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745 Aktuelle Fachpublikationen zum Thema Addition

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sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

01.02.2015 | Atul Kakrana; Reza Hammond; Parth Patel; Mayumi Nakano; Blake C. Meyers, Nucleic Acids Research, 2015

Parallel analysis of RNA ends (PARE) is a technique utilizing high-throughput sequencing to profile uncapped, mRNA cleavage or decay products on a genome-wide basis. Tools currently available to validate miRNA targets using PARE data employ only annotated genes, whereas important targets may be ...

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Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length

01.02.2015 | Jiyong Wang; Xavier Tadeo; Haitong Hou; Stuart Andrews; James J. Moresco; John R. Yates III; Peter L. Nagy; Songtao Jia, Nucleic Acids Research, 2015

Heterochromatin preferentially forms at repetitive DNA elements through RNAi-mediated targeting of histone-modifying enzymes. It was proposed that splicing factors interact with the RNAi machinery or regulate the splicing of repeat transcripts to directly participate in heterochromatin assembly. ...

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Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

01.02.2015 | Stefanie Kellner; Antonia Ochel; Kathrin Thüring; Felix Spenkuch; Jennifer Neumann; Sunny Sharma; Karl-Dieter Entian ..., Nucleic Acids Research, 2015

In the resurging field of RNA modifications, quantification is a bottleneck blocking many exciting avenues. With currently over 150 known nucleoside alterations, detection and quantification methods must encompass multiple modifications for a comprehensive profile. LC–MS/MS approaches offer a ...

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Degradation of DNA damage-independently stalled RNA polymerase II is independent of the E3 ligase Elc1

01.12.2014 | Eleni Karakasili; Cornelia Burkert-Kautzsch; Anja Kieser; Katja Sträßer, Nucleic Acids Research, 2014

Transcription elongation is a highly dynamic and discontinuous process, which includes frequent pausing of RNA polymerase II (RNAPII). RNAPII complexes that stall persistently on a gene during transcription elongation block transcription and thus have to be removed. It has been proposed that the ...

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Why double-stranded RNA resists condensation

01.12.2014 | Igor S. Tolokh; Suzette A. Pabit; Andrea M. Katz; Yujie Chen; Aleksander Drozdetski; Nathan Baker; Lois Pollack; Ale ..., Nucleic Acids Research, 2014

The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different ...

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A comprehensive survey of non-canonical splice sites in the human transcriptome

01.12.2014 | Guillermo E. Parada; Roberto Munita; Cledi A. Cerda; Katia Gysling, Nucleic Acids Research, 2014

We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites ...

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Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

01.11.2014 | Alexandre Lomsadze; Paul D. Burns; Mark Borodovsky, Nucleic Acids Research, 2014

We present a new approach to automatic training of a eukaryotic ab initio gene finding algorithm. With the advent of Next-Generation Sequencing, automatic training has become paramount, allowing genome annotation pipelines to keep pace with the speed of genome sequencing. Earlier we developed ...

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Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

01.11.2014 | Tino Köster; Katja Meyer; Claus Weinholdt; Lisa M. Smith; Martina Lummer; Corinna Speth; Ivo Grosse; Detlef Weigel; ..., Nucleic Acids Research, 2014

The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a ...

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Arginine methylation of hnRNPK negatively modulates apoptosis upon DNA damage through local regulation of phosphorylation

01.11.2014 | Jen-Hao Yang; Yi-Ying Chiou; Shu-Ling Fu; I-Yun Shih; Tsai-Hsuan Weng; Wey-Jinq Lin; Chao-Hsiung Lin, Nucleic Acids Research, 2014

Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an RNA/DNA-binding protein involved in chromatin remodeling, RNA processing and the DNA damage response. In addition, increased hnRNPK expression has been associated with tumor development and progression. A variety of post-translational ...

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The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription

01.11.2014 | María Carmen Mirón-García; Ana Isabel Garrido-Godino; Verónica Martínez-Fernández; Antonio Fernández-Pevida; Abel Cu ..., Nucleic Acids Research, 2014

Bud27, the yeast orthologue of human URI/RMP, is a member of the prefoldin-like family of ATP-independent molecular chaperones. It has recently been shown to mediate the assembly of the three RNA polymerases in an Rpb5-dependent manner. In this work, we present evidence of Bud27 modulating RNA ...

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