Sukno S

References (3)

Title : Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing - Redin_2014_J.Med.Genet_51_724
Author(s) : Redin C , Gerard B , Lauer J , Herenger Y , Muller J , Quartier A , Masurel-Paulet A , Willems M , Lesca G , El-Chehadeh S , Le Gras S , Vicaire S , Philipps M , Dumas M , Geoffroy V , Feger C , Haumesser N , Alembik Y , Barth M , Bonneau D , Colin E , Dollfus H , Doray B , Delrue MA , Drouin-Garraud V , Flori E , Fradin M , Francannet C , Goldenberg A , Lumbroso S , Mathieu-Dramard M , Martin-Coignard D , Lacombe D , Morin G , Polge A , Sukno S , Thauvin-Robinet C , Thevenon J , Doco-Fenzy M , Genevieve D , Sarda P , Edery P , Isidor B , Jost B , Olivier-Faivre L , Mandel JL , Piton A
Ref : Journal of Medical Genetics , 51 :724 , 2014
Abstract : BACKGROUND: Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation. METHODS: We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases. RESULTS: We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients' clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders. CONCLUSIONS: With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes implicated in ID and autism.
ESTHER : Redin_2014_J.Med.Genet_51_724
PubMedSearch : Redin_2014_J.Med.Genet_51_724
PubMedID: 25167861
Gene_locus related to this paper: human-NLGN3

Title : Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis - Alkan_2013_Mol.Plant.Microbe.Interact_26_1345
Author(s) : Alkan N , Meng X , Friedlander G , Reuveni E , Sukno S , Sherman A , Thon M , Fluhr R , Prusky D
Ref : Mol Plant Microbe Interact , 26 :1345 , 2013
Abstract : Colletotrichum gloeosporioides alkalinizes its surroundings during colonization of host tissue. The transcription factor pacC is a regulator of pH-controlled genes and is essential for successful colonization. We present here the sequence assembly of the Colletotrichum fruit pathogen and use it to explore the global regulation of pathogenicity by ambient pH. The assembled genome size was 54 Mb, encoding 18,456 genes. Transcriptomes of the wild type and DeltapacC mutant were established by RNA-seq and explored for their global pH-dependent gene regulation. The analysis showed that pacC upregulates 478 genes and downregulates 483 genes, comprising 5% of the fungal genome, including transporters, antioxidants, and cell-wall-degrading enzymes. Interestingly, gene families with similar functionality are both up- and downregulated by pacC. Global analysis of secreted genes showed significant pacC activation of degradative enzymes at alkaline pH and during fruit infection. Select genes from alkalizing-type pathogen C. gloeosporioides and from acidifying-type pathogen Sclerotinia sclerotiorum were verified by quantitative reverse-transcription polymerase chain reaction analysis at different pH values. Knock out of several pacC-activated genes confirmed their involvement in pathogenic colonization of alkalinized surroundings. The results suggest a global regulation by pacC of key pathogenicity genes during pH change in alkalinizing and acidifying pathogens.
ESTHER : Alkan_2013_Mol.Plant.Microbe.Interact_26_1345
PubMedSearch : Alkan_2013_Mol.Plant.Microbe.Interact_26_1345
PubMedID: 23902260
Gene_locus related to this paper: colgc-t0kps3 , colgc-t0kxm3 , colgc-t0jwq7 , colgc-t0ly43 , colgc-t0lk94 , colgc-t0jvv6 , colgn-l2fqx6 , colgc-t0klg2 , colgc-t0ky59 , colgc-t0jjv2 , colgn-l2fh91.1 , colgc-t0jp69 , colgn-l2g0g1 , colgn-l2g1k8 , colgn-l2fgv1 , colgc-t0lrv6 , colgc-t0kk78 , colgc-t0k080 , colgc-t0l215 , colgc-t0kui0 , colgn-l2g4i7 , colgn-l2ftf7 , colgc-t0jzf9 , colgc-t0k098 , colgc-t0ldf9 , colgc-t0k6d3 , colgc-t0kn97 , colgn-l2gi23 , colgc-t0ka43 , colgc-t0k3b9 , colgc-t0lm90 , colgc-t0m9n0 , colgn-l2ft30 , colgc-t0mb63 , colgn-l2ger6 , colgc-t0kbv4 , colgn-l2g8u3 , colgc-t0me46 , colgc-t0kkx8 , colgc-t0jqx0 , colgc-t0jmt1 , colgn-l2fdn5 , colgc-t0m156 , colgc-t0jwa2 , colgc-t0lv23 , colgc-t0l6a2 , colgc-t0k1u6 , colgn-l2fua0 , colgc-t0lk08 , colgc-t0ln91 , colgn-l2fmp3 , colgc-t0k5l9 , colgc-t0kne8 , colgc-t0ly52 , colgc-t0m513 , colgc-t0kem7 , colgc-t0m975

Title : Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma - Kubicek_2011_Genome.Biol_12_R40
Author(s) : Kubicek CP , Herrera-Estrella A , Seidl-Seiboth V , Martinez DA , Druzhinina IS , Thon M , Zeilinger S , Casas-Flores S , Horwitz BA , Mukherjee PK , Mukherjee M , Kredics L , Alcaraz LD , Aerts A , Antal Z , Atanasova L , Cervantes-Badillo MG , Challacombe J , Chertkov O , McCluskey K , Coulpier F , Deshpande N , von Dohren H , Ebbole DJ , Esquivel-Naranjo EU , Fekete E , Flipphi M , Glaser F , Gomez-Rodriguez EY , Gruber S , Han C , Henrissat B , Hermosa R , Hernandez-Onate M , Karaffa L , Kosti I , Le Crom S , Lindquist E , Lucas S , Lubeck M , Lubeck PS , Margeot A , Metz B , Misra M , Nevalainen H , Omann M , Packer N , Perrone G , Uresti-Rivera EE , Salamov A , Schmoll M , Seiboth B , Shapiro H , Sukno S , Tamayo-Ramos JA , Tisch D , Wiest A , Wilkinson HH , Zhang M , Coutinho PM , Kenerley CM , Monte E , Baker SE , Grigoriev IV
Ref : Genome Biol , 12 :R40 , 2011
Abstract : BACKGROUND: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.
RESULTS: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.
CONCLUSIONS: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
ESTHER : Kubicek_2011_Genome.Biol_12_R40
PubMedSearch : Kubicek_2011_Genome.Biol_12_R40
PubMedID: 21501500
Gene_locus related to this paper: hypai-g9nem6 , hypai-g9ng36 , hypai-g9ngu2 , hypai-g9nks5 , hypai-g9nks6 , hypai-g9nqe5 , hypai-g9nqk5 , hypai-g9nrx6 , hypai-g9nsx1 , hypai-g9ntn3 , hypai-g9nzc9 , hypai-g9nzd7 , hypai-g9p1t1 , hypai-g9p1v2 , hypai-g9p2n8 , hypai-g9p4z2 , hypai-g9p878 , hypai-g9pa17 , hypai-g9pbz9 , hypvg-g9mem8 , hypvg-g9mg52 , hypvg-g9mga2 , hypvg-g9mhi3 , hypvg-g9mjc7 , hypvg-g9mk44 , hypvg-g9mms1 , hypvg-g9mnf0 , hypvg-g9mng3 , hypvg-g9mpt0 , hypvg-g9mrp9 , hypvg-g9ms16 , hypvg-g9ms32 , hypvg-g9msv5 , hypvg-g9muh6 , hypvg-g9muk0 , hypvg-g9mwe2 , hypvg-g9my79 , hypvg-g9n0p7 , hypvg-g9n2g3 , hypvg-g9n2g4 , hypvg-g9n4k5 , hypvg-g9n9n0 , hypvg-g9n561 , hypvg-g9n988 , hypvg-g9nb12 , hypvg-g9nb54 , hypvg-g9nbh8 , hypai-g9npz7 , hypai-g9njw6 , hypvg-g9mx08 , hypvg-g9mlt2 , hypai-g9p4j3 , hypvg-g9nbd3 , hypai-g9nxf6 , hypvg-g9n3y9 , hypvg-g9mgs4 , hypai-g9p6m2 , hypvg-g9my62 , hypvg-g9nbv2 , hypvg-g9my22 , hypai-g9p2e2 , hypai-g9p596 , hypai-g9nf87 , hypvg-g9me87 , hypvg-g9ndn9 , hypai-g9niy5 , hypai-g9ntx6 , hypvg-g9n3e7 , hypai-g9nu29 , hypvg-g9n2z0 , hypvg-g9ndf4 , 9hypo-a0a2p4zt82 , hypvg-g9n0g0 , hypvg-g9muj2 , hypvg-g9mud0 , hypai-g9nkx5