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14.901 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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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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Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4)

01.02.2015 | James E. Thornton; Peng Du; Lili Jing; Ljiljana Sjekloca; Shuibin Lin; Elena Grossi; Piotr Sliz; Leonard I. Zon; Ric ..., Nucleic Acids Research, 2015

Recent small RNA sequencing data has uncovered 3' end modification of mature microRNAs (miRNAs). This non-templated nucleotide addition can impact miRNA gene regulatory networks through the control of miRNA stability or by interfering with the repression of target mRNAs. The miRNA modifying ...

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A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

01.02.2015 | Eliza J.R. Peterson; David J. Reiss; Serdar Turkarslan; Kyle J. Minch; Tige Rustad; Christopher L. Plaisier; William ..., Nucleic Acids Research, 2015

The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability to effectively counteract and even take advantage of the hostile environments of a host. In order to accelerate the discovery and characterization of these adaptive mechanisms, we have mined a compendium of 2325 ...

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Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae

01.02.2015 | Xin Deng; Haihua Liang; Kai Chen; Chuan He; Lefu Lan; Xiaoyan Tang, Nucleic Acids Research, 2015

Pseudomonas syringae uses the two-component system RhpRS to regulate the expression of type III secretion system (T3SS) genes and bacterial virulence. However, the molecular mechanisms and the regulons of RhpRS have yet to be fully elucidated. Here, we show that RhpS functions as a kinase and a ...

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MRTF-A steers an epigenetic complex to activate endothelin-induced pro-inflammatory transcription in vascular smooth muscle cells

01.12.2014 | Yuyu Yang; Xian Cheng; Wenfang Tian; Bisheng Zhou; Xiaoyan Wu; Huihui Xu; Fei Fang; Mingming Fang; Yong Xu, Nucleic Acids Research, 2014

Endothelin (ET-1) was initially identified as a potent vasoconstrictor contributing to the maintenance of vascular rhythm. Later studies have implicated ET-1, when aberrantly up-regulated within the vasculature, in a range of human pathologies associated with disruption of vascular homeostasis. ...

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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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Probing the elastic limit of DNA bending

01.12.2014 | Tung T. Le; Harold D. Kim, Nucleic Acids Research, 2014

Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using ...

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Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation

01.12.2014 | Matthew R. Grimmer; Sabine Stolzenburg; Ethan Ford; Ryan Lister; Pilar Blancafort; Peggy J. Farnham, Nucleic Acids Research, 2014

Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have ...

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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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