Search Results - "Lambowitz, Alan M"

Broad role for YBX1 in defining the small noncoding RNA composition of exosomes by Shurtleff, Matthew J., Yao, Jun, Qin, Yidan, Nottingham, Ryan M., Temoche-Diaz, Morayma M., Schekman, Randy, Lambowitz, Alan M.

“…RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with…”
Get full text

Efficient and quantitative high-throughput tRNA sequencing by Zheng, Guanqun, Qin, Yidan, Clark, Wesley C, Dai, Qing, Yi, Chengqi, He, Chuan, Lambowitz, Alan M, Pan, Tao

“…The combination of an engineered demthylase and a highly processive reverse transcriptase during tRNA library preparation for high-throughput sequencing allows…”
Get full text

Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes by Temoche-Diaz, Morayma M, Shurtleff, Matthew J, Nottingham, Ryan M, Yao, Jun, Fadadu, Raj P, Lambowitz, Alan M, Schekman, Randy

“…Extracellular vesicles (EVs) encompass a variety of vesicles secreted into the extracellular space. EVs have been implicated in promoting tumor metastasis, but…”
Get full text

Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase–Cas1 fusion protein by Silas, Sukrit, Mohr, Georg, Sidote, David J., Markham, Laura M., Sanchez-Amat, Antonio, Bhaya, Devaki, Lambowitz, Alan M., Fire, Andrew Z.

“…CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats…”
Get full text

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase by Nottingham, Ryan M, Wu, Douglas C, Qin, Yidan, Yao, Jun, Hunicke-Smith, Scott, Lambowitz, Alan M

“…Next-generation RNA sequencing (RNA-seq) has revolutionized our ability to analyze transcriptomes. Current RNA-seq methods are highly reproducible, but each…”
Get full text

Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching by Wu, Douglas C., Lambowitz, Alan M.

“…High-throughput single-stranded DNA sequencing (ssDNA-seq) of cell-free DNA from plasma and other bodily fluids is a powerful method for non-invasive prenatal…”
Get full text

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes by Boivin, Vincent, Deschamps-Francoeur, Gabrielle, Couture, Sonia, Nottingham, Ryan M, Bouchard-Bourelle, Philia, Lambowitz, Alan M, Scott, Michelle S, Abou-Elela, Sherif

“…Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific…”
Get full text

Limitations of alignment-free tools in total RNA-seq quantification by Wu, Douglas C, Yao, Jun, Ho, Kevin S, Lambowitz, Alan M, Wilke, Claus O

“…Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art…”
Get full text

Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5 by Katibah, George E., Qin, Yidan, Sidote, David J., Yao, Jun, Lambowitz, Alan M., Collins, Kathleen

“…Interferon (IFN) responses play key roles in cellular defense against pathogens. Highly expressed IFN-induced proteins with tetratricopeptide repeats (IFITs)…”
Get full text

Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling by Yao, Jun, Wu, Douglas C, Nottingham, Ryan M, Lambowitz, Alan M

“…Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II…”
Get full text

Mobile group II introns by Lambowitz, Alan M, Zimmerly, Steven

“…Mobile group II introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility…”
Get full text

Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p by Mallam, Anna L., Del Campo, Mark, Gilman, Benjamin, Sidote, David J., Lambowitz, Alan M.

“…Analysis of the yeast DEAD-box nucleic acid helicase Mss116p provides a structural model for how DEAD-box proteins recognize and unwind RNA duplexes. DEAD-box…”
Get full text

DEAD-Box Proteins Can Completely Separate an RNA Duplex Using a Single ATP by Chen, Yingfeng, Potratz, Jeffrey P., Tijerina, Pilar, Campo, Mark Del, Lambowitz, Alan M., Russell, Rick

“…DEAD-box proteins are ubiquitous in RNA metabolism and use ATP to mediate RNA conformational changes. These proteins have been suggested to use a fundamentally…”
Get full text

A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum by Mohr, Georg, Hong, Wei, Zhang, Jie, Cui, Gu-zhen, Yang, Yunfeng, Cui, Qiu, Liu, Ya-jun, Lambowitz, Alan M

“…Targetrons are gene targeting vectors derived from mobile group II introns. They consist of an autocatalytic intron RNA (a "ribozyme") and an intron-encoded…”
Get full text

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase by Mallam, Anna L, Sidote, David J, Lambowitz, Alan M

“…How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains…”
Get full text

Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core by Truong, David M, Sidote, David J, Russell, Rick, Lambowitz, Alan M

“…Mobile group II introns are bacterial retrotransposons thought to be evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They…”
Get full text

Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail by Mallam, Anna L, Jarmoskaite, Inga, Tijerina, Pilar, Del Campo, Mark, Seifert, Soenke, Guo, Liang, Russell, Rick, Lambowitz, Alan M

“…The mitochondrial DEAD-box proteins Mss116p of Saccharomyces cerevisiae and CYT-19 of Neurospora crassa are ATP-dependent helicases that function as general…”
Get full text

Mechanisms used for genomic proliferation by thermophilic group II introns by Mohr, Georg, Ghanem, Eman, Lambowitz, Alan M

“…Mobile group II introns, which are found in bacterial and organellar genomes, are site-specific retroelements hypothesized to be evolutionary ancestors of…”
Get full text

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires by Silas, Sukrit, Makarova, Kira S, Shmakov, Sergey, Páez-Espino, David, Mohr, Georg, Liu, Yi, Davison, Michelle, Roux, Simon, Krishnamurthy, Siddharth R, Fu, Becky Xu Hua, Hansen, Loren L, Wang, David, Sullivan, Matthew B, Millard, Andrew, Clokie, Martha R, Bhaya, Devaki, Lambowitz, Alan M, Kyrpides, Nikos C, Koonin, Eugene V, Fire, Andrew Z

“…Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of…”
Get full text

Generalized bacterial genome editing using mobile group II introns and Cre‐lox by Enyeart, Peter J, Chirieleison, Steven M, Dao, Mai N, Perutka, Jiri, Quandt, Erik M, Yao, Jun, Whitt, Jacob T, Keatinge‐Clay, Adrian T, Lambowitz, Alan M, Ellington, Andrew D

“…Efficient bacterial genetic engineering approaches with broad‐host applicability are rare. We combine two systems, mobile group II introns (‘targetrons’) and…”
Get full text