Enwerem, Isioma I I Elrod, Nathan D Chang, Chung-Te Lin, Ai Ji, Ping Bohn, Jennifer A Levdansky, Yevgen Wagner, Eric J Valkov, Eugene Goldstrohm, Aaron
...
Published in
RNA (New York, N.Y.)
Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified su...
Watson, Maegan Park, Yeonwoo Thoreen, Carson
Published in
RNA (New York, N.Y.)
The stability of mRNAs is fundamental to determining expression level and dynamics. Nonetheless, current approaches for measuring transcript half-lives (e.g. transcription shutoff) are generally toxic or technically complex. Here we describe an alternative strategy for targeted measurements of endogenous mRNA stability that is simple, inexpensive, ...
Passalacqua, Luiz F M Dingilian, Armine I Lupták, Andrej
Published in
RNA (New York, N.Y.)
RNA molecules can be conveniently synthesized in vitro by the T7 RNA polymerase (T7 RNAP). In some experiments, such as cotranscriptional biochemical analyses, continuous synthesis of RNA is not desired. Here, we propose a method for a single-pass transcription that yields a single transcript per template DNA molecule using the T7 RNAP system. We h...
Jahagirdar, Dushyant Jha, Vikash Basu, Kaustuv Gomez-Blanco, Josue Vargas, Javier Ortega, Joaquin
Published in
RNA (New York, N.Y.)
It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the struct...
Ancar, Rachel Li, Yize Kindler, Eveline Cooper, Daphne A Ransom, Monica Thiel, Volker Weiss, Susan R Hesselberth, Jay R Barton, David J
Published in
RNA (New York, N.Y.)
Coronavirus EndoU inhibits dsRNA-activated antiviral responses; however, the physiologic RNA substrates of EndoU are unknown. In this study, we used mouse hepatitis virus (MHV)-infected bone marrow-derived macrophage (BMM) and cyclic phosphate cDNA sequencing to identify the RNA targets of EndoU. EndoU targeted viral RNA, cleaving the 3' side of py...
Immer, Carina Hacker, Carolin Wöhnert, Jens
Published in
RNA (New York, N.Y.)
Small regulatory RNAs (sRNAs) play an important role for posttranscriptional gene regulation in bacteria. sRNAs recognize their target messenger RNAs (mRNAs) by base-pairing, which is often facilitated by interactions with the bacterial RNA-binding proteins Hfq or ProQ. The FinO/ProQ RNA-binding protein domain was first discovered in the bacterial ...
Boussier, Jeremy Munier, Sandie Achouri, Emna Crescenzo-Chaigne, Bernadette Behillil, Sylvie Enouf, Vincent van der Werf, Sylvie Naffakh, Nadia
Published in
RNA (New York, N.Y.)
Like most RNA viruses, influenza viruses generate defective viral genomes (DVGs) with large internal deletions during replication. There is accumulating evidence supporting a biological relevance of such DVGs. However, further understanding of the molecular mechanisms that underlie the production and biological activity of DVGs is conditioned upon ...
Qiu, Yushan Lyu, Jingyi Dunlap, Mikayla Harvey, Samuel E Cheng, Chonghui
Published in
RNA (New York, N.Y.)
During breast cancer metastasis, the developmental process epithelial-mesenchymal transition (EMT) is abnormally activated. Transcriptional regulatory networks controlling EMT are well-studied; however, alternative RNA splicing also plays a critical regulatory role during this process. A comprehensive understanding of alternative splicing (AS) and ...
Henry, Belle A Kanarek, Jack P Kotter, Annika Helm, Mark Lee, Nara
Published in
RNA (New York, N.Y.)
Many cellular noncoding RNAs contain chemically modified nucleotides that are essential for their function. The Epstein-Barr virus expresses two highly abundant noncoding RNAs called EBV-encoded RNA 1 (EBER1) and EBER2. To examine whether these viral RNAs contain modified nucleotides, we purified native EBERs from EBV-infected cells and performed m...
Smith, Benjamin A. Gelles, Jeff Goode, Bruce L.
Published in
Methods in Enzymology
The actin cytoskeleton is very dynamic and highly regulated by multiple associated proteins in vivo. Understanding how this system of proteins functions in the processes of actin network assembly and disassembly requires methods to dissect the mechanisms of activity of individual factors and of multiple factors acting in concert. The advent of sing...