EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates
暂无分享,去创建一个
Joshua D. Welch | Joshua D Welch | William F Marzluff | Michael K. Slevin | J. Prins | R. Duronio | W. Marzluff | D. Tatomer | Michael K Slevin | Deirdre C Tatomer | Robert J Duronio | Jan F Prins | Deirdre C. Tatomer
[1] G. Church,et al. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation , 2008, Nature Methods.
[2] Z. Dominski,et al. A 3' exonuclease that specifically interacts with the 3' end of histone mRNA. , 2003, Molecular cell.
[3] D. Hogness,et al. The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications. , 1978, Cold Spring Harbor symposia on quantitative biology.
[4] Julie L. Yang,et al. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression , 2013, Genes & development.
[5] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[6] Yongsheng Shi,et al. Global and quantitative profiling of polyadenylated RNAs using PAS-seq. , 2014, Methods in molecular biology.
[7] W. Marzluff,et al. The Oligo(A) Tail on Histone mRNA Plays an Active Role in Translational Silencing of Histone mRNA during Xenopus Oogenesis , 2004, Molecular and Cellular Biology.
[8] T. Jensen,et al. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells , 2009, Nature Structural &Molecular Biology.
[9] Thomas Tuschl,et al. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. , 2008, Methods.
[10] R. Graves,et al. Rapid reversible changes in the rate of histone gene transcription and histone mRNA levels in mouse myeloma cells , 1984, Molecular and cellular biology.
[11] Z. Dominski,et al. Characterization of 3′hExo, a 3′ Exonuclease Specifically Interacting with the 3′ End of Histone mRNA* , 2006, Journal of Biological Chemistry.
[12] Peter J. Shepard,et al. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. , 2011, RNA.
[13] R. Duronio,et al. Genetic and biochemical characterization of Drosophila Snipper: A promiscuous member of the metazoan 3'hExo/ERI-1 family of 3' to 5' exonucleases. , 2006, RNA.
[14] H. Kremer,et al. Two types of polyadenated mRNAs are synthesized from Drosophila replication-dependent histone genes. , 1997, European journal of biochemistry.
[15] C. Norbury,et al. Decapping is preceded by 3' uridylation in a novel pathway of bulk mRNA turnover. , 2009, Nature structural & molecular biology.
[16] S. Luo,et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. , 2011, RNA.
[17] Joshua D. Welch,et al. Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes. , 2014, Molecular cell.
[18] R. Duronio,et al. A sequence in the Drosophila H3-H4 Promoter triggers histone locus body assembly and biosynthesis of replication-coupled histone mRNAs. , 2013, Developmental cell.
[19] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[20] H. Goodman,et al. Uridine Addition After MicroRNA-Directed Cleavage , 2004, Science.
[21] Vidya Mani,et al. Deep sequencing of microRNA precursors reveals extensive 3' end modification. , 2011, RNA.
[22] Mihaela Zavolan,et al. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. , 2012, Cell reports.
[23] William F Marzluff,et al. Differences and similarities between Drosophila and mammalian 3' end processing of histone pre-mRNAs. , 2005, RNA.
[24] P. Schedl,et al. Two discrete modes of histone gene expression during oogenesis in Drosophila melanogaster. , 1985, Developmental biology.
[25] J. Steitz,et al. The site of 3′ end formation of histone messenger RNA is a fixed distance from the downstream element recognized by the U7 snRNP. , 1994, The EMBO journal.
[26] K. D. Sullivan,et al. Studies of the 5′ Exonuclease and Endonuclease Activities of CPSF-73 in Histone Pre-mRNA Processing , 2008, Molecular and Cellular Biology.
[27] D. Fargo,et al. Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. , 2013, Molecular cell.
[28] C. Norbury,et al. 3′ uridylation precedes decapping in a novel pathway of bulk mRNA turnover , 2009, Nature Structural &Molecular Biology.
[29] J. Deragon,et al. Uridylation prevents 3′ trimming of oligoadenylated mRNAs , 2013, Nucleic acids research.
[30] Wencheng Li,et al. Accurate mapping of cleavage and polyadenylation sites by 3' region extraction and deep sequencing. , 2014, Methods in molecular biology.
[31] E. Wagner,et al. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail , 2008, Nature Reviews Genetics.
[32] Wei Li,et al. CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression , 2014, Nature.
[33] Christus,et al. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .
[34] Jennifer Hesson,et al. Untemplated Oligoadenylation Promotes Degradation of RISC-Cleaved Transcripts , 2006, Science.
[35] E. Kremmer,et al. Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay , 2012, Nature Structural &Molecular Biology.
[36] A. Ruddell,et al. Biphasic pattern of histone gene expression during Drosophila oogenesis. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[37] C. Mayr,et al. Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.
[38] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[39] Michael K. Slevin,et al. mRNAs containing the histone 3' stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3' end. , 2013, RNA.
[40] T. Mullen,et al. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. , 2008, Genes & development.
[41] M. Pardue,et al. A portion of all major classes of histone messenger RNA in amphibian oocytes is polyadenylated. , 1978, The Journal of biological chemistry.
[42] V. Kim,et al. TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. , 2014, Molecular cell.