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  1. Article: Genomic and Transcriptomic Analysis of Pea (

    Zorin, Evgeny A / Sulima, Anton S / Zhernakov, Aleksandr I / Kuzmina, Daria O / Rakova, Valeria A / Kliukova, Marina S / Romanyuk, Daria A / Kulaeva, Olga A / Akhtemova, Gulnar A / Shtark, Oksana Y / Tikhonovich, Igor A / Zhukov, Vladimir A

    Plants (Basel, Switzerland)

    2023  Volume 13, Issue 1

    Abstract: Pea ( ...

    Abstract Pea (
    Language English
    Publishing date 2023-12-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants13010078
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  2. Article ; Online: Preparation and analysis of positioned mononucleosomes.

    Kulaeva, Olga I / Studitsky, Vasily M

    Methods in molecular biology (Clifton, N.J.)

    2015  Volume 1288, Page(s) 15–26

    Abstract: Short DNA fragments containing single nucleosomes have been extensively employed as simple model experimental systems for analysis of many intranuclear processes, including binding of proteins to nucleosomes, covalent histone modifications, transcription, ...

    Abstract Short DNA fragments containing single nucleosomes have been extensively employed as simple model experimental systems for analysis of many intranuclear processes, including binding of proteins to nucleosomes, covalent histone modifications, transcription, DNA repair, and ATP-dependent chromatin remodeling. Here we describe several recently developed procedures for obtaining and analysis of mononucleosomes assembled on 200-350-bp DNA fragments.
    MeSH term(s) Animals ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DNA/genetics ; DNA/metabolism ; Erythrocytes ; Histones/metabolism ; Nucleosomes/chemistry ; Nucleosomes/metabolism
    Chemical Substances Chromatin ; Histones ; Nucleosomes ; DNA (9007-49-2)
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-2474-5_2
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  3. Article ; Online: Experimental analysis of hFACT action during Pol II transcription in vitro.

    Hsieh, Fu-Kai / Kulaeva, Olga I / Studitsky, Vasily M

    Methods in molecular biology (Clifton, N.J.)

    2015  Volume 1276, Page(s) 315–326

    Abstract: FACT (facilitates chromatin transcription) is a histone chaperone that facilitates transcription through chromatin and promotes histone recovery during transcription. Here, we describe a highly purified experimental system that recapitulates many ... ...

    Abstract FACT (facilitates chromatin transcription) is a histone chaperone that facilitates transcription through chromatin and promotes histone recovery during transcription. Here, we describe a highly purified experimental system that recapitulates many important properties of transcribed chromatin and the key aspects of hFACT action during this process in vitro. We present the protocols describing how to prepare different forms of nucleosomes, including intact nucleosome, covalently conjugated nucleosome, nucleosome missing one of the two H2A/2B dimers (hexasome) and tetrasome (a nucleosome missing both H2A/2B dimers). These complexes allow analysis of various aspects of FACT's function. These approaches and other methods described below can also be applied to the study of other chromatin remodelers and chromatin-targeted factors.
    MeSH term(s) Chromatin/genetics ; Chromatin/physiology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; High Mobility Group Proteins/genetics ; High Mobility Group Proteins/metabolism ; Histones/metabolism ; Humans ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Oligonucleotides/genetics ; Plasmids/genetics ; RNA Polymerase II/metabolism ; Transcription, Genetic/physiology ; Transcriptional Elongation Factors/genetics ; Transcriptional Elongation Factors/metabolism
    Chemical Substances Chromatin ; DNA-Binding Proteins ; High Mobility Group Proteins ; Histones ; Nucleosomes ; Oligonucleotides ; SSRP1 protein, human ; Transcriptional Elongation Factors ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-2392-2_19
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  4. Article: A variable gene family encoding nodule-specific cysteine-rich peptides in pea (

    Zorin, Evgeny A / Kliukova, Marina S / Afonin, Alexey M / Gribchenko, Emma S / Gordon, Mikhail L / Sulima, Anton S / Zhernakov, Aleksandr I / Kulaeva, Olga A / Romanyuk, Daria A / Kusakin, Pyotr G / Tsyganova, Anna V / Tsyganov, Viktor E / Tikhonovich, Igor A / Zhukov, Vladimir A

    Frontiers in plant science

    2022  Volume 13, Page(s) 884726

    Abstract: Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule- ... ...

    Abstract Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume
    Language English
    Publishing date 2022-09-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2022.884726
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Mechanism of histone survival during transcription by RNA polymerase II.

    Kulaeva, Olga I / Studitsky, Vasily M

    Transcription

    2010  Volume 1, Issue 2, Page(s) 85–88

    Abstract: This work is related to and stems from our recent NSMB paper, "Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II" (December 2009). Synopsis. Recent genomic studies from many laboratories have suggested that nucleosomes ... ...

    Abstract This work is related to and stems from our recent NSMB paper, "Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II" (December 2009). Synopsis. Recent genomic studies from many laboratories have suggested that nucleosomes are not displaced from moderately transcribed genes. Furthermore, histones H3/H4 carrying the primary epigenetic marks are not displaced or exchanged (in contrast to H2A/H2B histones) during moderate transcription by RNA polymerase II (Pol II) in vivo. These exciting observations suggest that the large molecule of Pol II passes through chromatin structure without even transient displacement of H3/H4 histones. The most recent analysis of the RNA polymerase II (Pol II)-type mechanism of chromatin remodeling in vitro (described in our NSMB 2009 paper) suggests that nucleosome survival is tightly coupled with formation of a novel intermediate: a very small intranucleosomal DNA loop (Ø-loop) containing transcribing Pol II. In the submitted manuscript we critically evaluate one of the key predictions of this model: the lack of even transient displacement of histones H3/H4 during Pol II transcription in vitro. The data suggest that, indeed, histones H3/H4 are not displaced during Pol II transcription in vitro. These studies are directly connected with the observation in vivo on the lack of exchange of histones H3/H4 during Pol II transcription.
    MeSH term(s) Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DNA/genetics ; DNA/metabolism ; Histones/metabolism ; Models, Genetic ; Nucleosomes/genetics ; Nucleosomes/metabolism ; RNA Polymerase II/metabolism ; Transcription, Genetic/genetics
    Chemical Substances Chromatin ; Histones ; Nucleosomes ; DNA (9007-49-2) ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2010-08-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2646974-1
    ISSN 2154-1272 ; 2154-1264
    ISSN (online) 2154-1272
    ISSN 2154-1264
    DOI 10.4161/trns.1.2.12519
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  6. Article: Structure of transcribed chromatin is a sensor of DNA damage.

    Pestov, Nikolay A / Gerasimova, Nadezhda S / Kulaeva, Olga I / Studitsky, Vasily M

    Science advances

    2015  Volume 1, Issue 6, Page(s) e1500021

    Abstract: Early detection and repair of damaged DNA is essential for cell functioning and survival. Although multiple cellular systems are involved in the repair of single-strand DNA breaks (SSBs), it remains unknown how SSBs present in the nontemplate strand (NT- ... ...

    Abstract Early detection and repair of damaged DNA is essential for cell functioning and survival. Although multiple cellular systems are involved in the repair of single-strand DNA breaks (SSBs), it remains unknown how SSBs present in the nontemplate strand (NT-SSBs) of DNA organized in chromatin are detected. The effect of NT-SSBs on transcription through chromatin by RNA polymerase II was studied. NT-SSBs localized in the promoter-proximal region of nucleosomal DNA and hidden in the nucleosome structure can induce a nearly quantitative arrest of RNA polymerase downstream of the break, whereas more promoter-distal SSBs moderately facilitate transcription. The location of the arrest sites on nucleosomal DNA suggests that formation of small intranucleosomal DNA loops causes the arrest. This mechanism likely involves relief of unconstrained DNA supercoiling accumulated during transcription through chromatin by NT-SSBs. These data suggest the existence of a novel chromatin-specific mechanism that allows the detection of NT-SSBs by the transcribing enzyme.
    Language English
    Publishing date 2015-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.1500021
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  7. Article: Association Study of Symbiotic Genes in Pea (Pisum sativum L.) Cultivars Grown in Symbiotic Conditions

    Zhukov, Vladimir A. / Zhernakov, Aleksandr I. / Sulima, Anton S. / Kulaeva, Olga A. / Kliukova, Marina S. / Afonin, Alexey M. / Shtark, Oksana Y. / Tikhonovich, Igor A.

    Agronomy. 2021 Nov. 22, v. 11, no. 11

    2021  

    Abstract: In garden pea (Pisum sativum L.), several symbiotic genes are known to control the development of mutualistic symbioses with nodule bacteria (NB) and arbuscular mycorrhizal fungi (AMF). Here, we studied whether the allelic state of the symbiotic genes ... ...

    Abstract In garden pea (Pisum sativum L.), several symbiotic genes are known to control the development of mutualistic symbioses with nodule bacteria (NB) and arbuscular mycorrhizal fungi (AMF). Here, we studied whether the allelic state of the symbiotic genes was associated with the growth parameters of pea plants under single inoculation with NB and under double inoculation with NB + AMF. Using different statistical methods, we analyzed the dataset obtained from a pot experiment that involved 99 pea cultivars, 10 of which were characterized as having shortened internodes due to the presence of the natural mutation p.A229T in the developmental gene Le. The plant’s habitus strongly influenced most of the studied growth and yield parameters and the effectiveness of the symbiotic interactions under NB and NB + AMF inoculation. Double inoculation had different effects on Le⁺ (normal) and le⁻ (dwarf) plants with regard to nitrogen and phosphorus content in seeds. Regardless of the Le-status of plants, allelic states of the symbiotic gene LykX encoding the putative receptor of Nod factors (bacterial signal molecules) were shown to be associated with seed number, thousand-seed weight, and pod number at the level of FDR < 0.001, whereas associations of allelic states of the other studied symbiotic genes were less significant.
    Keywords Pisum sativum subsp. sativum var. sativum ; agronomy ; cultivars ; data collection ; genes ; mutation ; nitrogen ; peas ; phosphorus content ; vesicular arbuscular mycorrhizae
    Language English
    Dates of publication 2021-1122
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2607043-1
    ISSN 2073-4395
    ISSN 2073-4395
    DOI 10.3390/agronomy11112368
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: The Regulation of Pea (

    Ivanova, Kira A / Chernova, Ekaterina N / Kulaeva, Olga A / Tsyganova, Anna V / Kusakin, Pyotr G / Russkikh, Iana V / Tikhonovich, Igor A / Tsyganov, Viktor E

    Frontiers in plant science

    2022  Volume 13, Page(s) 843565

    Abstract: In this study, the roles of glutathione (GSH), homoglutathione (hGSH), and their ratio in symbiotic nodule development and functioning, as well as in defense responses accompanying ineffective nodulation in pea ( ...

    Abstract In this study, the roles of glutathione (GSH), homoglutathione (hGSH), and their ratio in symbiotic nodule development and functioning, as well as in defense responses accompanying ineffective nodulation in pea (
    Language English
    Publishing date 2022-03-30
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2022.843565
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  9. Article ; Online: Overcoming a nucleosomal barrier to replication.

    Chang, Han-Wen / Pandey, Manjula / Kulaeva, Olga I / Patel, Smita S / Studitsky, Vasily M

    Science advances

    2016  Volume 2, Issue 11, Page(s) e1601865

    Abstract: Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are ... ...

    Abstract Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are unknown. We have studied traversal of uniquely positioned mononucleosomes by T7 replisome in vitro. Nucleosomes present a strong, sequence-dependent barrier for replication, with particularly strong pausing of DNA polymerase at the +(31-40) and +(41-65) regions of the nucleosomal DNA. The exonuclease activity of T7 DNA polymerase increases the overall rate of progression of the replisome through a nucleosome, likely by resolving nonproductive complexes. The presence of nucleosome-free DNA upstream of the replication fork facilitates the progression of DNA polymerase through the nucleosome. After replication, at least 50% of the nucleosomes assume an alternative conformation, maintaining their original positions on the DNA. Our data suggest a previously unpublished mechanism for nucleosome maintenance during replication, likely involving transient formation of an intranucleosomal DNA loop.
    MeSH term(s) Animals ; Chickens ; DNA/blood ; DNA/chemistry ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry ; Nucleosomes/chemistry
    Chemical Substances Nucleosomes ; DNA (9007-49-2) ; bacteriophage T7 induced DNA polymerase (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2016-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.1601865
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  10. Article ; Online: Association Study of Symbiotic Genes in Pea ( Pisum sativum L.) Cultivars Grown in Symbiotic Conditions

    Vladimir A. Zhukov / Aleksandr I. Zhernakov / Anton S. Sulima / Olga A. Kulaeva / Marina S. Kliukova / Alexey M. Afonin / Oksana Y. Shtark / Igor A. Tikhonovich

    Agronomy, Vol 11, Iss 2368, p

    2021  Volume 2368

    Abstract: In garden pea ( Pisum sativum L.), several symbiotic genes are known to control the development of mutualistic symbioses with nodule bacteria (NB) and arbuscular mycorrhizal fungi (AMF). Here, we studied whether the allelic state of the symbiotic genes ... ...

    Abstract In garden pea ( Pisum sativum L.), several symbiotic genes are known to control the development of mutualistic symbioses with nodule bacteria (NB) and arbuscular mycorrhizal fungi (AMF). Here, we studied whether the allelic state of the symbiotic genes was associated with the growth parameters of pea plants under single inoculation with NB and under double inoculation with NB + AMF. Using different statistical methods, we analyzed the dataset obtained from a pot experiment that involved 99 pea cultivars, 10 of which were characterized as having shortened internodes due to the presence of the natural mutation p.A229T in the developmental gene Le . The plant’s habitus strongly influenced most of the studied growth and yield parameters and the effectiveness of the symbiotic interactions under NB and NB + AMF inoculation. Double inoculation had different effects on Le + (normal) and le − (dwarf) plants with regard to nitrogen and phosphorus content in seeds. Regardless of the Le -status of plants, allelic states of the symbiotic gene LykX encoding the putative receptor of Nod factors (bacterial signal molecules) were shown to be associated with seed number, thousand-seed weight, and pod number at the level of FDR < 0.001, whereas associations of allelic states of the other studied symbiotic genes were less significant.
    Keywords Pisum sativum ; symbiotic genes ; nodule bacteria ; arbuscular mycorrhiza ; symbiotic responsivity ; symbiotic effectiveness ; Agriculture ; S
    Subject code 580
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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