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Comparison of RNA-Sequencing Methods for Degraded RNA
International Journal of Molecular SciencesRNA sequencing (RNA-Seq) is a powerful technique and is increasingly being used in clinical research and drug development. Currently, several RNA-Seq methods have been developed. However, the relative advantage of each method for degraded RNA and low-input RNA, such as RNA samples collected in the field of clinical setting, has remained unknown.
Hiroki Ura, Yo Niida
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The type II poly(A)-binding protein PABP-2 is a downstream target of the "let-7" microRNA in the heterochronic pathway of "Caenorhabditis elegans" : mechanisms of microRNA-mediated gene silencing in "Caenorhabditis elegans" [PDF]
, 2012 microRNAs (miRNAs) are a large class of small, non-coding RNAs that post-transcriptionally regulate gene expression in animals, plants and protozoa. miRNAs are genomically encoded and transcribed by RNA polymerase II. Primary transcripts are sequentially
Hurschler, Benjamin
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, 2021 Robust methods are critical for testing the in vivo regulatory mechanism of RNA binding proteins. Here we report improvement of a protein–mRNA tethering assay to probe the function of an RNA binding protein in its natural context within the C.
Kimble, Judith +3 more
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Scientific ReportsOxygen shortage, known as hypoxia, occurs commonly in both physiological and pathological conditions. Transcriptional regulation by hypoxia-inducible factors is a dominant regulatory mechanism controlling hypoxia-responsive genes during acute hypoxia ...
Yoko Ogura +12 more
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Elucidation of pathways of ribosomal RNA degradation: an essential role for RNase E
RNA: A publication of the RNA Society, 2016 Although normally stable in growing cells, ribosomal RNAs are degraded under conditions of stress, such as starvation, and in response to misassembled or otherwise defective ribosomes in a process termed RNA quality control.
S. Sulthana +2 more
semanticscholar +1 more source
Molecular Oncology, EarlyView.We identify USP29 as the only DUB mirroring CA9 expression, a marker of hypoxia and HIF pathway activation associated with PCA aggressiveness. USP29 stabilizes HIF‐1α and HIF‐2α via a noncanonical mechanism that is independent of PHD/pVHL activity yet relies on proteasomal regulation, establishing USP29 as a previously unrecognized regulator of hypoxic
Amelie S Schober +16 more
wiley +1 more source
Domain orientation in the RNA helicase YxiN and the role of conformational changes for RNA unwinding [PDF]
, 2010 The RNA helicase YxiN from Bacillus subtilis is a member of the family of DEAD box proteins. YxiN is able to unwind RNA double strands in an ATP-dependent manner. The ability to catalyse RNA rearrangement is in vivo presumably necessary for the bacterial
Karow, Anne R.
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BiomoleculesThe exosome multiprotein complex plays a critical role in RNA processing and degradation. This system governs the regulation of mRNA quality, degradation in the cytoplasm, the processing of short noncoding RNA, and the breakdown of RNA fragments.
Seonha Park +7 more
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Bias in recent miRBase annotations potentially associated with RNA quality issues
Scientific Reports, 2017 Although microRNAs are supposed to be stable in-vivo, degradation processes potentially blur our knowledge on the small oligonucleotides. We set to quantify the effect of degradation on microRNAs in mouse to identify causes for distorted microRNAs ...
Nicole Ludwig +6 more
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Interferon-inducible ribonuclease ISG20 inhibits hepatitis B virus replication through directly binding to the epsilon stem-loop structure of viral RNA. [PDF]
PLoS Pathogens, 2017 Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of a viral RNA pregenome. We report herein that the interferon (IFN) stimulated exoribonuclease gene of 20 KD (ISG20) inhibits HBV replication through degradation of HBV RNA.
Yuanjie Liu +9 more
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