Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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High-resolution map of DNA double-stranded breaks in human genome

2011/02/A/NZ2/00014

Keywords:

genomics DNA double-stranded breaks (DSBs) genome stability next generation sequencing (NGS)

Descriptors:

  • NZ2_2: Genomics, transcriptomics, epigenomics
  • NZ2_7: Bioinformatics
  • NZ1_1: Molecular biology

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Uniwersytet Warszawski, Centrum Nowych Technologii Uniwersytetu Warszawskiego

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Krzysztof Ginalski 

Number of co-investigators in the project: 15

Call: MAESTRO 1 - announced on 2011-06-15

Amount awarded: 3 000 000 PLN

Project start date (Y-m-d): 2012-05-24

Project end date (Y-m-d): 2018-05-24

Project duration:: 72 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Rozbudowa systemu do sekwencjonowania nowej generacji HiSeq 2000 (do HiSeq 2500).
  2. Wirówka z kompletem rotorów (20 000 PLN)
  3. Serwer bioinformatyczny do przechowywania i przetwarzania danych (140 000 PLN)
  4. System do sekwencjonowania nowej generacji MiSeq.
  5. System oczyszczania wody z kompletem filtrów (35 000 PLN)
  6. Drobny sprzęt laboratoryjny: rozbudowa systemu do PCR (podstawa do termobloku), cieplarka (15 000 PLN)
  7. Inkubator do hodowli komórkowych (2 szt.) (60 000 PLN)
  8. Rozbudowa laptopa.
  9. Mikroskop.

Information in the final report

  • Publication in academic press/journals (26)
  1. Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity towards CTP and increased tendency for cytidine incorporation at the 3'-terminal positions of synthesized tails
    Authors:
    Kobylecki, K., Kuchta, K., Dziembowski, A., Ginalski, K., Tomecki, R.
    Academic press:
    RNA (rok: 2017, tom: 23, strony: 1902-1926), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.117 - link to the publication
  2. Phylogeny-based systematization of Arabidopsis proteins with histone H1 globular domain (GH1)
    Authors:
    Kotlinski, M., Knizewski, L., Muszewska, A., Rutowicz, K., Lirski, M., Schmidt, A., Baroux, C., Ginalski, K., Jerzmanowski, A.
    Academic press:
    Plant Physiology (rok: 2017, tom: 174, strony: 27-34), Wydawca: American Society of Plant Biologists
    Status:
    Published
    DOI:
    10.1104/pp.16.00214 - link to the publication
  3. Probabilistic approach to predicting substrate specificity of methyltransferases
    Authors:
    Szczepinska T, Kutner J, Kopczynski M, Pawlowski K, Dziembowski A, Kudlicki A, Ginalski K, Rowicka M
    Academic press:
    PLoS Computational Biology (rok: 2014, tom: 10, strony: e1003514), Wydawca: Public Library Science
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1003514 - link to the publication
  4. Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress
    Authors:
    Shi, W., Vu, T., Boucher, D., Biernacka, A., Nde, J., Pandita, R.K., Straube, J., Boyle, G.M., Al-Ejeh, F., Nag, P., Jeffery, J., Harris, J.L., Bain, A.L., Grzelak, M., Skrzypczak, M., Mitra, A., Dojer, N., Crosetto, N., Cloonan, N., Becherel, O.J., Finnie, J., Skaar, J.R., Walkley, C.R., Pandita, T.K., Rowicka, M., Ginalski, K., Lane, S.W., Khanna, K.K.
    Academic press:
    Blood (rok: 2017, tom: 129, strony: 2479-2492), Wydawca: American Society of Hematology
    Status:
    Published
    DOI:
    10.1182/blood-2016-06-725093 - link to the publication
  5. The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
    Authors:
    Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM
    Academic press:
    Nucleic Acids Research (rok: 2014, tom: 42, strony: 4160-4179), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkt1414 - link to the publication
  6. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing
    Authors:
    Crosetto N, Mitra A, Silva MJ, Bienko M, Dojer N, Wang Q, Karaca E, Chiarle R, Skrzypczak M, Ginalski K, Pasero P, Rowicka M, Dikic I
    Academic press:
    Nature Methods (rok: 2013, tom: 10, strony: 361-365), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/nmeth.2408 - link to the publication
  7. Systematic classification of the His-Me finger superfamily
    Authors:
    Jablonska, J., Matelska, D., Steczkiewicz, K., Ginalski, K.
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45, strony: 11479-11494), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx924 - link to the publication
  8. The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast
    Authors:
    Yoshida K, Bacal J, Desmarais D, Padioleau I, Tsaponina O, Chabes A, Pantesco V, Dubois E, Parrinello H, Skrzypczak M, Ginalski K, Lengronne A, Pasero P
    Academic press:
    Molecular Cell (rok: 2014, tom: 54, strony: 691-697), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.molcel.2014.04.03 - link to the publication
  9. Towards engineering novel PE-based immunotoxins by targeting them to the nucleus
    Authors:
    Borowiec, M., Gorzkiewicz, M., Grzesik, J., Walczak-Drzewiecka, A., Salkowska, A., Rodakowska, E., Steczkiewicz, K., Rychlewski, L., Dastych, J., Ginalski, K.
    Academic press:
    Toxins (rok: 2016, tom: 8, strony: E321), Wydawca: Multidisciplinary Digital Publishing Institute
    Status:
    Published
    DOI:
    10.3390/toxins8110321 - link to the publication
  10. Exome scale map of genetic alterations promoting metastasis in colorectal cancer
    Authors:
    Goryca, K., Kulecka, M., Paziewska, A., Dabrowska, M., Grzelak, M., Skrzypczak, M., Ginalski, K., Mroz, A., Rutkowski, A., Paczkowska, K., Mikula, M., Ostrowski, J.
    Academic press:
    BMC Genetics , Wydawca: BioMed Central
    Status:
    Submitted
    DOI:
    brak - link to the publication
  11. MRX, Set1 and Gcn5 modulate chromatin structure at stalled replication forks to promote resection of nascent DNA and cohesin loading
    Authors:
    Delamarre, A., Barthe, A., de la Roche Saint-Andre, C., Luciano, P., Forey, R., Padioleau, I., Skrzypczak, M., Ginalski, K., Geli, V., Lengronne, A., Pasero, P.
    Academic press:
    Molecular Cell , Wydawca: Cell Press
    Status:
    Submitted
    DOI:
    brak - link to the publication
  12. Comprehensive classification of the PIN domain-like superfamily
    Authors:
    Matelska, D., Steczkiewicz, K., Ginalski, K.
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45, strony: 6995-7020), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx494 - link to the publication
  13. Diverse cap-binding properties of Drosophila eIF4E isoforms
    Authors:
    Zuberek, J., Kuchta, K., Hermandez, G., Sonenberg, N., Ginalski, K.
    Academic press:
    Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics (rok: 2016, tom: 1864, strony: 1292-1303), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbapap.2016.06.015 - link to the publication
  14. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases
    Authors:
    Kuchta, K., Muszewska, A., Knizewski, L., Steczkiewicz, K., Wyrwicz, L.S., Pawlowski, K., Rychlewski, L., Ginalski, K.
    Academic press:
    Nucleic Acids Research (rok: 2016, tom: 44, strony: 3534-3548), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkw222 - link to the publication
  15. Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding
    Authors:
    Kropiwnicka A, Kuchta K, Lukaszewicz M, Kowalska J, Jemielity J, Ginalski K, Darzynkiewicz E, Zuberek J
    Academic press:
    Biochemical and Biophysical Research Communications (rok: 2015, tom: 456, strony: 47-52), Wydawca: Academic Press, Elsevier Science
    Status:
    Published
    DOI:
    10.1016/j.bbrc.2014.11.032 - link to the publication
  16. Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes
    Authors:
    Aymard, F., Aguirrebengoa, M., Guillou, E., Javierre, B.M., Bugler, B., Arnould, C., Rocher, V., Iacovoni, J.S., Biernacka, A., Skrzypczak, M., Ginalski, K., Rowicka, M., Fraser, P., Legube, G.
    Academic press:
    Nature Structural & Molecular Biology (rok: 2017, tom: 24, strony: 353-361), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/nsmb.3387 - link to the publication
  17. Hypermethylation of TRIM59 and KLF14 influences cell death signaling in familial Alzheimer's disease
    Authors:
    Wezyk, M., Spolnicka, M., Pospiech, E., Peplonska, B., Zbiec-Piekarska, R., Ilkowski, J., Styczynska, M., Barczak, A., Zboch, M., Filipek-Gliszczynska, A., Skrzypczak, M., Ginalski, K., Kabza, M., Makalowska, I., Barcikowska-Kotowicz, M., Branicki, W., Zekanowski, C.
    Academic press:
    Oxidative Medicine and Cellular Longevity (rok: 2018, tom: 2018, strony: 6918797), Wydawca: Hindawi
    Status:
    Published
    DOI:
    10.1155/2018/6918797 - link to the publication
  18. Histone H1 variants in Arabidopsis are subject to numerous post-translational modifications, both conserved and previously unknown in histones, suggesting complex functions of H1 in plants
    Authors:
    Kotlinski M, Rutowicz K, Knizewski L, Palusinski A, Oledzki J, Fogtman A, Rubel T, Koblowska M, Dadlez M, Ginalski K, Jerzmanowski A
    Academic press:
    PLoS One (rok: 2016, tom: 11, strony: e0147908), Wydawca: Public Library Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0147908 - link to the publication
  19. Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels
    Authors:
    Szczesny RJ, Hejnowicz MS, Steczkiewicz K, Muszewska A, Borowski LS, Ginalski K, Dziembowski A
    Academic press:
    Nucleic Acids Research (rok: 2013, tom: 41, strony: 3144-3161), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkt029 - link to the publication
  20. Overactive BRCA1 affects presenilin 1 in induced pluripotent stem cell-derived neurons in Alzheimer's disease
    Authors:
    Wezyk, M., Szybinska, A., Wojsiat, J., Szczerba, M., Day, K., Ronnholm, H., Kele, M., Berdynski, M., Peplonska, B., Fichna, J.P., Ilkowski, J., Styczynska, M., Barczak, A., Zboch, M., Filipek-Gliszczynska, A., Bojakowski, K., Skrzypczak, M., Ginalski, K., Kabza, M., Makalowska, I., Barcikowska-Kotowicz, M., Wojda, U., Falk, A., Zekanowski, C.
    Academic press:
    Journal of Alzheimer's Disease (rok: 2018, tom: 62, strony: 175-202), Wydawca: IOS Press
    Status:
    Published
    DOI:
    10.3233/JAD-170830 - link to the publication
  21. Predicting proteome dynamics using gene expression data
    Authors:
    Kuchta, K., Towpik, J., Biernacka, A., Kutner, J., Kudlicki, A., Ginalski, K., Rowicka, M.
    Academic press:
    Scientific Reports , Wydawca: Nature Publishing Group
    Status:
    Submitted
    DOI:
    brak - link to the publication
  22. A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis
    Authors:
    Rutowicz K, Puzio M, Halibart-Puzio J, Lirski M, Kotlinski M, Kroten MA, Knizewski L, Lange B, Muszewska A, Sniegowska-Swierk K, Koscielniak J, Iwanicka-Nowicka R, Buza K, Janowiak F, Zmuda K, Joesaar I, Laskowska-Kaszub K, Fogtman A, Kollist H, Zielenkiewicz P, Tiuryn J, Siedlecki P, Swiezewski S, Ginalski K, Koblowska M, Archacki R, Wilczynski B, Rapacz M, Jerzmanowski A
    Academic press:
    Plant Physiology (rok: 2015, tom: 169, strony: 2080-2101), Wydawca: American Society of Plant Biologists
    Status:
    Published
    DOI:
    10.1104/pp.15.00493 - link to the publication
  23. Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy
    Authors:
    Mikula, M., Skrzypczak, M., Goryca, K., Paczkowska, K., Ledwon, J.K., Statkiewicz, M., Kulecka, M., Grzelak, M., Dabrowska, M., Kuklinska, U., Karczmarski, J., Rumienczyk, I., Jastrzebski, K., Miaczynska, M., Ginalski, K., Bomsztyk, K., Ostrowski, J.
    Academic press:
    Nucleic Acids Research (rok: 2016, tom: 44, strony: 10150-10164), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkw763 - link to the publication
  24. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using Illumina platform
    Authors:
    Mitra A, Skrzypczak M, Ginalski K, Rowicka M
    Academic press:
    Plos One (rok: 2015, tom: 10, strony: e0120520), Wydawca: Public Library Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0120520 - link to the publication
  25. Comprehensive histone modification mapping at DNA Double Strand break deciphers repair pathways histone codes
    Authors:
    Clouaire, T., Rocher, V., Aguirrebengoa, M., Biernacka, A., Skrzypczak, M., Aymard, F., Fongfang, B., Dojer, N., Iacovoni, J.S., Rowicka, M., Ginalski, K., Legube, G.
    Academic press:
    Molecular Cell , Wydawca: Cell Press
    Status:
    Submitted
    DOI:
    brak - link to the publication
  26. i-BLESS: ultra-sensitive method for detection of DNA double-strand breaks
    Authors:
    Biernacka, A., Zhu, Y., Skrzypczak, M., Forey, R., Pardo, B., Grzelak, M., Nde, J., Mitra, A., Kudlicki, A., Crosetto, N., Pasero, P., Rowicka, M., Ginalski, K.
    Academic press:
    Communications Biology , Wydawca: Nature Publishing Group
    Status:
    Submitted
    DOI:
    brak - link to the publication

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