Transcriptional profiling of ventral tegmental area of male mice with alternative patterns of social behaviors

Poster (download) Olga Redina1, Vladimir Babenko2, Vadim Efimov3, Dmitry Smagin4, Irina Kovalenko5, Anna Galyamina6, Natalia Kudryavtseva71Laboratory of Neuropathology Modeling, Laboratory of Evolutional Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, oredina@bionet.nsc.ru2Laboratory of Neuropathology Modeling, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, bob@bionet.nsc.ru3Laboratory of Molecular Genetic Systems Modeling, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, efimov@bionet.nsc.ru4Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, smagin@bionet.nsc.ru5Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, koir@bionet.nsc.ru6Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, galyamina@bionet.nsc.ru7Laboratory of Neuropathology Modeling, Neurogenetics of Social Behavior Sector, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, n.n.kudryavtseva@gmail.com The activity of ventral tegmental area (VTA) neurons plays a crucial role in the reward circuit, emotional and addictive behaviors in animals and humans. To elucidate the molecular mechanisms underlying the functional changes in VTA neurons under stress arising from social interactions, RNA-Seq analysis was used to compare the transcriptome profiles in the VTA of three groups of male mice: chronically winning mice with positive social experience in daily agonistic interactions, chronically defeated mice with negative social experience in daily agonistic interactions, and control mice having no experience of agonistic interactions. The data obtained showed that both winning and defeated mice experience stress, however, in defeated animals, the repeated agonistic interactions have a stronger effect and cause more significant changes in the levels of gene transcription. Several genes have been identified that may be involved in the determination of alternative behavioral phenotypes in groups of male mice with alternative social experience.

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A study of genes controlling carcinogenesis in a regenerative model flatworm Macrostomum lignano

Poster (download) Kitill Ustyantsev1, Valeriya Vavilova2, Mikhail Biryukov3, Eugene Berezikov41Sector of molecular-genetic mechanisms of regeneration ICG SB RAS Novosibirsk, Russia, ustyantsev@bionet.nsc.ru2Sector of molecular-genetic mechanisms of regeneration ICG SB RAS Novosibirsk, Russia, valeriya-vavilova@bionet.nsc.ru3Interinstitutional laboratory of molecular paleogenetics and paleogenomics ICG SB RAS Novosibirsk, Russia, birykov@bionet.nsc.ru4Sector of molecular-genetic mechanisms of regeneration ICG SB RAS Novosibirsk, Russia European Research Institute for the Biology of Ageing Groningen, The Netherlands, eberez@bionet.nsc.ru В Free-living flatworm Macrostomum lignano is a novel model organism that provides a genetically tractable experimental system to specifically study the interplay between regulation of regeneration and cancer. Here, we tested two chemical carcinogens (MMS and CsA) and short wavelength ultraviolet irradiation (UVC) in M. lignano in order to identify genes and molecular pathways underlying carcinogenic response in this flatworms. For the first time, sensitivity of M. lignano to hard UV was evaluated, and it was shown that the worm can easily tolerate sterilization-level doses of higher than 100 mJ/cm2. Using differential gene expression analysis based on generated RNA-Seq data, common and individual patterns of M. lignano transcriptional response to the induced carcinogenesis by the tested stimuli were determined. This allowed us to select promising candidate genes for functional studies using RNAi knock-down screens and for determination of their role in stem cells regulation under regeneration and homeostasis in M. lignano.

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Genome-wide analysis of highly expressed plant retrotransposons

Murad Omarov1, Pavel Merkulov2, Sofia Gvaramia3, Liza Kolganova4, Ilya Kirov51All-Russia Research Institute of Agriculture biotechnology, muradok98@gmail.com2All-Russia Research Institute of Agriculture biotechnology, paulmerkulov97@gmail.com3All-Russia Research Institute of Agriculture biotechnology, sofia.gvaramia@gmail.com4All-Russia Research Institute of Agriculture biotechnology, liza.colg@gmail.com5All-Russia Research Institute of Agriculture biotechnology, kirovez@gmail.com Retrotransposons (TEs) are mobile genomic elements capable of transposition via reverse transcription of RNA intermediate. Transcription and mobility of TEs in a cell are under strong epigenetic silencing being partially recovered during stress and some development stages. But recent studies cast doubt on this axiomatic statement, revealing many transcripts of TEs (retrotranscriptome) in somatic organs under non-stressed conditions. The composition and structure of plant retrotranscriptome are still not clear. Here, we developed a pipeline for transcribed TEs identification and applied it to 7 plant species using RNA-seq data from different organs and under different conditions. Our results showed that TEs transcription under non-stressed conditions is the widespread phenomenon in plants and expressed TEs possess some distinctive genomic features

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lncRNAs – their potential in regulation of hypertension and behavior of ISIAH rats

Poster (download) Ivan Sidorenko1, Vladimir Babenko2, Arcady Markel3, Olga Redina41Institute of Cytology and Genetics SB RAS, vanyasidorenko22@gmail.com2Institute of Cytology and Genetics SB RAS, bob@bionet.nsc.ru3Institute of Cytology and Genetics SB RAS, markel@bionet.nsc.ru4Institute of Cytology and Genetics SB RAS, oredina@bionet.nsc.ru Long non-coding RNAs (lncRNAs) play an important role in the control of many biological processes in the body, including the development of cardiovascular diseases and hypertension. It is believed that lncRNAs play a central role in the epigenetic control of gene expression, however, the understanding of lncRNA biological functions and interactions is still far from being complete. In this work, we identified the lncRNAs differentially expressed in the hypothalami of hypertensive ISIAH and normotensive WAG rats, and revealed lncRNA-associated differentially expressed genes (DEGs) related to hypertension and behavioral characteristics of ISIAH rats (grooming, vertical activity, hyperactivity, abnormal emotion/affect behavior (including abnormal response to novelty). The work was carried out using transcriptome sequencing (RNA-Seq method). Three lncRNAs (Bc1, RGD1562890, and Snhg4) were found, the expression of which differed in the hypothalami of hypertensive ISIAH and normotensive WAG rats. The largest number of co-regulated genes, both associated with hypertension and behavior, was found for Snhg4. These findings may be useful for further understanding the role of lncRNAs in regulating the protein coding genes and modulating processes associated with both hypertension and behavior.

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STUDY OF THE ROOT TRANSCRIPTOME OF BREAD WHEAT USING HIGH-THROUGHPUT RNA SEQUENCING (RNA-SEQ)

Poster (download) Alexandr Vikhorev1, Nikolay Shmakov2, Anastasia Glagoleva3, Elena Khlestkina4, Olesya Shoeva51Novosibirsk State University, vikhorev@bionet.nsc.ru2Institute of Cytology and Genetics SB RAS, shmakov@bionet.nsc.ru3Institute of Cytology and Genetics SB RAS, glagoleva@bionet.nsc.ru4All-Russian Institute of Plant Recources, khlest@bionet.nsc.ru5Institute of Cytology and Genetics SB RAS, olesya_ter@bionet.nsc.ru Bread wheat (Triticum aestivum L.) is the most important crop in the world. It provides about 20% of the total calories consumed by humans. For a long time, wheat selection was mainly based on phenotypic traits of the shoot, but the roots were given little attention. As a result, the root system of modern wheat varieties has weakened. Therefore, the study of genetic control of wheat roots development is an urgent issue. In this study, sequencing of RNA libraries from roots and coleoptile of Russian spring variety “Saratovskaya, 29” was performed. De novo transcriptome was assembled. 31,488 up-regulated, 35,851 down-regulated and 18,040 roots-specific transcripts were found. The subsequent analysis of genes with differential expression will allow choosing the candidate genes for development of wheat varieties with resistant root system.

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RTrans: a pipeline for multi-way analysis of differential gene expression profiles

Poster (download) George Sergeevich Krasnov1, Anastasiya Andreevna Kobelyatskaya2, Anastasiya Vladimirovna Snezhkina3, Vladislav Sergeevich Pavlov4, Elena Anatolevna Pudova5, Anna Victorovna Kudryavtseva61EIMB RAS, gskrasnov@mail.ru2EIMB RAS, kaa.chel@mail.ru3EIMB RAS, leftger@rambler.ru4EIMB RAS, vladislav1pavlov@gmail.com5EIMB RAS, pudova_elena@inbox.ru6EIMB RAS, rhizamoeba@mail.ru RNA-Seq is a widespread technique routinely used to reveal differentially expressed (DE) genes, splicing events and affected signaling pathways. Usually, RNA-Seq data analysis needs skills in programming and bioinformatics. We aimed at developing easy-to-use pipeline covering multiple aspects of DE analysis. Here we present RTrans pipeline aimed at evaluating differential gene expression, pathway enrichment, WGCNA co-expression analysis and visualization. It provides rapid analysis of read counts data including MANOVA, paired tests, non-parametric tests. RTrans represents a versatile pipeline facilitating DE analysis based on RNA-Seq and other quantitative data.

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Comparison of Brain Transcriptome Profiles of Short-lived and Long-lived Species of Nothobranchius

Zulfiia Guvatova1, George Krasnov2, Sergey Simanovsky3, Alexander Frolov4, Nataliya Gladysh5, Anna Kudryavtseva61Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, guvatova.zulfiya@mail.ru2Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, gskrasnov@mail.ru3Laboratory for Ecological Monitoring of Nuclear Power Plant (NPP) Regions and Bioindication Russia A.N. Severtsov Institute of Ecology and Evolution Moscow, Russia, sergey.a.simanovsky@gmail.com4Laboratory for Ecological Monitoring of Nuclear Power Plant (NPP) Regions and Bioindication Russia A.N. Severtsov Institute of Ecology and Evolution Moscow, Russia, frolov@mail.ru5Veterinary biology faculty MSAVM&B – MVA named after K.I. Skryabin Moscow, Russia, natalyagladish@gmail.com6Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, rhizamoeba@mail.ru Annual fishes of the genus Nothobranchius from East Africa are promising vertebrate model in comparative and ageing studies. Nothobranchius show accelerated growth and age-related changes at all levels of organization. The present work aims to compare brain transcriptome profiles of short-lived N. rachovii with longer-lived N. korthausae and N. guntheri.

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Genes expression related to the effects of hypoxia in the marine mussel, Mytilus galloprovincialis

Ekaterina Vodiasova1, Aleksandra Andreyeva2, Рђnastasiya Lantushenko3, Yakov Meger4, Irina Deghtyar5, Dmitry Afonnikov61IBSS RAS, Sevastopol, Russia, eavodiasova@gmail.com2IBSS RAS, Sevastopol, Russia, andreevaal@gmail.com3SSU, Sevastopol, Russia, lantushenko@mail.ru4SSU, Sevastopol, Russia, meger_yakov@mail.ru5SSU, Sevastopol, Russia, skuratovskaya95@mail.ru6ICG SB RAS, Novosibirsk, Russia, ada@bionet.nsc.ru Despite that mussel is an important object of mariculture and can play the role of an ecosystem bio-indicator, the study of the effect of hypoxia on these mollusСЃs is limited only by biochemical and RT-PCR experiments for individual genes (enzymes). There is no data on changes in the expression profile of all genes based on RNA sequencing. At the same time, an understanding of physiological processes requires comprehensive studies based on the study of the expression of all genes in target tissues. At this work, the transcriptomes of the gills of Mytilus galloprovincialis exposed to hypoxic stress (DO 0.3 mg/l) for 24h were sequenced using Illumina technology for the first time. The raw reads assembled into 255,302 transcripts with an N50 value of 1,273 nt. A total of 65 transcripts that differed in abundance in the hypoxia-exposed mussels were identified. Their putative function was assigned using BLAST. The data obtained will allow further large-scale studies for other targeted tissues and to study all aspects of the physiological response of M. galloprovincialis to the emerging oxygen deficiency in the environment.

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The first insights into regulation of cell transdifferentiation during gut regeneration in Eupentacta fraudatrix

Alexey Boyko1, Igor Dolmatov21NSCMB FEB RAS, Vladivostok, Russia, Alteroldis@gmail.com2NSCMB FEB RAS, Vladivostok, Russia, idolmatov@mail.ru The holothurian Eupentacta fraudatrix is a unique organism for studying regeneration mechanisms. It has been repeatedly confirmed that regeneration is only due to the transformation of terminally differentiated cells. In this study, we examined changes in gene expression during gut regeneration of the holothurian E. fraudatrix and found 11 TFs, which are candidates for the role of transdifferentiation regulators.

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