea bream, which shows transparency in the juvenile stage because of delayed chromatophore development compared with normal individuals, and this finding suggested a genetic cause based on parentage assessments. To conduct marker-assisted selection to eliminate broodstock inheriting the causative gene, developing DNA markers associated with the phenotype was needed. We first conducted SNP mining based on AFLP analysis using bulked-DNA from normal and transparent individuals...
March 23, 2018: Marine Biotechnology
Francisco J Ruiz-Ruano, Jesús Castillo-Martínez, Josefa Cabrero, Ricardo Gómez, Juan Pedro M Camacho, María Dolores López-León
Satellite DNA (satDNA) constitutes an important fraction of repetitive DNA in eukaryotic genomes, but it is barely known in most species. The high-throughput analysis of satDNA in the grasshopper Pyrgomorpha conica revealed 87 satDNA variants grouped into 76 different families, representing 9.4% of the genome. Fluorescent in situ hybridization (FISH) analysis of the 38 most abundant satDNA families revealed four different patterns of chromosome distribution. Homology search between the 76 satDNA families showed the existence of 15 superfamilies, each including two or more families, with the most abundant superfamily representing more than 80% of all satDNA found in this species...
March 16, 2018: Chromosoma
Babita Sharma, Raman Preet Kaur, Sonali Raut, Anjana Munshi
BRCA1 gene mutations account for about 25-28% of hereditary Breast Cancer as BRCA1 is included in the category of high penetrance genes. Except for few commonmutations, there is a heterogenous spectrum of BRCA1 mutations in various ethnic groups. 185AGdel and 5382ins Care the most common BRCA1 alterations (founder mutations) which have been identified in most of the population. This review has been compiled with an aim to consolidate the information on genetic variants reported in BRCA1 found in various ethnic groups, their functional implications if known; involvement of BRCA1 in various cellular pathways/processes and potential BRCA1 targeted therapies...
January 8, 2018: Current Problems in Cancer
Ibrahim Kulac, Sehbal Arslankoz, George J Netto, Dilek Ertoy Baydar
Non-invasive low-grade papillary urothelial carcinoma (NILGPUC) of the bladder is regarded as a relatively indolent disease. However, its propensity for frequent recurrences constitutes a major clinical problem. Additionally, there is a progression risk of 10-15% to either a higher grade and/or a higher stage disease in these tumors. The molecular factors that will predict recurrence and progression in low-grade pTa bladder carcinoma have not yet been elucidated. Herein, we investigated the association of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) alterations with recurrence and progression in NILGPUC using immunohistochemistry...
January 24, 2018: Virchows Archiv: An International Journal of Pathology
Jiao Wang, Yingchun Liu, Ying Liu, Kaixin Du, Shuqi Xu, Yuchen Wang, Mart Krupovic, Xiangdong Chen
Genomes of halophilic archaea typically contain multiple loci of integrated mobile genetic elements (MGEs). Despite the abundance of these elements, however, mechanisms underlying their site-specific integration and excision have not been investigated. Here, we identified and characterized a novel recombination system encoded by the temperate pleolipovirus SNJ2, which infects haloarchaeon Natrinema sp. J7-1. SNJ2 genome is inserted into the tRNAMet gene and flanked by 14 bp direct repeats corresponding to attachment core sites...
March 16, 2018: Nucleic Acids Research
Preston Countryman, Yanlin Fan, Aparna Gorthi, Hai Pan, Jack Strickland, Parminder Kaur, Xuechun Wang, Jiangguo Lin, Xiaoying Lei, Christian White, Changjiang You, Nicolas Wirth, Ingrid Tessmer, Jacob Piehler, Robert Riehn, Alexander J R Bishop, Yizhi Jane Tao, Hong Wang
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single-molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA...
January 19, 2018: Journal of Biological Chemistry
Hannah H Vestergaard, Marcus R Christensen, Ulrik N Lassen
BACKGROUND: advanced-stage non-small cell lung cancer (NSCLC) is characterized by having limited treatment options and thus a poor prognosis. However, new treatment options, in the form of targeted agents (TA), have emerged during recent years. This systematic review aims to provide an overview of the accessible literature in PubMed evaluating TA used on NSCLC patients, and the resulting survival outcomes. METHOD: this systematic literature review was conducted by reviewing all relevant literature in PubMed...
February 2018: Acta Oncologica
Jiqing Wang, Longjie Che, Jon G H Hickford, Huitong Zhou, Zhiyun Hao, Yuzhu Luo, Jiang Hu, Xiu Liu, Shaobin Li
The gene encoding the high glycine/tyrosine keratin-associated protein 20-2 (KAP20-2) gene has been described in humans, but has not been identified in any livestock species. A search for similar sequences in the caprine genome using the human KAP20-2 gene ( KRTAP20-2 ) revealed a homologous sequence on chromosome 1. Three different banding patterns representing distinct sequences ( A - C ) in Longdong cashmere goats were identified using polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis...
November 17, 2017: Genes
Junxiu Sheng, Jinyao Zhao, Qiuhong Xu, Linlin Wang, Wenjing Zhang, Yang Zhang
Colorectal cancer is the third most common type of cancer and the fourth leading cause of cancer-associated mortality worldwide. Serine/arginine-rich splicing factor 1 (SRSF1) is a well-characterized oncogenic factor that promotes tumorigenesis by controlling a number of alternative splicing events. However, there is limited network analysis, from a global aspect, to study the effect of SRSF1 on colorectal cancer. In the present study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of available gene regulation data from The Cancer Genome Atlas database revealed the enriched functions and signaling pathways of SRSF1...
November 2017: Oncology Letters
Shanshan Nie, Minjuan Zhang, Lugang Zhang
BACKGROUND: Calmodulin-like (CML) proteins are a primary family of plant-specific Ca2+ sensors that specifically bind to Ca2+ and deliver a Ca2+ signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L...
November 2, 2017: BMC Genomics
Dong-Dong Yang, Gustavo M de Billerbeck, Jin-Jing Zhang, Frank Rosenzweig, Jean-Marie Francois
Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14 , encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns...
January 1, 2018: Applied and Environmental Microbiology
Shao-Jun Tang
The basic principles of chromosomal organization in eukaryotic cells remain elusive. Current mainstream research efforts largely concentrate on searching for critical packaging proteins involved in organizing chromosomes. I have taken a different perspective, by considering the role of genomic information in chromatins. In particular, I put forward the concept that repetitive DNA elements are key chromosomal packaging modules, and their intrinsic property of homology-based interaction can drive chromatin folding...
October 18, 2017: Genes
Kristina M Chapman, Megan M Wilkey, Kendall E Potter, Barbara C Waldman, Alan S Waldman
We investigated the impact of sequence divergence on DNA double-strand break (DSB) repair occurring via recombination in cultured thymidine kinase deficient mouse fibroblasts. We stably transfected cells with a DNA construct harboring a herpes thymidine kinase (tk) gene (the "recipient") rendered nonfunctional by insertion of an oligonucleotide containing the recognition site for endonuclease I-SceI. The construct also contained a closely linked truncated "donor" tk sequence. The donor could potentially restore function to the recipient gene via recombination provoked by induction of a DSB at the I-SceI site in the recipient...
December 2017: DNA Repair
Bailin Liu, Shuo Zhao, Xiaofei Wu, Xiaoyu Wang, Yunyou Nan, Dongdong Wang, Qin Chen
Phosphate transporter (PHTs) have important roles in Pi acquisition, allocation, and signal transduction. The aim of this study is to provide a comprehensive knowledge of PHTs in potato. Very strict homology search and subsequent domain verification using Hidden Markov Models revealed that the potato genome has 20 StPHT and StPHOs genes which were grouped into 5 phylogenetical clusters including 8 PHT1 homologs,1 PHT2 homolog, 2 PHT3 homologs, 5 PHT4 homologs and 4 PHO homologs. These genes were mapped on ten S...
October 18, 2017: Journal of Biotechnology
So Youn Won, Soo-Jin Kwon, Tae-Ho Lee, Jae-A Jung, Jung Sun Kim, Sang-Ho Kang, Seong-Han Sohn
Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C...
November 2017: Plant Molecular Biology
Salvatore Camiolo, Andrea Porceddu
Pseudogenes are gene copies that have lost the capability to encode a functional protein. Based on their structure, pseudogenes are classified in two types. Processed pseudogenes arise by a process of retrotranscription from a spliced mRNA and subsequent integration into the genome. Nonprocessed (or duplicated) pseudogenes are generated by genomic duplication and subsequent mutations that disable their functionality so that they cannot longer encode a functional protein. Differently from processed pseudogenes, duplicated pseudogenes are expected to conserve the exon-intron structure of their functional paralogs...
2018: Methods in Molecular Biology
Jin Xiao, Keli Dai, Lian Fu, Jan Vrána, Marie Kubaláková, Wentao Wan, Haojie Sun, Jing Zhao, Chunyan Yu, Yufeng Wu, Michael Abrouk, Haiyan Wang, Jaroslav Doležel, Xiue Wang
BACKGROUND: Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. RESULTS: In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1...
October 16, 2017: BMC Genomics
Chensong Yao, Hanwei Yan, Xiaodan Zhang, Rongfu Wang
Orphan genes refer to a group of protein-coding genes lacking recognizable homologs in the other organisms. Extensive studies have demonstrated that numerous newly sequenced genomes contain a significant number of orphan genes, which have important roles in plant's responses to the environment. Due to a lack of phylogenetic conservation, the origin of orphan genes and their functions are currently not well defined. In the present study, a Poaceae orphan genes database (POGD; was established to serve as a user-friendly web interface for entry browsing, searching and downloading orphan genes from various plants...
October 2017: Experimental and Therapeutic Medicine
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