InterPro in 2017—beyond protein family and domain annotations

We characterize the transcriptional splicing landscape of a prostate cancer cell line treated with a previously identified synergistic drug combination. We use a combination of third generation long-read RNA sequencing technology and short-read RNAseq to create a high-fidelity map of expressed isoforms and fusions to quantify splicing events triggered by treatment. We find strong evidence for drug-induced, coherent splicing changes which disrupt the function of oncogenic proteins, and detect novel transcripts arising from previously unreported fusion events.

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“…through InterPro [36]. We compared and visualized GO annotations for baseline and treated specific isoforms using WEGO [37].…”

Section: Functional Annotation Of Isoseq Transcriptsmentioning

confidence: 99%

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology

et al. 2017

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“…ebi.ac.uk/interpro/, Finn et al, 2017) search for collecting functional/ homology domain information; and (3) PredAlgo (https://giavap-genomes. ibpc.fr/cgi-bin/predalgodb.perl?page=main, Tardif et al, 2012) and/or TargetP (http://www.cbs.dtu.dk/services/TargetP/, Emanuelsson et al, 2007) search for N-terminal leader sequences.…”

Section: Annotation Of Ez-specific and G-lysin-inducible Genesmentioning

confidence: 99%

Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii

et al. 2017

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The sexual cycle of the unicellular Chlamydomonas reinhardtii culminates in the formation of diploid zygotes that differentiate into dormant spores that eventually undergo meiosis. Mating between gametes induces rapid cell wall shedding via the enzyme g-lysin; cell fusion is followed by heterodimerization of sex-specific homeobox transcription factors, GSM1 and GSP1, and initiation of zygote-specific gene expression. To investigate the genetic underpinnings of the zygote developmental pathway, we performed comparative transcriptome analysis of both pre-and post-fertilization samples. We identified 253 transcripts specifically enriched in early zygotes, 82% of which were not up-regulated in gsp1 null zygotes. We also found that the GSM1/GSP1 heterodimer negatively regulates the vegetative wall program at the posttranscriptional level, enabling prompt transition from vegetative wall to zygotic wall assembly. Annotation of the g-lysin-induced and early zygote genes reveals distinct vegetative and zygotic wall programs, supported by concerted up-regulation of genes encoding cell wall-modifying enzymes and proteins involved in nucleotide-sugar metabolism. The haploid-to-diploid transition in Chlamydomonas is masterfully controlled by the GSM1/GSP1 heterodimer, translating fertilization and gamete coalescence into a bona fide differentiation program. The fertilization-triggered integration of genes required to make related, but structurally and functionally distinct organelles-the vegetative versus zygote cell wall-presents a likely scenario for the evolution of complex developmental gene regulatory networks.

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“…The Artemis platform was used to combine evidence and produce the final annotation, and its ACT tool (Carver et al 2008) allowed us to compare the 'Florina' and GDDH13 genomic regions. The functional annotation of present genes was inferred from best homologous genes in the Arabidopsis genome (Berardini et al 2015) and results of Interproscan for conserved domains and gene ontology (Jones et al 2014;Finn et al 2016Finn et al , 2017.…”

Section: Bac Clone Sequencing and Contig Assemblymentioning

confidence: 99%

“…Their localization is relative to the targeted region of the 95 Kb between SSR_377 and SSR_4; the corresponding gene name in GDDH13 is specified if possible. Biochemical functions are described through homologies and relative PFAM (Finn et al 2016) and INTERPRO (Finn et al 2017) (Vaddepalli et al 2014). In vascular plants, such as apple, plasmodesmata permit the movement of sap through the sieve element.…”

Section: Candidate Genes For the Tolerance Phenotypementioning

confidence: 99%

Identification of candidate genes at the Dp-fl locus conferring resistance against the rosy apple aphid Dysaphis plantaginea

Dall’Agata

Pagliarani

Padmarasu

et al. 2018

Tree Genetics & Genomes

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The cultivated apple is susceptible to several pests including the rosy apple aphid (RAA; Dysaphis plantaginea Passerini), control of which is mainly based on chemical treatments. A few cases of resistance to aphids have been described in apple germplasm resources, laying the basis for the development of new resistant cultivars by breeding. The cultivar 'Florina' is resistant to RAA, and recently, the Dp-fl locus responsible for its resistance was mapped on linkage group 8 of the apple genome. In this paper, a chromosome walking approach was performed by using a 'Florina' bacterial artificial chromosome (BAC) library. The walking started from the available tightly linked molecular markers flanking the resistance region. Various walking steps were performed in order to identify the minimum tiling path of BAC clones covering the Dp-fl region from both the Bresistant^and Bsusceptibleĉ hromosomes of 'Florina'. A genomic region of about 279 Kb encompassing the Dp-fl resistance locus was fully sequenced by the PacBio technology. Through the development of new polymorphic markers, the mapping interval around the resistance locus was narrowed down to a physical region of 95 Kb. The annotation of this sequence resulted in the identification of four candidate genes putatively involved in the RAA resistance response.

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InterPro in 2017—beyond protein family and domain annotations

Cited by 1,326 publications

References 47 publications

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology

Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii

Identification of candidate genes at the Dp-fl locus conferring resistance against the rosy apple aphid Dysaphis plantaginea

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