small ORFs: A new class of essential genes for development

Albuquerque, João Paulo; Tobias-Santos, Vitória; Rodrigues, Aline Cáceres; Mury, Flávia Borges; Fonseca, Rodrigo Nunes da

doi:10.1590/s1415-475738320150009

Cited by 19 publications

(24 citation statements)

References 23 publications

(59 reference statements)

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“…Beause mlpt does not act as a gap gene in Drosophila (Galindo et al, ), this smORF was recruited into the gene regulatory network of early patterning during insect evolution. Whether mlpt acts as a gap gene role in basal hemiptera such as Rhodnius is an important question (Albuquerque et al ., ). Preliminary analysis indicates that mlpt is a gap gene in Rhodnius and also essential for nymphal metamorphosis during post embryonic stages (Tobias‐Santos and Nunes da Fonseca, unpublished observation).…”

Section: Embryonic Developmentmentioning

confidence: 97%

Rhodnius prolixus: From classical physiology to modern developmental biology

Fonseca

Berni

Tobias-Santos

et al. 2017

Genesis

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The hemiptera Rhodnius prolixus is a blood-feeding insect and a primary vector of Trypanosoma cruzi, the etiological agent of the Chagas disease. Over the past century, Rhodnius has been the subject of intense investigations, which have contributed to unveil important aspects of metabolism and physiology in insects. Recent technological innovations are helping dissect the genetic and molecular underpinnings of Rhodnius embryogenesis and organogenesis, thus fostering the use of this important species in the fields of developmental and evolutionary biology. Rhodnius represents also an excellent system to study development under stressful conditions, since the embryo must develop in the presence of a large amount of blood-derived reactive oxygen species. With a recently sequenced genome, small among other Hemiptera, and the identification of basic elements for all classical development pathways, functional studies in this species are revealing novel aspects of insect development and evolution. Here we review early studies on this model insect and how this paved the way for recent functional studies using the kissing bug.

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Section: Embryonic Developmentmentioning

confidence: 97%

Rhodnius prolixus: From classical physiology to modern developmental biology

Fonseca

Berni

Tobias-Santos

et al. 2017

Genesis

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“…These criteria result in an important underestimation of translated ORFs in the genome (Andrews and Rothnagel 2014;Saghatelian and Couso 2015;Couso and Patraquim 2017;Plaza et al 2017). With functional evidence for previously unannotated ORFs in bacteria (Wadler and Vanderpool 2007;Hemm et al 2008Hemm et al , 2010Storz et al 2014;Lluch-Senar et al 2015;Baek et al 2017), Drosophila (Galindo et al 2007;Kondo et al 2007;Reinhardt et al 2013;Aspden et al 2014;Albuquerque et al 2015;Li et al 2016a;Pueyo et al 2016a), plants (Hanada et al 2013;Juntawong et al 2014;Hsu et al 2016;Hsu and Benfey 2017), and other eukaryotes (Oyama et al 2007;Ingolia et al 2011;Vanderperre et al 2013;Ma et al 2014), genome annotations will need to be revised.…”

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confidence: 99%

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

et al. 2018

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Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts. This has important consequences for the correlation of phenotypes and genotypes. Most alternative ORFs are not yet annotated because of a lack of evidence, and this absence from databases precludes their detection by standard proteomic methods, such as mass spectrometry. Here, we demonstrate how current approaches tend to overlook alternative ORFs, hindering the discovery of new genetic drivers and fundamental research. We discuss available tools and techniques to improve identification of proteins from alternative ORFs and finally suggest a novel annotation system to permit a more complete representation of the transcriptomic and proteomic information contained within a gene. Given the crucial challenge of distinguishing functional ORFs from random ones, the suggested pipeline emphasizes both experimental data and conservation signatures. The addition of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current genome annotations and thus permit their inclusion in hypotheses and models, which relate phenotypes and genotypes.

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“…These two classes of peptides are now acknowledged to be present in the cell but with rare functional annotation . The likely reason for this disparity is the lack of tools to measure the presence and activity of these peptides.…”

Section: Targeted Proteomics: What Does It Bring For Researchers At Bmentioning

confidence: 99%

“…[64] These two classes of peptides are now acknowledged to be present in the cell but with rare functional annotation. [65][66][67] The likely reason for this disparity is the lack of tools to measure the presence and activity of these peptides. While there is emerging literature regarding the structural roles played by noncoding RNAs to inhibit or activate proteins, it is even more feasible for small peptides capable of mimicking folds and turns of a protein, which can easily block the active site or result in a change of confirmation.…”

Section: Peptidomics: Targeted Proteomics For Annotated or Unannotatedmentioning

confidence: 99%

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

Arora

Somasundaram

2019

BioEssays

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While mass spectrometry (MS)‐based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is the proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided. A special emphasis is placed on upcoming areas such as peptidomics, proteoform research, and mass spectrometry imaging, where the utilization of targeted proteomics is expected to bring forth new avenues. The limitations associated with the acceptance of this technique for mainstream usage are also highlighted. Also see the video abstract here https://youtu.be/mieB47B8gZw.

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small ORFs: A new class of essential genes for development

Cited by 19 publications

References 23 publications

Rhodnius prolixus: From classical physiology to modern developmental biology

Rhodnius prolixus: From classical physiology to modern developmental biology

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

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