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https://www.readbyqxmd.com/read/28724077/physical-map-of-the-short-arm-of-bread-wheat-chromosome-3d
#1
Kateřina Holušová, Jan Vrána, Jan Šafář, Hana Šimková, Barbora Balcárková, Zeev Frenkel, Benoit Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel, Jan Bartoš
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#2
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28716627/membrane-proteins-structures-a-review-on-computational-modeling-tools
#3
REVIEW
Jose G Almeida, Antonio J Preto, Panagiotis I Koukos, Alexandre M J J Bonvin, Irina S Moreira
BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28715506/analysis-of-aquaporins-from-the-euryhaline-barnacle-balanus-improvisus-reveals-differential-expression-in-response-to-changes-in-salinity
#4
Ulrika Lind, Michael Järvå, Magnus Alm Rosenblad, Piero Pingitore, Emil Karlsson, Anna-Lisa Wrange, Emelie Kamdal, Kristina Sundell, Carl André, Per R Jonsson, Jon Havenhand, Leif A Eriksson, Kristina Hedfalk, Anders Blomberg
Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms...
2017: PloS One
https://www.readbyqxmd.com/read/28715472/a-novel-isoform-of-il-33-revealed-by-screening-for-transposable-element-promoted-genes-in-human-colorectal-cancer
#5
Frances E Lock, Artem Babaian, Ying Zhang, Liane Gagnier, Sabrina Kuah, Antonia Weberling, Mohammad M Karimi, Dixie L Mager
Remnants of ancient transposable elements (TEs) are abundant in mammalian genomes. These sequences contain multiple regulatory motifs and hence are capable of influencing expression of host genes. TEs are known to be released from epigenetic repression and can become transcriptionally active in cancer. Such activation could also lead to lineage-inappropriate activation of oncogenes, as previously described in lymphomas. However, there are few reports of this mechanism occurring in non-blood cancers. Here, we re-analyzed whole transcriptome data from a large cohort of patients with colon cancer, compared to matched normal colon control samples, to detect genes or transcripts ectopically expressed through activation of TE promoters...
2017: PloS One
https://www.readbyqxmd.com/read/28709003/3d-chromatin-structures-of-mature-gametes-and-structural-reprogramming-during-mammalian-embryogenesis
#6
Yuwen Ke, Yanan Xu, Xuepeng Chen, Songjie Feng, Zhenbo Liu, Yaoyu Sun, Xuelong Yao, Fangzhen Li, Wei Zhu, Lei Gao, Haojie Chen, Zhenhai Du, Wei Xie, Xiaocui Xu, Xingxu Huang, Jiang Liu
High-order chromatin structure plays important roles in gene expression regulation. Knowledge of the dynamics of 3D chromatin structures during mammalian embryo development remains limited. We report the 3D chromatin architecture of mouse gametes and early embryos using an optimized Hi-C method with low-cell samples. We find that mature oocytes at the metaphase II stage do not have topologically associated domains (TADs). In sperm, extra-long-range interactions (>4 Mb) and interchromosomal interactions occur frequently...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28704353/organization-and-function-of-the-3d-genome
#7
Boyan Bonev, Giacomo Cavalli
No abstract text is available yet for this article.
December 2016: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28703188/allelic-reprogramming-of-3d-chromatin-architecture-during-early-mammalian-development
#8
Zhenhai Du, Hui Zheng, Bo Huang, Rui Ma, Jingyi Wu, Xianglin Zhang, Jing He, Yunlong Xiang, Qiujun Wang, Yuanyuan Li, Jing Ma, Xu Zhang, Ke Zhang, Yang Wang, Michael Q Zhang, Juntao Gao, Jesse R Dixon, Xiaowo Wang, Jianyang Zeng, Wei Xie
In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs) and chromatin compartments...
July 12, 2017: Nature
https://www.readbyqxmd.com/read/28702048/aegilops-tauschii-accessions-with-geographically-diverse-origin-show-differences-in-chromosome-organization-and-polymorphism-of-molecular-markers-linked-to-leaf-rust-and-powdery-mildew-resistance-genes
#9
Maciej Majka, Michał T Kwiatek, Joanna Majka, Halina Wiśniewska
Aegilops tauschii (2n = 2x = 14) is a diploid wild species which is reported as a donor of the D-genome of cultivated bread wheat. The main goal of this study was to examine the differences and similarities in chromosomes organization among accessions of Ae. tauschii with geographically diversed origin, which is believed as a potential source of genes, especially determining resistance to fungal diseases (i.e., leaf rust and powdery mildew) for breeding of cereals. We established and compared the fluorescence in situ hybridization patterns of 21 accessions of Ae...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28702010/comparison-among-the-quantification-of-bacterial-pathogens-by-qpcr-dpcr-and-cultural-methods
#10
Matteo Ricchi, Cristina Bertasio, Maria B Boniotti, Nadia Vicari, Simone Russo, Michela Tilola, Marco A Bellotti, Barbara Bertasi
The demand for rapid methods for the quantification of pathogens is increasing. Among these methods, those based on nucleic acids amplification (quantitative PCRs) are the most widespread worldwide. Together with the qPCR, a new approach named digital PCR (dPCR), has rapidly gained importance. The aim of our study was to compare the results obtained using two different dPCR systems and one qPCR in the quantification of three different bacterial pathogens: Listeria monocytogenes, Francisella tularensis, and Mycobacterium avium subsp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28693426/evolution-gene-expression-profiling-and-3d-modeling-of-csld-proteins-in-cotton
#11
Yanpeng Li, Tiegang Yang, Dandan Dai, Ying Hu, Xiaoyang Guo, Hongxia Guo
BACKGROUND: Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes. RESULTS: A total of 23 full-length CSLD proteins were identified in Gossypium raimondii, Gossypium arboreum and Gossypium hirsutum...
July 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28692038/par-terra-directs-homologous-sex-chromosome-pairing
#12
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...
July 10, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28679078/structural-modelling-and-molecular-dynamics-of-a-multi-stress-responsive-wrky-tf-dna-complex-towards-elucidating-its-role-in-stress-signalling-mechanisms-in-chickpea
#13
Aravind Kumar Konda, Rohit Farmer, Khela Ram Soren, P S Shanmugavadivel, Aravind Setti
Chickpea is a premier food legume crop with high nutritional quality and attains prime importance in the current era of 795 million people being undernourished worldwide. Chickpea production encounters setbacks due to various stresses and understanding the role of key transcription factors involved in multiple stresses becomes inevitable. We have recently identified a multi-stress responsive WRKY transcription factor (TF) in chickpea. The present study was conducted to predict the structure of WRKY TF to identify the DNA interacting residues and decipher DNA-protein interactions...
July 5, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28678427/clear-cell-and-endometrioid-carcinomas-are-their-differences-attributable-to-distinct-cells-of-origin
#14
Dawn R Cochrane, Basile Tessier-Cloutier, Katherine M Lawrence, Tayyebeh Nazeran, Anthony N Karnezis, Clara Salamanca, Angela S Cheng, Jessica N McAlpine, Lien N Hoang, C Blake Gilks, David G Huntsman
Endometrial epithelium is the presumed tissue of origin for both eutopic and endometriosis-derived clear cell and endometrioid carcinomas. We had previously hypothesized that the morphological, biological and clinical differences between these carcinomas are due to histotype-specific mutations. Although some mutations and genomic landscape features are more likely to be found in one of these histotypes, we were not able to identify a single class of mutations that was exclusively present in one histotype and not the other...
July 5, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28671686/the-methyltransferase-setdb1-regulates-a-large-neuron-specific-topological-chromatin-domain
#15
Yan Jiang, Yong-Hwee Eddie Loh, Prashanth Rajarajan, Teruyoshi Hirayama, Will Liao, Bibi S Kassim, Behnam Javidfar, Brigham J Hartley, Lisa Kleofas, Royce B Park, Benoit Labonte, Seok-Man Ho, Sandhya Chandrasekaran, Catherine Do, Brianna R Ramirez, Cyril J Peter, Julia T C W, Brian M Safaie, Hirofumi Morishita, Panos Roussos, Eric J Nestler, Anne Schaefer, Benjamin Tycko, Kristen J Brennand, Takeshi Yagi, Li Shen, Schahram Akbarian
We report locus-specific disintegration of megabase-scale chromosomal conformations in brain after neuronal ablation of Setdb1 (also known as Kmt1e; encodes a histone H3 lysine 9 methyltransferase), including a large topologically associated 1.2-Mb domain conserved in humans and mice that encompasses >70 genes at the clustered protocadherin locus (hereafter referred to as cPcdh). The cPcdh topologically associated domain (TAD(cPcdh)) in neurons from mutant mice showed abnormal accumulation of the transcriptional regulator and three-dimensional (3D) genome organizer CTCF at cryptic binding sites, in conjunction with DNA cytosine hypomethylation, histone hyperacetylation and upregulated expression...
July 3, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28669984/cancer-genetics-a-3d-view-of-genome-rearrangements
#16
Linda Koch
No abstract text is available yet for this article.
August 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28667649/analysis-of-transcription-factors-among-differentially-expressed-genes-induced-by-drought-stress-in-populus-davidiana
#17
Bong-Gyu Mun, Sang-Uk Lee, Eung-Jun Park, Hyun-Ho Kim, Adil Hussain, Qari Muhammad Imran, In-Jung Lee, Byung-Wook Yun
Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively...
July 2017: 3 Biotech
https://www.readbyqxmd.com/read/28667427/variation-of-synechococcus-pigment-genetic-diversity-along-two-turbidity-gradients-in-the-china-seas
#18
Xiaomin Xia, Hongbin Liu, Donghan Choi, Jae Hoon Noh
Synechococcus are important and widely distributed picocyanobacteria that encompass a high pigment diversity. In this study, we developed a primer set (peBF/peAR) for amplifying the cpeBA operon sequence from Synechococcus genomic DNA to study Synechococcus pigment diversity along two turbidity gradients in the China seas. Our data revealed that all previously reported pigment types occurred in the South (SCS) and East (ECS) China Seas. In addition, a novel pigment genetic type (type 3f), represented by the high phycourobilin Synechococcus sp...
July 1, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28667246/genetic-profile-and-biological-implication-of-pin2-trf1-interacting-telomerase-inhibitor-1-pinx1-in-human-cancers-an-analysis-using-the-cancer-genome-atlas
#19
Wei-Juan Huang, Mei Li, Xiao-Han Jin, Xiao-Jia Huang, Wei Zhao, Xiao-Peng Tian
Pin2/TRF1-interacting telomere inhibitor 1 (PinX1) was originally identified as a telomerase inhibitor, involved in maintaining telomerase activity, telomere length, and chromosomal stability. However, research has shown that PinX1 can have opposing molecular status in its expression patterns in several other tumor types. We thus investigated the genetic profile and biological implication of PinX1 in several human cancers using the cBioportal database. Our results showed that PinX1 deletion accounted for the most alterations, with the frequency of its deletion regularly occurring in pathological types of carcinosarcoma and adenocarcinoma...
June 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28659472/crystal-structure-and-thermostability-characterization-of-ev-d68-3d-pol
#20
Chunnian Wang, Caiyan Wang, Qing Li, Zhong Wang, Wei Xie
Enterovirus-D68 (EV-D68) is one of the many non-polio enteroviruses that cause mild-to-severe respiratory illness. The non-structural protein 3D(pol) is an RNA-dependent RNA polymerase (RdRP) of EV-D68, which plays a critical role in the replication of the viral genome and represents a promising drug target. Here we report the first three-dimensional crystal structure of RdRP from EV-D68 in complex with the substrate GTP to 2.3-Å resolution. The RdRP structure is similar to those of other viral RdRPs, where the three domains termed the palm, fingers, and thumb form a structure resembling a cupped right hand...
June 28, 2017: Journal of Virology
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