The Definition of Open Reading Frame Revisited

Sieber, Patricia; Platzer, Matthias; Schuster, Stefan

doi:10.1016/j.tig.2017.12.009

Cited by 54 publications

(50 citation statements)

References 9 publications

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“…All sgRNAs were targeted to the non-template strand of the Open Reading Frame (ORF), defined as the distance between a bioinformatically identified start and stop codon 27 , to block transcription elongation.…”

Section: A Crispri Library Targeting M Smegmatis Homologues Of M Tumentioning

confidence: 99%

CRISPRi-Seq for the Identification and Characterisation of Essential Mycobacterial Genes and Transcriptional Units

Wet

Gobe

Mhlanga

et al. 2018

Preprint

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High-throughput essentiality screens have enabled genome-wide assessments of the genetic requirements for growth and survival of a variety of bacteria in different experimental models. The reliance in many of these studies on transposon (Tn)-based gene inactivation has, however, limited the ability to probe essential gene function or design targeted screens. We interrogated the potential of targeted, large-scale, pooled CRISPR interference (CRISPRi)-based screens to extend conventional Tn approaches in mycobacteria through the capacity for positionally regulable gene repression. Here, we report the utility of the "CRISPRi-Seq" method for targeted, pooled essentiality screening, confirming strong overlap with TnSeq datasets. In addition, we exploit this high-throughput approach to provide insight into CRISPRi functionality. By interrogating polar effects and combining image-based phenotyping with CRISPRimediated depletion of selected essential genes, we demonstrate that CRISPRi-Seq can functionally validate Transcriptional Units within operons. Together, these observations suggest the utility of CRISPRiSeq to provide insights into (myco)bacterial gene regulation and expression on a genome-wide scale.

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Section: A Crispri Library Targeting M Smegmatis Homologues Of M Tumentioning

confidence: 99%

CRISPRi-Seq for the Identification and Characterisation of Essential Mycobacterial Genes and Transcriptional Units

Wet

Gobe

Mhlanga

et al. 2018

Preprint

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“…Furthermore, the well-resolved mammalian phylogeny [19,20] provides a robust foundation for which to test for homology and confirm orthology. For most non-model mammalian species with whole-genome sequences, genes are predicted using algorithms that locate open reading frames (e.g., [21]), yet rarely are the predicted genes validated experimentally [22,23]. Some algorithms compare putative open reading frames with model-species to confirm length and expected sequence variation.…”

Section: Introductionmentioning

confidence: 99%

Unexpected predicted length variation for the coding sequence of the sleep related gene, BHLHE41 in gorilla amidst strong purifying selection across mammals

Unadkat

Whittall

2020

PLoS ONE

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There is a molecular basis for many sleep patterns and disorders involving circadian clock genes. In humans, "short-sleeper" behavior has been linked to specific amino acid substitutions in BHLHE41 (DEC2), yet little is known about variation at these sites and across this gene in mammals. We compare BHLHE41 coding sequences for 27 mammals. Approximately half of the coding sequence was invariable at the nucleotide level and close to threequarters of the amino acid alignment was identical. No other mammals had the same "shortsleeper" amino acid substitutions previously described from humans. Phylogenetic analyses based on the nucleotides of the coding sequence alignment are consistent with established mammalian relationships confirming orthology among the sampled sequences. Significant purifying selection was detected in about two-thirds of the variable codons and no codons exhibited significant signs of positive selection. Unexpectedly, the gorilla BHLHE41 sequence has a 318 bp insertion at the 5' end of the coding sequence and a deletion of 195 bp near the 3' end of the coding sequence (including the two short sleeper variable sites). Given the strong signal of purifying selection across this gene, phylogenetic congruence with expected relationships and generally conserved function among mammals investigated thus far, we suggest the indels predicted in the gorilla BHLHE41 may represent an annotation error and warrant experimental validation.

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“…Contudo, a identificação de ORFs nãoé suficiente para a identificação de genes, uma vez que, embora todo gene corresponda a uma ORF, a recíproca nãoé verdadeira. Ao longo do genomas dos organismos, existem diversas ORFs que não correspondem a genes [Sieber et al 2018].…”

Section: Introductionunclassified

“…A Figura 1 ilustra um trecho de um genoma fictício de um procarioto em que podemos observar dentro dele a existência de 1 CDS e 3 ORFs, denominadas como ORF A, ORF B e ORF C. Por meio da ilustração, pode-se observar 3 cenários relevantes relacionados com as ORFs: 1) a existência de ORFs que não correspondem a genes -cenário ilustrado pela ORF A; 2) a existência de ORF que corresponde a CDS -representado pela ORF B; e 3) a existência de ORF dentro de outra ORF, aqui denominado sub ORFrepresentado pela ORF C. Dessa forma, conclui-se que, embora uma ORF tenha potencial para ser uma CDS,é possível a existência de ORFs dentro das regiões do genoma que não correspondem a CDS -chamadas de regiões intergênicas -, bem como a existência de sub ORFs tanto nas regiões intergênicas quanto nas próprias CDS [Sieber et al 2018].…”

Section: Introductionunclassified

Análise de composição de conjunto de treinamento para avaliação de aprendizagem de máquina aplicada à predição de genes

Silva¹,

Padovani²,

Santos³

et al. 2018

Anais Estendidos Do XI Simpósio Brasileiro De Bioinformática (BSB Estendido 2018)

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A metagenômica realiza o estudo de comunidades microbianas, conhecidas como metagenomas, descrevendo-as por meio de suas composições e das relações e atividades dos microrganismos que ali coabitam, permitindo assim um maior conhecimento a respeito dos fundamentos da vida e da ampla e ainda pouco conhecida — diversidade microbiológica. Uma das formas de se realizar tal descrição é por meio da análise de informações de genes contidos em (meta)genomas, extraídas através do processo de identificação de genes em sequências de DNA denominado predicão de genes. Este trabalho apresenta um estudo de caso que permite a analise do impacto da composição do conjunto de treinamento ao se utilizar aprendizagem de maquina na predição de genes codificadores de proteína.

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The Definition of Open Reading Frame Revisited

Cited by 54 publications

References 9 publications

CRISPRi-Seq for the Identification and Characterisation of Essential Mycobacterial Genes and Transcriptional Units

CRISPRi-Seq for the Identification and Characterisation of Essential Mycobacterial Genes and Transcriptional Units

Unexpected predicted length variation for the coding sequence of the sleep related gene, BHLHE41 in gorilla amidst strong purifying selection across mammals

Análise de composição de conjunto de treinamento para avaliação de aprendizagem de máquina aplicada à predição de genes

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