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《Molecular & cellular proteomics : MCP》2023,22(1):100480
Alternative ORFs (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry as the only direct way of identification is hampered by the short lengths and relative low abundance of AltProts. There is an urgent need for improvement of mass spectrometry methodologies for AltProt identification. Here, we report an approach based on size-exclusion chromatography for simultaneous enrichment and fractionation of AltProts from complex proteome. This method greatly simplifies the variance of AltProts discovery by enriching small proteins smaller than 40 kDa. In a systematic comparison between 10 methods, the approach we reported enabled the discovery of more AltProts with overall higher intensities, with less cost of time and effort compared to other workflows. We applied this approach to identify 89 novel AltProts from mouse liver, 39 of which were differentially expressed between embryonic and adult mice. During embryonic development, the upregulated AltProts were mainly involved in biological pathways on RNA splicing and processing, whereas the AltProts involved in metabolisms were more active in adult livers. Our study not only provides an effective approach for identifying AltProts but also novel AltProts that are potentially important in developmental biology. 相似文献
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Double-Stranded RNA in Rice 总被引:2,自引:0,他引:2
Toshiyuki Fukuhara 《Journal of plant research》1999,112(1):131-138
Oryza sativa ) and wild rice (O. rufipogon) tissues. It is detected at every developmental stage, and is transmitted very efficiently to progeny via seeds (more than
98%). The dsRNA is maintained at a constant level (approximately 100 copies/cell) in almost all tissues. However, the number
of copies increases about 10-fold when host cells are grown in suspension culture. Complete nucleotide sequences of cultivated
rice (temperate japonica rice, cv. Nipponbare, J-dsRNA) and wild rice (W-1714, W-dsRNA) dsRNAs have been determined. Both wild and cultivated rice
dsRNAs have a single long open reading frame (ORF) containing the conserved motifs of RNA-dependent RNA polymerase and RNA
helicase. The coding strands of both contain a site-specific discontinuity (nick) at nt 1,211 (J-dsRNA) or at nt 1,197 (W-dsRNA)
from the 5′ end of their coding strand. Rice dsRNA has several unique properties and can be regarded as a novel RNA replicon.
This paper discusses the origin and evolution of the rice dsRNA.
Received 23 October 1998/ Accepted in revised form 15 December 1998 相似文献
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Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer
Elizabeth A. Bowling Jarey H. Wang Fade Gong William Wu Nicholas J. Neill Ik Sun Kim Siddhartha Tyagi Mayra Orellana Sarah J. Kurley Rocio Dominguez-Vidaña Hsiang-Ching Chung Tiffany Y.-T. Hsu Julien Dubrulle Alexander B. Saltzman Heyuan Li Jitendra K. Meena Gino M. Canlas Srinivas Chamakuri Thomas F. Westbrook 《Cell》2021,184(2):384-403.e21
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《Cell》2021,184(20):5215-5229.e17
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《Cell》2021,184(25):6037-6051.e14