Chernev, Aleksandar

[["dc.bibliographiccitation.firstpage","1082"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Cell"],["dc.bibliographiccitation.lastpage","1093"],["dc.bibliographiccitation.volume","171"],["dc.contributor.author","Hillen, Hauke S."],["dc.contributor.author","Parshin, Andrey V."],["dc.contributor.author","Agaronyan, Karen"],["dc.contributor.author","Morozov, Yaroslav I."],["dc.contributor.author","Graber, James J."],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Schwinghammer, Kathrin"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Anikin, Michael"],["dc.contributor.author","Cramer, Patrick"],["dc.contributor.author","Temiakov, Dmitry"],["dc.date.accessioned","2018-01-09T12:26:24Z"],["dc.date.available","2018-01-09T12:26:24Z"],["dc.date.issued","2017"],["dc.description.abstract","In human mitochondria, transcription termination events at a G-quadruplex region near the replication origin are thought to drive replication of mtDNA by generation of an RNA primer. This process is suppressed by a key regulator of mtDNA-the transcription factor TEFM. We determined the structure of an anti-termination complex in which TEFM is bound to transcribing mtRNAP. The structure reveals interactions of the dimeric pseudonuclease core of TEFM with mobile structural elements in mtRNAP and the nucleic acid components of the elongation complex (EC). Binding of TEFM to the DNA forms a downstream \"sliding clamp,\" providing high processivity to the EC. TEFM also binds near the RNA exit channel to prevent formation of the RNA G-quadruplex structure required for termination and thus synthesis of the replication primer. Our data provide insights into target specificity of TEFM and mechanisms by which it regulates the switch between transcription and replication of mtDNA."],["dc.identifier.doi","10.1016/j.cell.2017.09.035"],["dc.identifier.pmid","29033127"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11586"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1097-4172"],["dc.title","Mechanism of Transcription Anti-termination in Human Mitochondria"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Nature"],["dc.contributor.author","Kokic, Goran"],["dc.contributor.author","Wagner, Felix R."],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2021-10-01T09:57:44Z"],["dc.date.available","2021-10-01T09:57:44Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract Transcription-coupled DNA repair removes bulky DNA lesions from the genome 1,2 and protects cells against ultraviolet (UV) irradiation 3 . Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4 CSA and UV-stimulated scaffold protein A (UVSSA) 3 . Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published 3,4 data, the structures provide a model for transcription–repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, EC TCR , uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4 CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4 CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA."],["dc.identifier.doi","10.1038/s41586-021-03906-4"],["dc.identifier.pii","3906"],["dc.identifier.pmid","34526721"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/89904"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/340"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-469"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1476-4687"],["dc.relation.issn","0028-0836"],["dc.relation.workinggroup","RG Cramer"],["dc.rights","CC BY 4.0"],["dc.title","Structural basis of human transcription–DNA repair coupling"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3441"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Journal of Proteome Research"],["dc.bibliographiccitation.lastpage","3448"],["dc.bibliographiccitation.volume","15"],["dc.contributor.author","Veit, Johannes"],["dc.contributor.author","Sachsenberg, Timo"],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Aicheler, Fabian"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Kohlbacher, Oliver"],["dc.date.accessioned","2018-11-07T10:09:48Z"],["dc.date.available","2018-11-07T10:09:48Z"],["dc.date.issued","2016"],["dc.description.abstract","Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNxl for UV-induced peptide RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark (Ramus, C.; et al. J. Proteomics 2016, 132, 51-62). The second workflow, RNPxl, represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results."],["dc.identifier.doi","10.1021/acs.jproteome.6b00407"],["dc.identifier.isi","000382713300044"],["dc.identifier.pmid","27476824"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/39721"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Chemical Soc"],["dc.relation.issn","1535-3907"],["dc.relation.issn","1535-3893"],["dc.title","LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","11310"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Hiragami-Hamada, Kyoko"],["dc.contributor.author","Soeroes, Szabolcs"],["dc.contributor.author","Nikolov, Miroslav"],["dc.contributor.author","Wilkins, Bryan J."],["dc.contributor.author","Kreuz, Sarah"],["dc.contributor.author","Chen, Carol"],["dc.contributor.author","De La Rosa-Velazquez, Inti A."],["dc.contributor.author","Zenn, Hans Michael"],["dc.contributor.author","Kost, Nils"],["dc.contributor.author","Pohl, Wiebke"],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Schwarzer, Dirk"],["dc.contributor.author","Jenuwein, Thomas"],["dc.contributor.author","Lorincz, Matthew"],["dc.contributor.author","Zimmermann, Bastian"],["dc.contributor.author","Walla, Peter Jomo"],["dc.contributor.author","Neumann, Heinz"],["dc.contributor.author","Baubec, Tuncay"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Fischle, Wolfgang"],["dc.date.accessioned","2018-11-07T10:16:11Z"],["dc.date.available","2018-11-07T10:16:11Z"],["dc.date.issued","2016"],["dc.description.abstract","Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins of the heterochromatin protein 1 (HP1) family are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin condensation have been speculative and controversial. Here we demonstrate that human HP1 beta is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. HP1 beta bridges condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1 beta genome-wide localization follows H3K9me3-enrichment and artificial bridging of chromatin fibres is sufficient for maintaining cellular heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which might contribute to the plastic nature of condensed chromatin."],["dc.identifier.doi","10.1038/ncomms11310"],["dc.identifier.isi","000374291900001"],["dc.identifier.pmid","27090491"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13282"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/40987"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","2041-1723"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Dynamic and flexible H3K9me3 bridging via HP1 beta dimerization establishes a plastic state of condensed chromatin"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Stützer, Alexandra"],["dc.contributor.author","Welp, Luisa M."],["dc.contributor.author","Raabe, Monika"],["dc.contributor.author","Sachsenberg, Timo"],["dc.contributor.author","Kappert, Christin"],["dc.contributor.author","Wulf, Alexander"],["dc.contributor.author","Lau, Andy M."],["dc.contributor.author","David, Stefan-Sebastian"],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Politis, Argyris"],["dc.contributor.author","Kohlbacher, Oliver"],["dc.contributor.author","Fischle, Wolfgang"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2021-04-14T08:31:49Z"],["dc.date.available","2021-04-14T08:31:49Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1038/s41467-020-19047-7"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83722"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","2041-1723"],["dc.title","Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","10313"],["dc.bibliographiccitation.issue","19"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","10326"],["dc.bibliographiccitation.volume","47"],["dc.contributor.author","Ayoubi, Leyla El"],["dc.contributor.author","Dumay-Odelot, Hélène"],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Boissier, Fanny"],["dc.contributor.author","Minvielle-Sébastia, Lionel"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Fribourg, Sébastien"],["dc.contributor.author","Teichmann, Martin"],["dc.date.accessioned","2019-12-11T14:59:57Z"],["dc.date.accessioned","2021-10-27T13:21:52Z"],["dc.date.available","2019-12-11T14:59:57Z"],["dc.date.available","2021-10-27T13:21:52Z"],["dc.date.issued","2019"],["dc.description.abstract","In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3'-5' DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα."],["dc.identifier.doi","10.1093/nar/gkz788"],["dc.identifier.isbn","31529052"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16928"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/92050"],["dc.language.iso","en"],["dc.notes.intern","Migrated from goescholar"],["dc.relation.eissn","1362-4962"],["dc.relation.issn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.relation.orgunit","Universitätsmedizin Göttingen"],["dc.rights","CC BY-NC 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/4.0"],["dc.subject.ddc","610"],["dc.title","The hRPC62 subunit of human RNA polymerase III displays helicase activity"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","2885"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Kokic, Goran"],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Tegunov, Dimitry"],["dc.contributor.author","Dienemann, C."],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2019-07-22T12:01:28Z"],["dc.date.available","2019-07-22T12:01:28Z"],["dc.date.issued","2019"],["dc.description.abstract","Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway."],["dc.identifier.doi","10.1038/s41467-019-10745-5"],["dc.identifier.pmid","31253769"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16290"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61789"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","2041-1723"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Structural basis of TFIIH activation for nucleotide excision repair"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]