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Authors = Piero Carninci

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12 pages, 976 KiB  
Review
Genome-Wide Technologies to Study RNA–Chromatin Interactions
by Masaki Kato and Piero Carninci
Non-Coding RNA 2020, 6(2), 20; https://doi.org/10.3390/ncrna6020020 - 27 May 2020
Cited by 19 | Viewed by 8241
Abstract
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the [...] Read more.
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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17 pages, 863 KiB  
Article
Telomerase Reverse Transcriptase Regulates microRNAs
by Timo Lassmann, Yoshiko Maida, Yasuhiro Tomaru, Mami Yasukawa, Yoshinari Ando, Miki Kojima, Vivi Kasim, Christophe Simon, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki and Kenkichi Masutomi
Int. J. Mol. Sci. 2015, 16(1), 1192-1208; https://doi.org/10.3390/ijms16011192 - 6 Jan 2015
Cited by 23 | Viewed by 8292
Abstract
MicroRNAs are small non-coding RNAs that inhibit the translation of target mRNAs. In humans, most microRNAs are transcribed by RNA polymerase II as long primary transcripts and processed by sequential cleavage of the two RNase III enzymes, DROSHA and DICER, into precursor and [...] Read more.
MicroRNAs are small non-coding RNAs that inhibit the translation of target mRNAs. In humans, most microRNAs are transcribed by RNA polymerase II as long primary transcripts and processed by sequential cleavage of the two RNase III enzymes, DROSHA and DICER, into precursor and mature microRNAs, respectively. Although the fundamental functions of microRNAs in RNA silencing have been gradually uncovered, less is known about the regulatory mechanisms of microRNA expression. Here, we report that telomerase reverse transcriptase (TERT) extensively affects the expression levels of mature microRNAs. Deep sequencing-based screens of short RNA populations revealed that the suppression of TERT resulted in the downregulation of microRNAs expressed in THP-1 cells and HeLa cells. Primary and precursor microRNA levels were also reduced under the suppression of TERT. Similar results were obtained with the suppression of either BRG1 (also called SMARCA4) or nucleostemin, which are proteins interacting with TERT and functioning beyond telomeres. These results suggest that TERT regulates microRNAs at the very early phases in their biogenesis, presumably through non-telomerase mechanism(s). Full article
(This article belongs to the Collection Regulation by Non-coding RNAs)
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