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https://www.readbyqxmd.com/read/28338982/rna-editing-during-sexual-development-occurs-in-distantly-related-filamentous-ascomycetes
#1
Ines Teichert, Tim Dahlmann, Ulrich Kück, Minou Nowrousian
RNA editing is a posttranscriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete Fusarium graminearum that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from Sordaria macrospora and Pyronema confluens, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete Schizosaccharomyces pombe...
March 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334779/targeted-gene-knock-in-by-homology-directed-genome-editing-using-cas9-ribonucleoprotein-and-aav-donor-delivery
#2
Thomas Gaj, Brett T Staahl, Gonçalo M C Rodrigues, Prajit Limsirichai, Freja K Ekman, Jennifer A Doudna, David V Schaffer
Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334154/ethical-issues-of-crispr-technology-and-gene-editing-through-the-lens-of-solidarity
#3
John J Mulvihill, Benjamin Capps, Yann Joly, Tamra Lysaght, Hub A E Zwart, Ruth Chadwick
Background: The avalanche of commentaries on CRISPR-Cas9 technology, a bacterial immune system modified to recognize any short DNA sequence, cut it out, and insert a new one, has rekindled hopes for gene therapy and other applications and raised criticisms of engineering genes in future generations. Sources of data: This discussion draws on articles that emphasize ethics, identified partly through PubMed and Google, 2014-2016. Areas of agreement: CRISPR-Cas9 has taken the pace and prospects for genetic discovery and applications to a high level, stoking anticipation for somatic gene engineering to help patients...
February 23, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/28325688/current-and-emerging-molecular-tests-for-human-papillomavirus-related-neoplasia-in-the-genomic-era
#4
REVIEW
Sixto M Leal, Margaret L Gulley
Laboratory tests have a key role in preventing human papillomavirus (HPV)-driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelial cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential, driven largely by viral interference with cell cycle regulation and the DNA damage response to promote continuous cell division while thwarting apoptosis, which enables mutation accumulation...
March 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28324494/analysis-of-average-telomere-length-in-human-telomeric-protein-knockout-cells-generated-by-crispr-cas9
#5
Jun Xu, Zhou Songyang, Dan Liu, Hyeung Kim
Telomeres play an important role in ensuring the integrity of the genome. Telomere shortening can lead to loss of genetic information and trigger DNA damage responses. Cultured mammalian cells have served as critical model systems for studying the function of telomere binding proteins and telomerase. Tremendous heterogeneity can be observed both between species and within a single cell population. Recent advances in genome editing (such as the development of the CRISPR/Cas9 platform) have further enabled researchers to carry out loss-of-function analysis of how disrupting key players in telomere maintenance affects telomere length regulation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28323069/minicircle-classes-heterogeneity-within-the-tciii-and-tciv-discrete-typing-units-of-trypanosoma-cruzi
#6
S Ortiz, G Osorio, A Solari
The taxon Trypanosoma cruzi, causative agent of Chagas disease, is composed of several discrete typing units (DTUs) named TcI-TcVI, and Tcbat. The history of the taxon T. cruzi is known, even though several controversial aspects remain as the relationships between TcIII and TcIV. We analyzed cloned T. cruzi stocks pertaining to the seven DTUs by filter hybridization tests of PCR amplicons from minicircle variable regions and kinetoplast DNA probes. Minicircle DNA blots from the cloned stocks and filter hybridization with one TcI, one TcII, one TcV, one TcVI, three TcIII, one TcIV from North America and one TcIV kinetoplast DNA probes from South America revealed minicircle variable region cross-reaction in some T...
March 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28323062/new-strategies-and-approaches-for-engineering-biosynthetic-gene-clusters-of-microbial-natural-products
#7
REVIEW
Lei Li, Weihong Jiang, Yinhua Lu
With the rapidly growing number of sequenced microbial (meta)genomes, enormous cryptic natural product (NP) biosynthetic gene clusters (BGCs) have been identified, which are regarded as a rich reservoir for novel drug discovery. A series of powerful tools for engineering BGCs has accelerated the discovery and development of pharmaceutically active NPs. Here, we describe recent advances in the strategies for BGCs manipulation, which are driven by emerging technologies, including efficient DNA recombination systems, versatile CRISPR/Cas9 genome editing tools and diverse DNA assembly methods...
March 16, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28322595/improving-the-quality-of-aav-vector-preparations-the-challenge-of-product-related-impurities
#8
Maria Schnödt, Hildegard Büning
Adeno-associated viral (AAV) vectors have emerged as one of the most popular gene transfer systems in both, research and clinical gene therapy. As AAV vectors are derived from a stealth, nonpathogenic virus and lack an active integrase activity, vectors are frequently applied for in vivo gene therapy of liver, muscle and other post-mitotic tissues. While long-term transgene expression from AAV vector episomes is reported from these tissues, AAV's episomal nature - once regarded as disadvantage - has become an attractive feature for gene editing approaches targeting proliferating cells...
March 21, 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28321286/crispr-cas9-mediated-heterozygous-knockout-of-the-autism-gene-chd8-and-characterization-of-its-transcriptional-networks-in-cerebral-organoids-derived-from-ips-cells
#9
Ping Wang, Ryan Mokhtari, Erika Pedrosa, Michael Kirschenbaum, Can Bayrak, Deyou Zheng, Herbert M Lachman
BACKGROUND: CHD8 (chromodomain helicase DNA-binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is one of the most commonly mutated genes in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities and influence cancer cell proliferation. We previously reported an RNA-seq analysis carried out on neural progenitor cells (NPCs) and monolayer neurons derived from induced pluripotent stem (iPS) cells that were heterozygous for CHD8 knockout (KO) alleles generated using CRISPR-Cas9 gene editing...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28320736/arabidopsis-retinoblastoma-related-directly-regulates-dna-damage-responses-through-functions-beyond-cell-cycle-control
#10
Beatrix M Horvath, Hana Kourova, Szilvia Nagy, Edit Nemeth, Zoltan Magyar, Csaba Papdi, Zaki Ahmad, Gabino F Sanchez-Perez, Serena Perilli, Ikram Blilou, Aladár Pettkó-Szandtner, Zsuzsanna Darula, Tamas Meszaros, Pavla Binarova, Laszlo Bogre, Ben Scheres
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci...
March 20, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28315713/maternal-senp7-programs-meiosis-architecture-and-embryo-survival-in-mouse
#11
ChunJie Huang, Di Wu, XiaoFei Jiao, Faheem Ahmed Khan, ChengLiang Xiong, XiaoMing Liu, Jing Yang, TaiLang Yin, LiJun Huo
Understanding the mechanisms underlying abnormal egg production and pregnancy loss is significant for human fertility. SENP7, a SUMO poly-chain editing enzyme, has been regarded as a mitotic regulator of heterochromatin integrity and DNA repair. Herein, we report the roles of SENP7 in mammalian reproductive scenario. Mouse oocytes deficient in SENP7 experienced meiotic arrest at prophase I and metaphase I stages, causing substantial decrease of mature eggs. Hyperaceylation and hypomethylation of histone H3 and up-regulation of Cdc14B/C accompanied by down-regulation of CyclinB1 and CyclinB2 were further recognized as contributors to defective M-phase entry and spindle assembly in oocytes...
March 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28315663/enhancing-the-catalytic-deamination-activity-of-apobec3c-is-insufficient-to-inhibit-vif-deficient-hiv-1
#12
Ananda Ayyappan Jaguva Vasudevan, Henning Hofmann, Dieter Willbold, Dieter Häussinger, Bernd W Koenig, Carsten Münk
The retroviral restriction factors of the APOBEC3 (A3) cytidine deaminase family catalyze the deamination of cytidines in single-stranded viral DNA. APOBEC3C (A3C) is a strong antiviral factor against viral infectivity factor (vif)-deficient simian immunodeficiency (SIV) Δvif, however, a weak inhibitor against human immunodeficiency virus (HIV)-1 for reasons unknown. The precise link between the antiretroviral effect of A3C and its catalytic activity is incompletely understood. Here we show that the S61P mutation in human A3C (A3C...
March 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28306506/crystal-structure-of-the-minimal-cas9-from-campylobacter-jejuni-reveals-the-molecular-diversity-in-the-crispr-cas9-systems
#13
Mari Yamada, Yuto Watanabe, Jonathan S Gootenberg, Hisato Hirano, F Ann Ran, Takanori Nakane, Ryuichiro Ishitani, Feng Zhang, Hiroshi Nishimasu, Osamu Nureki
The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28296678/endocervical-adenocarcinoma-with-morphologic-features-of-both-usual-and-gastric-types-clinicopathologic-and-immunohistochemical-analyses-and-high-risk-hpv-detection-by-in-situ-hybridization
#14
Tomoko Wada, Yoshihiro Ohishi, Tsunehisa Kaku, Murasaki Aman, Hiroko Imamura, Nobuko Yasutake, Kenzo Sonoda, Kiyoko Kato, Yoshinao Oda
The fourth edition of the World Health Organization classification set up new entities of endocervical adenocarcinoma (ECA), namely the "usual type" and "gastric type." These 2 types are considered to be distinct histogenetically because of their differing immunophenotypes, human papillomavirus (HPV) status, and prognoses. Usual-type ECAs (U-ECAs) are virtually always associated with high-risk human papillomavirus (HR-HPV) infection. Gastric-type ECAs (G-ECAs) are believed not to be associated with HR-HPV infection...
March 14, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28295376/both-maternally-and-paternally-imprinted-genes-regulate-seed-development-in-rice
#15
Jingya Yuan, Sushu Chen, Wu Jiao, Longfei Wang, Limei Wang, Wenxue Ye, Jie Lu, Delin Hong, Siliang You, Zhukuan Cheng, Dong-Lei Yang, Z Jeffrey Chen
Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated. We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology...
March 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28288828/functional-interrogation-of-non-coding-dna-through-crispr-genome-editing
#16
REVIEW
Matthew C Canver, Daniel E Bauer, Stuart H Orkin
ologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence...
March 10, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28288698/crispr-system-for-genome-engineering-the-application-for-autophagy-study
#17
Jianzhou Cui, Shirley Jia Li Chew, Yin Shi, Zhiyuan Gong, Han-Ming Shen
CRISPR/Cas9 is the latest tool introduced in the field of genome engineering and is so far the best genome-editing tool as compared to its precedents such as, meganucleases, zinc finger nucleases (ZFNs) and transcription activator-like effectors (TALENs). The simple design and assembly of the CRISPR/Cas9 system makes genome editing easy to perform as it uses small guide RNAs that correspond to their DNA targets for high efficiency editing. This has helped open the doors for multiplexible genome targeting in many species that were intractable using old genetic perturbation techniques...
March 14, 2017: BMB Reports
https://www.readbyqxmd.com/read/28287101/identification-of-common-non-coding-variants-at-1p22-that-are-functional-for-non-syndromic-orofacial-clefting
#18
Huan Liu, Elizabeth J Leslie, Jenna C Carlson, Terri H Beaty, Mary L Marazita, Andrew C Lidral, Robert A Cornell
Genome-wide association studies (GWAS) do not distinguish between single nucleotide polymorphisms (SNPs) that are causal and those that are merely in linkage-disequilibrium with causal mutations. Here we describe a versatile, functional pipeline and apply it to SNPs at 1p22, a locus identified in several GWAS for non-syndromic cleft lip with or without cleft palate (NS CL/P). First we amplified DNA elements containing the ten most-highly risk-associated SNPs and tested their enhancer activity in vitro, identifying three SNPs with allele-dependent effects on such activity...
March 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28278120/new-gmo-regulations-for-old-determining-a-new-future-for-eu-crop-biotechnology
#19
John Davison, Klaus Ammann
In this review, current EU GMO regulations are subjected to a point-by point analysis to determine their suitability for agriculture in modern Europe. Our analysis concerns present GMO regulations as well as suggestions for possible new regulations for genome editing and New Breeding Techniques (for which no regulations presently exist). Firstly, the present GMO regulations stem from the early days of recombinant DNA and are not adapted to current scientific understanding on this subject. Scientific understanding of GMOs has changed and these regulations are now, not only unfit for their original purpose, but, the purpose itself is now no longer scientifically valid...
January 2, 2017: GM Crops & Food
https://www.readbyqxmd.com/read/28277978/targeted-dna-demethylation-in-human-cells-by-fusion-of-a-plant-5-methylcytosine-dna-glycosylase-to-a-sequence-specific-dna-binding-domain
#20
Jara Teresa Parrilla-Doblas, Rafael R Ariza, Teresa Roldán-Arjona
DNA methylation is a crucial epigenetic mark associated to gene silencing, and its targeted removal is a major goal of epigenetic editing. In animal cells, DNA demethylation involves iterative 5mC oxidation by TET enzymes followed by replication-dependent dilution and/or replication-independent DNA repair of its oxidized derivatives. In contrast, plants use specific DNA glycosylases that directly excise 5mC and initiate its substitution for unmethylated C in a base excision repair process. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5mC DNA glycosylase (ROS1_CD) to the DNA binding domain of yeast GAL4 (GBD)...
February 23, 2017: Epigenetics: Official Journal of the DNA Methylation Society
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