Statistical problems of clusters of transcription factor binding sites in plant genomes

Artur Dergilev11Institute of Cytology and Genetics SB RAS, arturd1993@yandex.ru AbstractВ В В В  This work presents the results of using computer scripts to analyze ChIP-seq data, calculate clusters, and visualize them in the form of heat maps. In the work, ChIP-seq peaks were used to study the stem cell niche of three plants, among which the well-known Talus (Arabidopsis Thailana), Physcomitrella patens, Chlamydomonas reinhardti. What about the tendency of co-localization of transcription factors in plant genomes? What are the features of this co-localization?

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Functional study of potential regulatory SNPs

Arina Degtyareva1, Elena Leberfarb2, Ilya Brusentsov3, Tatiana Kuzina4, Tatiana Merkulova51ICG SB RAS, degtyareva_rso@mail.ru2ICG SB RAS, lieberfarb@bionet.nsc.ru3ICG SB RAS, brusentsovi@gmail.com4NSU, t.kuzina@g.nsu.ru5ICG SB RAS, merkulova@bionet.nsc.ru In a previous study using a new bioinformatic approach based on Chip-Seq data with antibodies to various transcription factors , histone markers , and ChiA-PET and RNA-seq data, 32 potentially regulatory single -nucleotide polymorphisms (SNPs) were associated with colorectal cancer . In this study, a functional analysis of 6 of these polymorphisms was performed using EMSA and the luciferase reporter system. These nucleotide substitutions have been shown to alter the binding of oligonucleotides to nuclear extract proteins and alter the expression of the reporter gene.

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Altered expression of genes Npas4 and Nr1d1 in adult female mice with history of early-life stress

Poster (download) Yuliya Ryabushkina1, Vasiliy Reshetnikov2, Natalya Bondar31ICG SB RAS, Novosibirsk, Russia, ryabushkina@bionet.nsc.ru2ICG SB RAS, Novosibirsk, Russia, vasiliyreshetnikov@bionet.nsc.ru3ICG SB RAS, Novosibirsk, Russia, nbondar@bionet.nsc.ru Stressful events early in life alter neuronal plasticity of the brain regions that regulate social behavior. Previous works have shown that brief and prolonged separation of pups from their mothers leads to enhanced social behavior in adult female mice. In this study, we performed Egr1, Npas4, Arc, and Homer1 gene expression level analysis in the prefrontal cortex and dorsal hippocampus of adult female mice after exposure to early life stress. Also was evaluated expression level of stress-related genes glucocorticoid and mineralocorticoid receptors (Nr3c1 and Nr3c2) as well as Nr1d1, which encodes a transcription factor REVERBО±, which regulates sociability and anxiety-related behavior. C57Bl/6 mice were exposed to maternal separation (MS, 3 h once a day) or handling (HD, 15 min once a day) on postnatal days 2 through 14. As adults, female mice behavior was analyzed by behavioral tests, on the day after last testing gene expression level analysis was performed. We found evaluation of Npas4 expression in prefrontal cortex and Nr1d1 both in prefrontal cortex and dorsal hippocampus of adult female mice of MS group, not in HD group. The expression of stress-related genes Nr3c1 and Nr3c2 was unchanged in both groups. This upregulation of Npas4 and Nr1d1 genes in female mice with stressful events early in life and enhanced social behavior may be an adaptation mechanism reversing possible aberrations caused by early-life stress.

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Placental transcriptome co-expression analysis reveals key biomarkers and pathways of preeclampsia

Poster (download) Trifonova E.1, Zarubin A.2, Babovskaya A.3, Markov A.4, Stepanov V.51TNRMC RAS, Tomsk, Russia; SibMed, Tomsk, Russia, ekaterina.trifonova@medgenetics.ru2TNRMC RAS, Tomsk, Russia, aleksei.zarubin@medgenetics.ru3TNRMC RAS, Tomsk, Russia, anastasia.babovskaya@medgenetics.ru4TNRMC RAS, Tomsk, Russia, anton.markov@medgenetics.ru5TNRMC RAS, Tomsk, Russia, vadim.stepanov@medgenetics.ru Preeclampsia is a complication of pregnancy characterized by new-onset hypertension and proteinuria of gestation, with serious consequences for mother and infant. Although a vast amount of research has been performed on the pathogenesis of preeclampsia, the underlying mechanisms of this multisystemic disease have remained to be fully elucidated. We identified the significant role of disturbance of intercellular interactions and regulation of proteins modification in placental tissue during the development of the PE. Among the genes involved in these key pathways, 9 hub genes and 3 master regulators were identified from the co-expression and upstream analysis networks. The present study may provide a basis for exploring potential novel genes and pathways as therapeutic targets for preeclampsia.

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Promoter expression landscape in skeletal muscle in hindlimb suspension and recovery model in rat

Poster (download) Guzel Gazizova1, Ruslan Deviatiiarov2, Islam Nigmetzyanov3, Oksana Tyapkina4, Leniz Nurullin5, Oleg Gusev61Kazan Federal University, grgazizova@gmail.com2Kazan Federal University, ruselusalbus@gmail.com3Kazan Federal University, islamka32@gmail.com4Federal Research Center “Kazan Scientific Center of the RAS\”, antitoxin@icloud.com5Federal Research Center “Kazan Scientific Center of the RAS\”, leniz2009@gmail.com6Kazan Federal University, RIKEN, oleg.gusev@riken.jp Loss of muscle mass and function during long period of physical inactivity still remains a clinical problem for humanity because the significant reducing of life quality and increasing mortality. In recent studies global gene expression in atrophied and recovered skeletal muscles on different animal models was analyzed. However, previously whole-genome regulation of atrophy and following recovery at promoter and enhancer level has not been studied. To identify transcription initiation sites (TSS), and evaluate full-genome RNA expression at the level of individual promoters and enhancers during unloading and subsequent recovery in rats two types of muscles, \”slow\” (m. Soleus) and \”fast\” (m. EDL), were examined in rats in normal conditions, after 1, 3 and 7 days of hindlimb suspension and following 1, 3 and 7 days of recovery using CAGE (Cap Analysis of Gene Expression) method followed by Illumina HiSeq 2500 sequencing. We obtained 9971 unique CAGE clusters, among which 6377 were promoters associated with genes. Differential expression of genes and their promoter activity were strongly varied in m. EDL and m. soleus within suspension-recovery time course. This study provides the first systematic annotation of promoters landscape and genes activated in \”fast\” and \”slow\” muscle types under induced atrophy and following recovery in rats.

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Expression of DNA reparation genes in anhydrobiotic insect Polypedilum vanderplanki

Video (download) Alexander Nesmelov1, Sabina Kondratyeva2, Taisiya Voronina31IFMB KFU, Kazan, Russia, nesmelov@gmail.com2IFMB KFU, Kazan, Russia, sabinakondr@gmail.com3IFMB KFU, Kazan, Russia, vorotaisiya@gmail.com Anhydrobiosis is survival of complete body desiccation, tightly linked to the ability to cope with a massive DNA damage. However, in anhydrobiotic midge Polypedilum vanderplanki this ability is not accompanied by a huge induction of genes of DNA reparation system which is typical for many other anhydrobiosis-related genes in this insect.

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Detection and investigation of genes with circadian expression pattern in common wheat

Poster (download) Antonina Kiseleva1, Maria Bragina2, Elena Salina31ICG SB RAS, Novosibirsk, Russia, antkiseleva@bionet.nsc.ru2ICG SB RAS, Novosibirsk, Russia, koltunova@bionet.nsc.ru3ICG SB RAS, Novosibirsk, Russia, salina@bionet.nsc.ru The study of daily oscillations of the wheat transcriptome, the identification of both the core circadian genes and the genes of metabolic pathways under the influence of daily rhythms is the main topic of this work.

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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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Functional study of potential regulatory SNPs (rs590352, rs11542583, rs3829202, rs78317230, rs2072580, rs4796672)

Poster (download) Arina Degtyareva1, Elena Leberfarb2, Ilya Brusentsov3, Tatiana Kuzina4, Tatiana Merkulova51ICG SB RAS, degtyareva_rso@mail.ru2ICG SB RAS, lieberfarb@bionet.nsc.ru3ICG SB RAS, brusentsovi@gmail.com4NSU, t.kuzina@g.nsu.ru5ICG SB RAS, merkulova@bionet.nsc.ru In a previous study using a new bioinformatic approach based on Chip-Seq data with antibodies against various transcription factors and histone modifications, ChiA-PET, RNA-seq and ICGC data, 32 potentially regulatory single -nucleotide polymorphisms (rSNPs) were associated with colorectal cancer. In this study, a functional analysis of 6 of these polymorphisms was performed using EMSA and the luciferase reporter system. These nucleotide substitutions have been shown to alter the binding of nuclear extract proteins and influence the expression of the reporter gene.  

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