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Phillip D Zamore

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https://www.readbyqxmd.com/read/29499946/transcriptome-profiling-of-neovascularized-corneas-reveals-mir-204-as-a-multi-target-biotherapy-deliverable-by-raavs
#1
Yi Lu, Phillip W L Tai, Jianzhong Ai, Dominic J Gessler, Qin Su, Xieyi Yao, Qiang Zheng, Phillip D Zamore, Xun Xu, Guangping Gao
Corneal neovascularization (NV) is the major sight-threatening pathology caused by angiogenic stimuli. Current drugs that directly target pro-angiogenic factors to inhibit or reverse the disease require multiple rounds of administration and have limited efficacies. Here, we identify potential anti-angiogenic corneal microRNAs (miRNAs) and demonstrate a framework that employs discovered miRNAs as biotherapies deliverable by recombinant adeno-associated viruses (rAAVs). By querying differentially expressed miRNAs in neovascularized mouse corneas induced by alkali burn, we have revealed 39 miRNAs that are predicted to target more than 5,500 differentially expressed corneal mRNAs...
March 2, 2018: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/29438062/inhibiting-mirna-function-by-antisense-oligonucleotides-in-drosophila-s2-cells
#2
Chengjian Li, Phillip D Zamore
This protocol describes methods to transfect antisense oligonucleotides (ASOs) into Drosophila S2 cells for suppression of miRNA function. The effects of ASOs on the miRNA are evaluated by measuring the protein level of the putative miRNA target or the activity of a reporter bearing a 3' UTR derived from the putative miRNA target.
February 1, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29438061/inhibiting-mirna-function-by-antisense-oligonucleotides-in-cultured-mammalian-cells
#3
Chengjian Li, Phillip D Zamore
Methods for transfecting antisense oligonucleotides (ASOs) into mammalian cells for suppression of miRNA function are described in this protocol. The effects of ASOs on the miRNA are evaluated by measuring the protein level of the putative miRNA target or the activity of a reporter bearing a 3' untranslated region (3' UTR) derived from the putative miRNA target.
February 1, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29438060/preparation-of-antisense-oligonucleotides-to-inhibit-mirna-function
#4
Chengjian Li, Phillip D Zamore
This protocol is used to design antisense oligonucleotides (ASOs) for specific inhibition of miRNA function in cultured cells. The incorporation of 2'- O -methyl-modifications in ASOs enhances their potency and resistance to degradation, whereas 3'-terminal cholesterol-conjugation facilitates delivery of ASOs into cells.
February 1, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29432571/comparison-of-partially-and-fully-chemically-modified-sirna-in-conjugate-mediated-delivery-in-vivo
#5
Matthew R Hassler, Anton A Turanov, Julia F Alterman, Reka A Haraszti, Andrew H Coles, Maire F Osborn, Dimas Echeverria, Mehran Nikan, William E Salomon, Loïc Roux, Bruno M D C Godinho, Sarah M Davis, David V Morrissey, Phillip D Zamore, S Ananth Karumanchi, Melissa J Moore, Neil Aronin, Anastasia Khvorova
Small interfering RNA (siRNA)-based drugs require chemical modifications or formulation to promote stability, minimize innate immunity, and enable delivery to target tissues. Partially modified siRNAs (up to 70% of the nucleotides) provide significant stabilization in vitro and are commercially available; thus are commonly used to evaluate efficacy of bio-conjugates for in vivo delivery. In contrast, most clinically-advanced non-formulated compounds, using conjugation as a delivery strategy, are fully chemically modified (100% of nucleotides)...
March 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29376823/the-genome-of-the-hi5-germ-cell-line-from-trichoplusia-ni-an-agricultural-pest-and-novel-model-for-small-rna-biology
#6
Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A Quarles, Zhiping Weng, Phillip D Zamore
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni , assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni -specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins...
January 29, 2018: ELife
https://www.readbyqxmd.com/read/29203920/pan-arthropod-analysis-reveals-somatic-pirnas-as-an-ancestral-defence-against-transposable-elements
#7
Samuel H Lewis, Kaycee A Quarles, Yujing Yang, Melanie Tanguy, Lise Frézal, Stephen A Smith, Prashant P Sharma, Richard Cordaux, Clément Gilbert, Isabelle Giraud, David H Collins, Phillip D Zamore, Eric A Miska, Peter Sarkies, Francis M Jiggins
In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods...
January 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/28880287/molecular-biology-rhino-gives-voice-to-silent-chromatin
#8
COMMENT
Phillip D Zamore
No abstract text is available yet for this article.
September 6, 2017: Nature
https://www.readbyqxmd.com/read/28428565/small-methyltransferase-rlmh-assembles-a-composite-active-site-to-methylate-a-ribosomal-pseudouridine
#9
Cha San Koh, Rohini Madireddy, Timothy J Beane, Phillip D Zamore, Andrei A Korostelev
Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27543296/rapid-screening-for-crispr-directed-editing-of-the-drosophila-genome-using-white-coconversion
#10
Daniel Tianfang Ge, Cindy Tipping, Michael H Brodsky, Phillip D Zamore
Adoption of a streamlined version of the bacterial clustered regular interspersed short palindromic repeat (CRISPR)/Cas9 defense system has accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, directed by a simplified, CRISPR-like single-guide RNA, catalyzes a double-stranded DNA break at a specific genomic site; subsequent repair by end joining can introduce mutagenic insertions or deletions, while repair by homologous recombination using an exogenous DNA template can incorporate new sequences at the target locus...
October 13, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/26340424/slicing-and-binding-by-ago3-or-aub-trigger-piwi-bound-pirna-production-by-distinct-mechanisms
#11
Wei Wang, Bo W Han, Cindy Tipping, Daniel Tianfang Ge, Zhao Zhang, Zhiping Weng, Phillip D Zamore
In Drosophila ovarian germ cells, PIWI-interacting RNAs (piRNAs) direct Aubergine and Argonaute3 to cleave transposon transcripts and instruct Piwi to repress transposon transcription, thereby safeguarding the germline genome. Here, we report that RNA cleavage by Argonaute3 initiates production of most Piwi-bound piRNAs. We find that the cardinal function of Argonaute3, whose piRNA guides predominantly correspond to sense transposon sequences, is to produce antisense piRNAs that direct transcriptional silencing by Piwi, rather than to make piRNAs that guide post-transcriptional silencing by Aubergine...
September 3, 2015: Molecular Cell
https://www.readbyqxmd.com/read/26140592/single-molecule-imaging-reveals-that-argonaute-reshapes-the-binding-properties-of-its-nucleic-acid-guides
#12
William E Salomon, Samson M Jolly, Melissa J Moore, Phillip D Zamore, Victor Serebrov
Argonaute proteins repress gene expression and defend against foreign nucleic acids using short RNAs or DNAs to specify the correct target RNA or DNA sequence. We have developed single-molecule methods to analyze target binding and cleavage mediated by the Argonaute:guide complex, RISC. We find that both eukaryotic and prokaryotic Argonaute proteins reshape the fundamental properties of RNA:RNA, RNA:DNA, and DNA:DNA hybridization—a small RNA or DNA bound to Argonaute as a guide no longer follows the well-established rules by which oligonucleotides find, bind, and dissociate from complementary nucleic acid sequences...
July 2, 2015: Cell
https://www.readbyqxmd.com/read/26007652/tailor-a-computational-framework-for-detecting-non-templated-tailing-of-small-silencing-rnas
#13
Min-Te Chou, Bo W Han, Chiung-Po Hsiao, Phillip D Zamore, Zhiping Weng, Jui-Hung Hung
Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3' end, namely tailing, was found to associate with the processing and stability of small silencing RNAs...
September 30, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25977554/noncoding-rna-pirna-guided-transposon-cleavage-initiates-zucchini-dependent-phased-pirna-production
#14
Bo W Han, Wei Wang, Chengjian Li, Zhiping Weng, Phillip D Zamore
PIWI-interacting RNAs (piRNAs) protect the animal germ line by silencing transposons. Primary piRNAs, generated from transcripts of genomic transposon "junkyards" (piRNA clusters), are amplified by the "ping-pong" pathway, yielding secondary piRNAs. We report that secondary piRNAs, bound to the PIWI protein Ago3, can initiate primary piRNA production from cleaved transposon RNAs. The first ~26 nucleotides (nt) of each cleaved RNA becomes a secondary piRNA, but the subsequent ~26 nt become the first in a series of phased primary piRNAs that bind Piwi, allowing piRNAs to spread beyond the site of RNA cleavage...
May 15, 2015: Science
https://www.readbyqxmd.com/read/25866926/assessing-long-distance-rna-sequence-connectivity-via-rna-templated-dna-dna-ligation
#15
Christian K Roy, Sara Olson, Brenton R Graveley, Phillip D Zamore, Melissa J Moore
Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules...
2015: ELife
https://www.readbyqxmd.com/read/25805138/pitfalls-of-mapping-high-throughput-sequencing-data-to-repetitive-sequences-piwi-s-genomic-targets-still-not-identified
#16
Georgi K Marinov, Jie Wang, Dominik Handler, Barbara J Wold, Zhiping Weng, Gregory J Hannon, Alexei A Aravin, Phillip D Zamore, Julius Brennecke, Katalin Fejes Toth
Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors' genome-wide conclusions...
March 23, 2015: Developmental Cell
https://www.readbyqxmd.com/read/25453759/the-initial-uridine-of-primary-pirnas-does-not-create-the-tenth-adenine-that-is-the-hallmark-of-secondary-pirnas
#17
Wei Wang, Mayu Yoshikawa, Bo W Han, Natsuko Izumi, Yukihide Tomari, Zhiping Weng, Phillip D Zamore
PIWI-interacting RNAs (piRNAs) silence transposons in animal germ cells. PIWI proteins bind and amplify piRNAs via the "Ping-Pong" pathway. Because PIWI proteins cleave RNAs between target nucleotides t10 and t11-the nucleotides paired to piRNA guide positions g10 and g11-the first ten nucleotides of piRNAs participating in the Ping-Pong amplification cycle are complementary. Drosophila piRNAs bound to the PIWI protein Aubergine typically begin with uridine (1U), while piRNAs bound to Argonaute3, which are produced by Ping-Pong amplification, often have adenine at position 10 (10A)...
December 4, 2014: Molecular Cell
https://www.readbyqxmd.com/read/25342065/pipipes-a-set-of-pipelines-for-pirna-and-transposon-analysis-via-small-rna-seq-rna-seq-degradome-and-cage-seq-chip-seq-and-genomic-dna-sequencing
#18
Bo W Han, Wei Wang, Phillip D Zamore, Zhiping Weng
MOTIVATION: PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile...
February 15, 2015: Bioinformatics
https://www.readbyqxmd.com/read/25137579/pirnas
#19
Bo W Han, Phillip D Zamore
No abstract text is available yet for this article.
August 18, 2014: Current Biology: CB
https://www.readbyqxmd.com/read/25062733/increased-steady-state-mutant-huntingtin-mrna-in-huntington-s-disease-brain
#20
Wanzhao Liu, Joanna Chaurette, Edith L Pfister, Lori A Kennington, Kathryn O Chase, Jocelyn Bullock, Jean Paul G Vonsattel, Richard L M Faull, Douglas Macdonald, Marian DiFiglia, Phillip D Zamore, Neil Aronin
BACKGROUND: Huntington's disease is caused by expansion of CAG trinucleotide repeats in the first exon of the huntingtin gene, which is essential for both development and neurogenesis. Huntington's disease is autosomal dominant. The normal allele contains 6 to 35 CAG triplets (average, 18) and the mutant, disease-causing allele contains >36 CAG triplets (average, 42). OBJECTIVE: We examined 279 postmortem brain samples, including 148 HD and 131 non-HD controls...
2013: Journal of Huntington's Disease
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