LaPeruta, Amber J Micic, Jelena Woolford, John L Jr
Published in
Nucleic acids research
During eukaryotic ribosome biogenesis, pre-ribosomes travel from the nucleolus, where assembly is initiated, to the nucleoplasm and then are exported to the cytoplasm, where assembly concludes. Although nuclear export of pre-ribosomes has been extensively investigated, the release of pre-ribosomes from the nucleolus is an understudied phenomenon. I...
Chen, Chuan Wang, Zening Kang, Minhyo Lee, Ki Baek Ge, Xin
Published in
Nucleic acids research
Mammalian cells carrying defined genetic variations have shown great potentials in both fundamental research and therapeutic development. However, their full use was limited by lack of a robust method to construct large monoclonal high-quality combinatorial libraries. This study developed cell cycle arrested recombinase-mediated cassette exchange (...
Lee, Hongwoo Seo, Pil Joon
Published in
Nucleic acids research
Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associatin...
Mayayo-Peralta, Isabel Gregoricchio, Sebastian Schuurman, Karianne Yavuz, Selçuk Zaalberg, Anniek Kojic, Aleksandar Abbott, Nina Geverts, Bart Beerthuijzen, Suzanne Siefert, Joseph
...
Published in
Nucleic acids research
How steroid hormone receptors (SHRs) regulate transcriptional activity remains partly understood. Upon activation, SHRs bind the genome together with a co-regulator repertoire, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited co-regulator complex are essential to drive transcription following horm...
Ghosh, Ishita Kwon, Youngho Shabestari, Aida Badamchi Chikhale, Rupesh Chen, Jing Wiese, Claudia Sung, Patrick De Benedetti, Arrigo
Published in
Nucleic acids research
Environmental agents like ionizing radiation (IR) and chemotherapeutic drugs can cause severe damage to the DNA, often in the form of double-strand breaks (DSBs). Remaining unrepaired, DSBs can lead to chromosomal rearrangements, and cell death. One major error-free pathway to repair DSBs is homologous recombination repair (HRR). Tousled-like kinas...
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...
Ponnienselvan, Karthikeyan Liu, Pengpeng Nyalile, Thomas Oikemus, Sarah Maitland, Stacy A Lawson, Nathan D Luban, Jeremy Wolfe, Scot A
Published in
Nucleic acids research
Prime editing systems have enabled the incorporation of precise edits within a genome without introducing double strand breaks. Previous studies defined an optimal primer binding site (PBS) length for the pegRNA of ∼13 nucleotides depending on the sequence composition. However, optimal PBS length characterization has been based on prime editing out...
Ottesen, Eric W Singh, Natalia N Luo, Diou Kaas, Bailey Gillette, Benjamin J Seo, Joonbae Jorgensen, Hannah J Singh, Ravindra N
Published in
Nucleic acids research
Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule wh...
Singh, Himanshu Das, Chandan K Buchmuller, Benjamin C Schäfer, Lars V Summerer, Daniel Linser, Rasmus
Published in
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...
