Short open reading frame genes in innate immunity: from discovery to characterization

Malekos, Eric; Carpenter, Susan

doi:10.1016/j.it.2022.07.005

Cited by 15 publications

(14 citation statements)

References 143 publications

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“…Ribosome profiling is performed to recognize sORF transcription within ncRNAs that encode micropeptides. It mainly includes ncRNA samples enrichment, ribosome footprints obtaining, RNA purification, and deep sequencing 27 . MS‐based proteomics is used to obtain evidence for the stable expression of micropeptides 26 .…”

Section: Methods and Technologies For Predicting And Characterizing S...mentioning

confidence: 99%

“…It mainly includes ncRNA samples enrichment, ribosome footprints obtaining, RNA purification, and deep sequencing. 27 MS-based proteomics is used to obtain evidence for the stable expression of micropeptides. 26 Micropeptides are screened from protein extract and analyzed by LC-MS/MS to obtain the sample mass spectrum.…”

Section: Micropeptides Localized In the Nucleusmentioning

confidence: 99%

“…25,26 For example, ribosome profiling is performed to recognize sORF transcription within ncRNAs that encode micropeptides. 27,28 Furthermore, mass spectrometry (MS)-based proteomics analysis is performed for identifying and validating endogenously expressed microproteins. 26 Nonetheless, several sORFs remain unexplored, and only a few micropeptides have been established owing to the limitations of multiple omics and databases.…”

Section: Introductionmentioning

confidence: 99%

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Subcellular localization and relevant mechanisms of human cancer‐related micropeptides

Deng,

Xu,

Jie

et al. 2023

The FASEB Journal

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Rapid advances in high‐quality sequencing and bioinformatics have invalidated the argument that noncoding RNAs (ncRNAs) are junk transcripts that do not encode proteins. Increasing evidence suggests that small open reading frames (sORFs) in ncRNAs can encode micropeptides and polypeptides within 100 amino acids in length. Several micropeptides have been characterized and proven to have various functions in human physiology and pathology, particularly in cancer. The present review mainly highlights the latest studies on ncRNA‐encoded micropeptides in different cancers and categorizes them based on their subcellular localization, thereby providing a theoretical basis for micropeptide applications in the early diagnosis and prognosis of cancer and as therapeutic targets. However, considering the inherent characteristics of micropeptides and the limitations of the assay technology methods, more detailed information is warranted.

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Section: Methods and Technologies For Predicting And Characterizing S...mentioning

confidence: 99%

Section: Micropeptides Localized In the Nucleusmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Subcellular localization and relevant mechanisms of human cancer‐related micropeptides

Deng,

Xu,

Jie

et al. 2023

The FASEB Journal

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“…Similar to the above considered evolution of molecular genetic diagnostics, decades passed from the discovery that about 99% of the human genome do not encode proteins, but instead generate a broad spectrum of non-coding RNAs (ncRNAs) many of whom are involved in the immune response [44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60], until finally successful clinical exploitation of ncRNAs and of novel drugs developed using them as blueprints was achieved [1,2]. Across the entire spectrum of medical disciplines it has been ascertained that the noncoding genome plays a key role in genetic programming and gene regulation during development as well as in health and disease.…”

Section: Novel Immune Players From the Human Non-coding Genomementioning

confidence: 99%

Innate Immunity in Cardiovascular Diseases – Identification of Novel Molecular Players and Targets

Poller¹,

Heidecker²,

Ammirati³

et al. 2022

Preprint

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During the past few years unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking ad-vantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss emerging clinical relevance of advanced diagnostics for cardiovascular diseases - includ-ing those associated with COVID-19 - with a focus on the role of inflammation in cardiomyopa-thies and arrhythmias. Second, we consider newly identified immunological interactions at or-gan and systems level which affect cardiovascular pathogenesis. Thus, studies into immune in-fluences arising from the intestinal system are moving towards therapeutic exploitation. Fur-ther, powerful new research tools have enabled novel insight into brain – immune system inter-actions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress - acting through defined brain regions - upon viral and cardiovas-cular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.

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“…Furthermore, some RNAs presumed to be non-coding are found to encode novel functional peptides by recent studies [6][7][8][9][10]. While such non-canonical ORFs play essential roles in diverse biological processes [11][12][13][14][15], they were often overlooked in traditional studies due to difficulties in detection.…”

Section: Introductionmentioning

confidence: 99%

A systematic evaluation revealed that detecting translated non-canonical ORFs from ribosome profiling data remains challenging

Lei

Chang

Yao

et al. 2022

Preprint

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Non-canonical open reading frames (ORFs), which are ORFs that are not included in reference genome annotations, are gaining more and more research interest in recent years. While vast numbers of non-canonical ORFs have been identified with ribosome profiling (Ribo-Seq) by various state-of-the-art computational methods, the performance of these methods has not been assessed systematically. To this end, we evaluated the four most popular methods for translated non-canonical ORF prediction using various public datasets. We found that non-canonical ORFs predicted by different methods differ substantially and are not saturated at typical sequence depths. Furthermore, the precision and accuracy of all four methods are not satisfactory, especially for ORFs with near-cognate start codons. Based on these results, we suggest that improved sequence depth, biological repetitions, and translation initiation site profiling should be considered to obtain a high-quality catalog of translated non-canonical ORFs in future studies.

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Short open reading frame genes in innate immunity: from discovery to characterization

Cited by 15 publications

References 143 publications

Subcellular localization and relevant mechanisms of human cancer‐related micropeptides

Subcellular localization and relevant mechanisms of human cancer‐related micropeptides

Innate Immunity in Cardiovascular Diseases – Identification of Novel Molecular Players and Targets

A systematic evaluation revealed that detecting translated non-canonical ORFs from ribosome profiling data remains challenging

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