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Chromosome homology search

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https://www.readbyqxmd.com/read/29175904/cohesin-sa2-is-a-sequence-independent-dna-binding-protein-that-recognizes-dna-replication-and-repair-intermediates
#1
Preston Countryman, Yanlin Fan, Aparna Gorthi, Hai Pan, Jack Strickland, Parminder Kaur, Xuechun Wang, Jianggguo Lin, Xiaoying Lei, Christian White, Changjiang You, Nicolas Wirth, Ingrid Tessmer, Jacob Pieler, 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...
November 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29172833/a-systematic-review-of-targeted-agents-for-non-small-cell-lung-cancer
#2
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...
November 25, 2017: Acta Oncologica
https://www.readbyqxmd.com/read/29149036/identification-of-the-caprine-keratin-associated-protein-20-2-kap20-2-gene-and-its-effect-on-cashmere-traits
#3
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
https://www.readbyqxmd.com/read/29113173/bioinformatics-analysis-of-srsf1-controlled-gene-networks-in-colorectal-cancer
#4
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
https://www.readbyqxmd.com/read/29096605/genome-wide-identification-and-expression-analysis-of-calmodulin-like-cml-genes-in-chinese-cabbage-brassica-rapa-l-ssp-pekinensis
#5
Shanshan Nie, Minjuan Zhang, Lugang Zhang
BACKGROUND: Calmodulin-like (CML) proteins are a primary family of plant-specific Ca(2+) sensors that specifically bind to Ca(2+) and deliver a Ca(2+) 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
https://www.readbyqxmd.com/read/29079624/deciphering-the-origin-evolution-and-physiological-function-of-the-subtelomeric-aryl-alcohol-dehydrogenase-gene-family-in-the-yeast-saccharomyces-cerevisiae
#6
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 AADs 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 oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns...
October 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29057826/potential-role-of-phase-separation-of-repetitive-dna-in-chromosomal-organization
#7
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
https://www.readbyqxmd.com/read/29055804/high-homology-is-not-required-at-the-site-of-strand-invasion-during-recombinational-double-strand-break-repair-in-mammalian-chromosomes
#8
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
https://www.readbyqxmd.com/read/29055693/identification-and-characterization-of-phosphate-transporter-genes-in-potato
#9
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
https://www.readbyqxmd.com/read/29052098/comparative-transcriptome-analysis-reveals-whole-genome-duplications-and-gene-selection-patterns-in-cultivated-and-wild-chrysanthemum-species
#10
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
https://www.readbyqxmd.com/read/29039010/identification-of-pseudogenes-in-brachypodium-distachyon-chromosomes
#11
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
https://www.readbyqxmd.com/read/29037165/sequencing-flow-sorted-short-arm-of-haynaldia-villosa-chromosome-4v-provides-insights-into-its-molecular-structure-and-virtual-gene-order
#12
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
https://www.readbyqxmd.com/read/28966675/a-database-for-orphan-genes-in-poaceae
#13
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; http://bioinfo.ahau.edu.cn/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
https://www.readbyqxmd.com/read/28838355/sixteen-years-of-meiotic-silencing-by-unpaired-dna
#14
T M Hammond
The filamentous fungus Neurospora crassa possesses a process called meiotic silencing by unpaired DNA (MSUD). MSUD has a remarkable ability to scan homologous chromosomes for unpaired DNA during meiosis. After unpaired DNA is identified, MSUD silences all RNA from the unpaired DNA along with any RNA transcribed from homologous sequences at other locations in the genome, regardless of their pairing state. The mechanism by which unpaired DNA is detected is unknown. Unpaired DNA segments can be as short as 1.3kb, if not shorter, and DNA sequences with only a small level of polymorphism (6%) can be considered unpaired by MSUD...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/28799009/genome-wide-survey-and-characterization-of-fatty-acid-desaturase-gene-family-in-brassica-napus-and-its-parental-species
#15
Yufei Xue, Baojun Chen, Rui Wang, Aung Naing Win, Jiana Li, Yourong Chai
Rapeseed (Brassica napus) is an important oilseed crop worldwide, and fatty acid (FA) compositions determine the nutritional and economic value of its seed oil. Fatty acid desaturases (FADs) play a pivotal role in regulating FA compositions, but to date, no comprehensive genome-wide analysis of FAD gene family in rapeseed and its parent species has been reported. In this study, using homology searches, 84, 45, and 44 FAD genes were identified in rapeseed, Brassica rapa, and Brassica oleracea genomes, respectively...
August 10, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28708824/tex19-1-promotes-spo11-dependent-meiotic-recombination-in-mouse-spermatocytes
#16
James H Crichton, Christopher J Playfoot, Marie MacLennan, David Read, Howard J Cooke, Ian R Adams
Meiosis relies on the SPO11 endonuclease to generate the recombinogenic DNA double strand breaks (DSBs) required for homologous chromosome synapsis and segregation. The number of meiotic DSBs needs to be sufficient to allow chromosomes to search for and find their homologs, but not excessive to the point of causing genome instability. Here we report that the mammal-specific gene Tex19.1 promotes Spo11-dependent recombination in mouse spermatocytes. We show that the chromosome asynapsis previously reported in Tex19...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28700723/position-effects-influencing-intrachromosomal-repair-of-a-double-strand-break-in-budding-yeast
#17
Ruoxi W Wang, Cheng-Sheng Lee, James E Haber
Repair of a double-strand break (DSB) by an ectopic homologous donor sequence is subject to the three-dimensional arrangement of chromosomes in the nucleus of haploid budding yeast. The data for interchromosomal recombination suggest that searching for homology is accomplished by a random collision process, strongly influenced by the contact probability of the donor and recipient sequences. Here we explore how recombination occurs on the same chromosome and whether there are additional constraints imposed on repair...
2017: PloS One
https://www.readbyqxmd.com/read/28693746/so-similar-yet-so-different-the-two-ends-of-a-double-strand-break
#18
REVIEW
Keun P Kim, Ekaterina V Mirkin
Homologous recombination (HR) is essential for ensuring proper segregation of chromosomes in the first round of meiotic division. HR is also crucial for preserving genomic integrity of somatic cells due to its ability to rescue collapsed replication forks and eliminate deleterious DNA lesions, such as double-strand breaks (DSBs), interstrand crosslinks, and single-strand DNA gaps. Here, we review the early steps of HR (homology search and strand exchange), focusing on the roles of the two ends of a DSB. A detailed overview of the basic HR machinery and its mechanism for template selection and capture of duplex DNA via strand exchange is provided...
June 27, 2017: Mutation Research
https://www.readbyqxmd.com/read/28692038/par-terra-directs-homologous-sex-chromosome-pairing
#19
Hsueh-Ping Chu, John E Froberg, Barry Kesner, Hyun Jung Oh, Fei Ji, Ruslan Sadreyev, Stefan F Pinter, Jeannie T Lee
In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts...
August 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28667016/an-rna-recognition-motif-containing-protein-functions-in-meiotic-silencing-by-unpaired-dna
#20
Dilini A Samarajeewa, Pennapa Manitchotpisit, Miranda Henderson, Hua Xiao, David G Rehard, Kevin A Edwards, Patrick K T Shiu, Thomas M Hammond
Meiotic silencing by unpaired DNA (MSUD) is a biological process that searches pairs of homologous chromosomes (homologs) for segments of DNA that are unpaired. Genes found within unpaired segments are silenced for the duration of meiosis. In this report, we describe the identification and characterization of Neurospora crassa sad-7, a gene that encodes a protein with an RNA recognition motif (RRM). Orthologs of sad-7 are found in a wide range of ascomycete fungi. In N. crassa, sad-7 is required for a fully efficient MSUD response to unpaired genes...
August 7, 2017: G3: Genes—Genomes—Genetics
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