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  1. Article ; Online: Global repair is the primary nucleotide excision repair subpathway for the removal of pyrimidine-pyrimidone (6-4) damage from the Arabidopsis genome.

    Kaya, Sezgi / Erdogan, Dugcar Ebrar / Sancar, Aziz / Adebali, Ogun / Oztas, Onur

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 3308

    Abstract: Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant genomes. (6-4)PPs disrupt growth and development by interfering with transcription and DNA ... ...

    Abstract Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant genomes. (6-4)PPs disrupt growth and development by interfering with transcription and DNA replication. To resist UV stress, plants employ both photoreactivation and nucleotide excision repair that excises oligonucleotide containing (6-4)PPs through two subpathways: global and transcription-coupled excision repair (TCR). Here, we analyzed the genome-wide excision repair-mediated repair of (6-4)PPs in Arabidopsis thaliana and found that (6-4)PPs can be repaired by TCR; however, the main subpathway to remove (6-4)PPs from the genome is global repair. Our analysis showed that open chromatin genome regions are more rapidly repaired than heterochromatin regions, and the repair level peaks at the promoter, transcription start site and transcription end site of genes. Our study revealed that the repair of (6-4)PP in plants showed a distinct genome-wide repair profile compared to the repair of other major UV-induced DNA lesion called cyclobutane pyrimidine dimers (CPDs).
    MeSH term(s) DNA Repair ; Arabidopsis/genetics ; Pyrimidinones ; Excision Repair ; Pyrimidine Dimers ; DNA Damage ; Receptors, Antigen, T-Cell/genetics ; Ultraviolet Rays
    Chemical Substances Pyrimidinones ; Pyrimidine Dimers ; Receptors, Antigen, T-Cell
    Language English
    Publishing date 2024-02-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-53472-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genome-wide Excision Repair Map of Cyclobutane Pyrimidine Dimers in Arabidopsis and the Roles of CSA1 and CSA2 Proteins in Transcription-coupled Repair.

    Kaya, Sezgi / Adebali, Ogun / Oztas, Onur / Sancar, Aziz

    Photochemistry and photobiology

    2021  Volume 98, Issue 3, Page(s) 707–712

    Abstract: Plants depend on light for energy production. However, the UV component in sunlight also inflicts DNA damage, mostly in the form of cyclobutane pyrimidine dimers (CPD) and (6-4) pyrimidine-pyrimidone photoproducts, which are mutagenic and lethal to the ... ...

    Abstract Plants depend on light for energy production. However, the UV component in sunlight also inflicts DNA damage, mostly in the form of cyclobutane pyrimidine dimers (CPD) and (6-4) pyrimidine-pyrimidone photoproducts, which are mutagenic and lethal to the plant cells. These lesions are repaired by blue-light-dependent photolyases and the nucleotide excision repair enzymatic systems. Here, we characterize nucleotide excision repair in Arabidopsis thaliana genome-wide and at single nucleotide resolution with special focus on transcription-coupled repair and the role of the CSA1 and CSA2 genes/proteins in dictating the efficiency and the strand preference of repair of transcribed genes. We demonstrate that CSA1 is the dominant protein in coupling repair to transcription with minor contribution from CSA2.
    MeSH term(s) Arabidopsis/genetics ; Arabidopsis/metabolism ; DNA Damage ; DNA Repair ; Deoxyribodipyrimidine Photo-Lyase/genetics ; Deoxyribodipyrimidine Photo-Lyase/metabolism ; Pyrimidine Dimers/metabolism ; Ultraviolet Rays
    Chemical Substances Pyrimidine Dimers ; Deoxyribodipyrimidine Photo-Lyase (EC 4.1.99.3)
    Language English
    Publishing date 2021-10-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 123540-0
    ISSN 1751-1097 ; 0031-8655
    ISSN (online) 1751-1097
    ISSN 0031-8655
    DOI 10.1111/php.13519
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Long Non-coding RNA in Plants in the Era of Reference Sequences.

    Budak, Hikmet / Kaya, Sezgi Biyiklioglu / Cagirici, Halise Busra

    Frontiers in plant science

    2020  Volume 11, Page(s) 276

    Abstract: The discovery of non-coding RNAs (ncRNAs), and the subsequent elucidation of their functional roles, was largely delayed due to the misidentification of non-protein-coding parts of DNA as "junk DNA," which forced ncRNAs into the shadows of their protein- ... ...

    Abstract The discovery of non-coding RNAs (ncRNAs), and the subsequent elucidation of their functional roles, was largely delayed due to the misidentification of non-protein-coding parts of DNA as "junk DNA," which forced ncRNAs into the shadows of their protein-coding counterparts. However, over the past decade, insight into the important regulatory roles of ncRNAs has led to rapid progress in their identification and characterization. Of the different types of ncRNAs, long non-coding RNAs (lncRNAs), has attracted considerable attention due to their mRNA-like structures and gene regulatory functions in plant stress responses. While RNA sequencing has been commonly used for mining lncRNAs, a lack of widespread conservation at the sequence level in addition to relatively low and highly tissue-specific expression patterns challenges high-throughput
    Language English
    Publishing date 2020-03-12
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.00276
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Pan-Genome miRNomics in Brachypodium

    Muslu, Tugdem / Biyiklioglu-Kaya, Sezgi / Akpinar, Bala Ani / Yuce, Meral / Budak, Hikmet

    Plants. 2021 May 16, v. 10, no. 5

    2021  

    Abstract: Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute ... ...

    Abstract Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.
    Keywords Brachypodium distachyon ; computer simulation ; gene expression regulation ; genomics ; microRNA ; stress tolerance
    Language English
    Dates of publication 2021-0516
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants10050991
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Pan-Genome miRNomics in

    Muslu, Tugdem / Biyiklioglu-Kaya, Sezgi / Akpinar, Bala Ani / Yuce, Meral / Budak, Hikmet

    Plants (Basel, Switzerland)

    2021  Volume 10, Issue 5

    Abstract: Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute ... ...

    Abstract Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of
    Language English
    Publishing date 2021-05-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants10050991
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes.

    Muslu, Tugdem / Akpinar, Bala Ani / Biyiklioglu-Kaya, Sezgi / Yuce, Meral / Budak, Hikmet

    International journal of molecular sciences

    2021  Volume 22, Issue 22

    Abstract: Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple ... ...

    Abstract Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (
    MeSH term(s) Animals ; Avena/genetics ; Avena/immunology ; Avena/parasitology ; Chromosome Mapping/methods ; Diptera/pathogenicity ; Diptera/physiology ; Disease Resistance/genetics ; Edible Grain ; Genetic Code ; Genome, Plant ; Hordeum/genetics ; Hordeum/immunology ; Hordeum/parasitology ; Humans ; Hymenoptera/pathogenicity ; Hymenoptera/physiology ; Oryza/genetics ; Oryza/immunology ; Oryza/parasitology ; Plant Diseases/genetics ; Plant Diseases/immunology ; Plant Diseases/parasitology ; Quantitative Trait Loci ; Quantitative Trait, Heritable ; Secale/genetics ; Secale/immunology ; Secale/parasitology ; Species Specificity ; Triticum/genetics ; Triticum/immunology ; Triticum/parasitology
    Language English
    Publishing date 2021-11-16
    Publishing country Switzerland
    Document type Comparative Study ; Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms222212349
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

    Rabanus-Wallace, M Timothy / Hackauf, Bernd / Mascher, Martin / Lux, Thomas / Wicker, Thomas / Gundlach, Heidrun / Baez, Mariana / Houben, Andreas / Mayer, Klaus F X / Guo, Liangliang / Poland, Jesse / Pozniak, Curtis J / Walkowiak, Sean / Melonek, Joanna / Praz, Coraline R / Schreiber, Mona / Budak, Hikmet / Heuberger, Matthias / Steuernagel, Burkhard /
    Wulff, Brande / Börner, Andreas / Byrns, Brook / Čížková, Jana / Fowler, D Brian / Fritz, Allan / Himmelbach, Axel / Kaithakottil, Gemy / Keilwagen, Jens / Keller, Beat / Konkin, David / Larsen, Jamie / Li, Qiang / Myśków, Beata / Padmarasu, Sudharsan / Rawat, Nidhi / Sesiz, Uğur / Biyiklioglu-Kaya, Sezgi / Sharpe, Andy / Šimková, Hana / Small, Ian / Swarbreck, David / Toegelová, Helena / Tsvetkova, Natalia / Voylokov, Anatoly V / Vrána, Jan / Bauer, Eva / Bolibok-Bragoszewska, Hanna / Doležel, Jaroslav / Hall, Anthony / Jia, Jizeng / Korzun, Viktor / Laroche, André / Ma, Xue-Feng / Ordon, Frank / Özkan, Hakan / Rakoczy-Trojanowska, Monika / Scholz, Uwe / Schulman, Alan H / Siekmann, Dörthe / Stojałowski, Stefan / Tiwari, Vijay K / Spannagl, Manuel / Stein, Nils

    Nature genetics

    2021  Volume 53, Issue 4, Page(s) 564–573

    Abstract: Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is ... ...

    Abstract Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
    MeSH term(s) Adaptation, Physiological/genetics ; Chromosome Mapping/methods ; Crops, Agricultural/genetics ; Crops, Agricultural/immunology ; Gene Expression Regulation, Plant ; Genetic Introgression ; Genome, Plant ; Karyotype ; Plant Breeding/methods ; Plant Immunity/genetics ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Secale/genetics ; Secale/immunology ; Stress, Physiological ; Triticum/genetics
    Chemical Substances Plant Proteins
    Language English
    Publishing date 2021-03-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-021-00807-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 46: Show issues

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  8. Article ; Online: Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

    Rabanus-Wallace, M. Timothy / Hackauf, Bernd / Mascher, Martin / Lux, Thomas / Wicker, Thomas / Gundlach, Heidrun / Baez, Mariana / Houben, Andreas / Mayer, Klaus F. X. / Guo, Liangliang / Poland, Jesse / Pozniak, Curtis J. / Walkowiak, Sean / Melonek, Joanna / Praz, Coraline R. / Schreiber, Mona / Budak, Hikmet / Heuberger, Matthias / Steuernagel, Burkhard /
    Wulff, Brande / Börner, Andreas / Byrns, Brook / Čížková, Jana / Fowler, D. Brian / Fritz, Allan / Himmelbach, Axel / Kaithakottil, Gemy / Keilwagen, Jens / Keller, Beat / Konkin, David / Larsen, Jamie / Li, Qiang / Myśków, Beata / Padmarasu, Sudharsan / Rawat, Nidhi / Sesiz, Uğur / Biyiklioglu-Kaya, Sezgi / Sharpe, Andy / Šimková, Hana / Small, Ian / Swarbreck, David / Toegelová, Helena / Tsvetkova, Natalia / Voylokov, Anatoly V. / Vrána, Jan / Bauer, Eva / Bolibok-Bragoszewska, Hanna / Doležel, Jaroslav / Hall, Anthony / Jia, Jizeng / Korzun, Viktor / Laroche, André / Ma, Xue-Feng / Ordon, Frank / Özkan, Hakan / Rakoczy-Trojanowska, Monika / Scholz, Uwe / Schulman, Alan H. / Siekmann, Dörthe / Stojałowski, Stefan / Tiwari, Vijay K. / Spannagl, Manuel / Stein, Nils

    2021  

    Abstract: Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is ... ...

    Abstract Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
    Keywords Text ; ddc:630
    Language English
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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