Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

Lopes, Kátia de Paiva; Campos‐Laborie, Francisco J.; Vialle, Ricardo Assunção; Ortega, Josè Miguel; Rivas, Javier De Las

doi:10.1186/s12864-016-3062-y

Cited by 4 publications

(2 citation statements)

References 48 publications

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“…We compared genes specific for 16 different tissues against (presumed) housekeeping genes [40]. Our assumption was that the ubiquitously and generally more highly expressed housekeeping genes [54] should have globally higher scores than tissue-specific genes. Although the absolute effect size was small, significantly higher scores were attributed to genes specific to cerebellum, eye, neuronal and muscle tissue.…”

Section: Discussionmentioning

confidence: 99%

“…On the one hand, brain tissue has experienced major development changes during the time period between 535 and 310 Mya ago, i.e. increased expression and gain of functions of paralogs of brain-specific genes [54,55]. Since then and during the entire mammalian development, the expression of paralogs of brain-specific genes is lower than that observed in other tissues [56], which indicates the fine balancing that acts to keep the brain functional.…”

Section: Discussionmentioning

confidence: 99%

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pCADD: SNV prioritisation in Sus scrofa

et al. 2020

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Background: In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. Results:To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. Conclusions:We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

pCADD: SNV prioritisation in Sus scrofa

et al. 2020

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Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures

Rivas

Bonavides-Martínez

Campos‐Laborie

2017

Briefings in Bioinformatics

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Owing to the emerging impact of bioinformatics and computational biology, in this article, we present an overview of the history and current state of the research on this field in Latin America (LA). It will be difficult to cover without inequality all the efforts, initiatives and works that have happened for the past two decades in this vast region (that includes >19 million km2 and >600 million people). Despite the difficulty, we have done an analytical search looking for publications in the field made by researchers from 19 LA countries in the past 25 years. In this way, we find that research in bioinformatics in this region should develop twice to approach the average world scientific production in the field. We also found some of the pioneering scientists who initiated and led bioinformatics in the region and were promoters of this new scientific field. Our analysis also reveals that spin-off began around some specific areas within the biomolecular sciences: studies on genomes (anchored in the new generation of deep sequencing technologies, followed by developments in proteomics) and studies on protein structures (supported by three-dimensional structural determination technologies and their computational advancement). Finally, we show that the contribution to this endeavour of the Iberoamerican Society for Bioinformatics, founded in Mexico in 2009, has been significant, as it is a leading forum to join efforts of many scientists from LA interested in promoting research, training and education in bioinformatics.

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The origins and evolutionary history of human non-coding RNA regulatory networks

Sherafatian

Mowla

2017

J. Bioinform. Comput. Biol.

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The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

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Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

Cited by 4 publications

References 48 publications

pCADD: SNV prioritisation in Sus scrofa

pCADD: SNV prioritisation in Sus scrofa

Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures

The origins and evolutionary history of human non-coding RNA regulatory networks

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