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16.743 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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Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites

01.02.2015 | Keisuke Shoji; Kahori Hara; Munetaka Kawamoto; Takashi Kiuchi; Shinpei Kawaoka; Sumio Sugano; Toru Shimada; Yutaka S ..., Nucleic Acids Research, 2015

Heterochromatin protein 1 (HP1) is an evolutionarily conserved protein across different eukaryotic species and is crucial for heterochromatin establishment and maintenance. The silkworm, Bombyx mori, encodes two HP1 proteins, BmHP1a and BmHP1b. In order to investigate the role of BmHP1a in ...

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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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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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Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians

15.12.2014 | Kyung-Won Hong; Ji Eun Lim; Jong Wook Kim; Yasuharu Tabara; Hirotsugu Ueshima; Tetsuro Miki; Fumihiko Matsuda; Yoon ..., Human Molecular Genetics, 2014

The electrocardiogram has several advantages in detecting cardiac arrhythmia—it is readily available, noninvasive and cost-efficient. Recent genome-wide association studies have identified single-nucleotide polymorphisms that are associated with electrocardiogram measures. We performed 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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Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site

01.12.2014 | Agata L. Starosta; Jürgen Lassak; Lauri Peil; Gemma C. Atkinson; Kai Virumäe; Tanel Tenson; Jaanus Remme; Kirsten Ju ..., Nucleic Acids Research, 2014

The polymerization of amino acids into proteins occurs on ribosomes, with the rate influenced by the amino acids being polymerized. The imino acid proline is a poor donor and acceptor for peptide-bond formation, such that translational stalling occurs when three or more consecutive prolines (PPP) ...

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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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