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Relevant bibliographies by topics / SmORF peptide

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Journal articles

Academic literature on the topic 'SmORF peptide'

Author: Grafiati

Published: 18 May 2024

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Journal articles on the topic "SmORF peptide"

1

Markus, Damien, Aurore Pelletier, Muriel Boube, et al. "The pleiotropic functions of Pri smORF peptides synchronize leg development regulators." PLOS Genetics 19, no. 10 (2023): e1011004. http://dx.doi.org/10.1371/journal.pgen.1011004.

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The last decade witnesses the emergence of the abundant family of smORF peptides, encoded by small ORF (<100 codons), whose biological functions remain largely unexplored. Bioinformatic analyses here identify hundreds of putative smORF peptides expressed in Drosophila imaginal leg discs. Thanks to a functional screen in leg, we found smORF peptides involved in morphogenesis, including the pioneer smORF peptides Pri. Since we identified its target Ubr3 in the epidermis and pri was known to control leg development through poorly understood mechanisms, we investigated the role of Ubr3 in media

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2

Lyapina, Irina, Vadim Ivanov, and Igor Fesenko. "Peptidome: Chaos or Inevitability." International Journal of Molecular Sciences 22, no. 23 (2021): 13128. http://dx.doi.org/10.3390/ijms222313128.

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Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the

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3

Douka, Katerina, Isabel Birds, Dapeng Wang, et al. "Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation." RNA 27, no. 9 (2021): 1082–101. http://dx.doi.org/10.1261/rna.078782.121.

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The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%–70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we f

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4

Bonilauri, Bernardo, Fabiola Barbieri Holetz, and Bruno Dallagiovanna. "Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins." Biomolecules 11, no. 11 (2021): 1673. http://dx.doi.org/10.3390/biom11111673.

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Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transc

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5

Dozier, Christine, Audrey Montigny, Mireia Viladrich, et al. "Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila." International Journal of Molecular Sciences 23, no. 10 (2022): 5764. http://dx.doi.org/10.3390/ijms23105764.

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MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). However, several lnc pri-miRNAs contain translatable small open reading frames (smORFs). If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis-regu

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6

Southan, Christopher. "Last rolls of the yoyo: Assessing the human canonical protein count." F1000Research 6 (April 7, 2017): 448. http://dx.doi.org/10.12688/f1000research.11119.1.

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In 2004, when the protein estimate from the finished human genome was only 24,000, the surprise was compounded as reviewed estimates fell to 19,000 by 2014. However, variability in the total canonical protein counts (i.e. excluding alternative splice forms) of open reading frames (ORFs) in different annotation portals persists. This work assesses these differences and possible causes. A 16-year analysis of Ensembl and UniProtKB/Swiss-Prot shows convergence to a protein number of ~20,000. The former had shown some yo-yoing, but both have now plateaued. Nine major annotation portals, reviewed at

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7

Wan, Linrong, Wenfu Xiao, Ziyan Huang, et al. "Systematic identification of smORFs in domestic silkworm (Bombyx mori)." PeerJ 11 (January 13, 2023): e14682. http://dx.doi.org/10.7717/peerj.14682.

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The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our

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8

Cao, Yipeng, Rui Yang, Imshik Lee, et al. "Prediction of LncRNA-encoded small peptides in glioma and oligomer channel functional analysis using in silico approaches." PLOS ONE 16, no. 3 (2021): e0248634. http://dx.doi.org/10.1371/journal.pone.0248634.

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Glioma is a lethal malignant brain cancer, and many reports have shown that abnormalities in the behavior of water and ion channels play an important role in regulating tumor proliferation, migration, apoptosis, and differentiation. Recently, new studies have suggested that some long noncoding RNAs containing small open reading frames can encode small peptides and form oligomers for water or ion regulation. However, because the peptides are difficult to identify, their functional mechanisms are far from being clearly understood. In this study, we used bioinformatics methods to identify and eva

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9

Magny, Emile G., Jose Ignacio Pueyo, Frances M. G. Pearl, et al. "Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames." Science 341, no. 6150 (2013): 1116–20. http://dx.doi.org/10.1126/science.1238802.

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Small open reading frames (smORFs) are short DNA sequences that are able to encode small peptides of less than 100 amino acids. Study of these elements has been neglected despite thousands existing in our genomes. We and others previously showed that peptides as short as 11 amino acids are translated and provide essential functions during insect development. Here, we describe two peptides of less than 30 amino acids regulating calcium transport, and hence influencing regular muscle contraction, in the Drosophila heart. These peptides seem conserved for more than 550 million years in a range of

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10

Dragomir, Mihnea P., Ganiraju C. Manyam, Leonie Florence Ott, et al. "FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs." Non-Coding RNA 6, no. 4 (2020): 41. http://dx.doi.org/10.3390/ncrna6040041.

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Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually b

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