Tomoda, Ena Nagao, Asuteka Shirai, Yuki Asano, Kana Suzuki, Takeo Battersby, Brendan J Suzuki, Tsutomu
Published in
Nucleic acids research
Mutations in mitochondrial (mt-)tRNAs frequently cause mitochondrial dysfunction. Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), and myoclonus epilepsy associated with ragged red fibers (MERRF) are major clinical subgroups of mitochondrial diseases caused by pathogenic point mutations in tRNA genes encode...
Singh, Himanshu Das, Chandan K Buchmuller, Benjamin C Schäfer, Lars V Summerer, Daniel Linser, Rasmus
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Nucleic acids research
5-methylcytosine (mC) and its TET-oxidized derivatives exist in CpG dyads of mammalian DNA and regulate cell fate, but how their individual combinations in the two strands of a CpG act as distinct regulatory signals is poorly understood. Readers that selectively recognize such novel 'CpG duplex marks' could be versatile tools for studying their bio...
Zuo, Zheng Billings, Timothy Walker, Michael Petkov, Petko M Fordyce, Polly M Stormo, Gary D
Published in
Nucleic acids research
The human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger arrays should recognize longer DNA-binding sites. However, recent experimental efforts to identify in vivo ZFP binding sites contradict this assumption, with many ex...
Pham, Phuong Wood, Elizabeth A Cox, Michael M Goodman, Myron F
Published in
Nucleic acids research
Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated 'ssGap-seq', we explore RecA and SSB binding to ssDNA on a genomic scale in E. coli in a wide range of genetic backgrounds. Some results are expected. During log phase growth, Re...
Levin, Itay Štrajbl, Marek Fastman, Yair Baran, Dror Twito, Shir Mioduser, Jessica Keren, Adi Fischman, Sharon Zhenin, Michael Nimrod, Guy
...
Published in
Nucleic acids research
Deep parallel sequencing (NGS) is a viable tool for monitoring scFv and Fab library dynamics in many antibody engineering high-throughput screening efforts. Although very useful, the commonly used Illumina NGS platform cannot handle the entire sequence of scFv or Fab in a single read, usually focusing on specific CDRs or resorting to sequencing VH ...
Jennings, Martin D Srivastava, Priya Kershaw, Christopher J Talavera, David Grant, Christopher M Pavitt, Graham D
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Nucleic acids research
In response to oxidative stress cells reprogram gene expression to enhance levels of antioxidant enzymes and promote survival. In Saccharomyces cerevisiae the polysome-interacting La-related proteins (LARPs) Slf1 and Sro9 aid adaptation of protein synthesis during stress by undetermined means. To gain insight in their mechanisms of action in stress...
Cerqueira, Paula G Meyer, Damon Zhang, Lilin Mallory, Benjamin Liu, Jie Hua Fu, Becky Xu Zhang, Xiaoping Heyer, Wolf-Dietrich
Published in
Nucleic acids research
Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat re...
Milenkovic, Ivan Santos Vieira, Helaine Graziele Lucas, Morghan C Ruiz-Orera, Jorge Patone, Giannino Kesteven, Scott Wu, Jianxin Feneley, Michael Espadas, Guadalupe Sabidó, Eduard
...
Published in
Nucleic acids research
Ribosomes are macromolecular machines responsible for protein synthesis in all living beings. Recent studies have shown that ribosomes can be heterogeneous in their structure, possibly leading to a specialized function. Here, we focus on RPL3L, a ribosomal protein expressed exclusively in striated muscles. We find that the deletion of the Rpl3l gen...
Hernández-Carralero, Esperanza Cabrera, Elisa Rodríguez-Torres, Gara Hernández-Reyes, Yeray Singh, Abhay N Santa-María, Cristina Fernández-Justel, José Miguel Janssens, Roel C Marteijn, Jurgen A Evert, Bernd O
...
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Nucleic acids research
The deubiquitinating enzyme Ataxin-3 (ATXN3) contains a polyglutamine (PolyQ) region, the expansion of which causes spinocerebellar ataxia type-3 (SCA3). ATXN3 has multiple functions, such as regulating transcription or controlling genomic stability after DNA damage. Here we report the role of ATXN3 in chromatin organization during unperturbed cond...
FitzPatrick, Vincent D Leemans, Christ van Arensbergen, Joris van Steensel, Bas Bussemaker, Harmen J
Published in
Nucleic acids research
Classic promoter mutagenesis strategies can be used to study how proximal promoter regions regulate the expression of particular genes of interest. This is a laborious process, in which the smallest sub-region of the promoter still capable of recapitulating expression in an ectopic setting is first identified, followed by targeted mutation of putat...
