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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 ...


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. ...


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 ...


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 ...


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 ...


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 ...


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 ...


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 ...


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 ...


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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