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Article ; Online: PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency.

Dobrinić, Paula / Szczurek, Aleksander T / Klose, Robert J

2021 Volume 28, Issue 10, Page(s) 811–824

Abstract: The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback ... ...

Abstract	The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The inter-relatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics, we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.
MeSH term(s)	Animals ; Cell Line ; Chromatin Immunoprecipitation Sequencing ; Gene Expression Regulation ; Histones/genetics ; Histones/metabolism ; Lysine/genetics ; Male ; Mice ; Mouse Embryonic Stem Cells/physiology ; Polycomb Repressive Complex 1/genetics ; Polycomb Repressive Complex 1/metabolism ; Polycomb Repressive Complex 2/genetics ; Polycomb Repressive Complex 2/metabolism ; RNA Polymerase II/metabolism ; Single-Cell Analysis ; Transcription Initiation, Genetic
Chemical Substances	Histones ; Polycomb Repressive Complex 2 (EC 2.1.1.43) ; Polycomb Repressive Complex 1 (EC 2.3.2.27) ; RNA Polymerase II (EC 2.7.7.-) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2021-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-021-00661-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 4101: 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)
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Book ; Online ; Thesis: Single molecule localisation microscopy by photoconversion and dynamic labelling using DNA-binding dyes resolves chromatin compaction in model ischemia

Szczurek, Aleksander [Verfasser]

2017

Author's details	Aleksander Szczurek
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek Mainz
Publishing place	Mainz
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Sister chromatid cohesion is mediated by individual cohesin complexes.

Ochs, Fena / Green, Charlotte / Szczurek, Aleksander Tomasz / Pytowski, Lior / Kolesnikova, Sofia / Brown, Jill / Gerlich, Daniel Wolfram / Buckle, Veronica / Schermelleh, Lothar / Nasmyth, Kim Ashley

Science (New York, N.Y.)

2024 Volume 383, Issue 6687, Page(s) 1122–1130

Abstract: Eukaryotic genomes are organized by loop extrusion and sister chromatid cohesion, both mediated by the multimeric cohesin protein complex. Understanding how cohesin holds sister DNAs together, and how loss of cohesion causes age-related infertility in ... ...

Abstract	Eukaryotic genomes are organized by loop extrusion and sister chromatid cohesion, both mediated by the multimeric cohesin protein complex. Understanding how cohesin holds sister DNAs together, and how loss of cohesion causes age-related infertility in females, requires knowledge as to cohesin's stoichiometry in vivo. Using quantitative super-resolution imaging, we identified two discrete populations of chromatin-bound cohesin in postreplicative human cells. Whereas most complexes appear dimeric, cohesin that localized to sites of sister chromatid cohesion and associated with sororin was exclusively monomeric. The monomeric stoichiometry of sororin:cohesin complexes demonstrates that sister chromatid cohesion is conferred by individual cohesin rings, a key prediction of the proposal that cohesion arises from the co-entrapment of sister DNAs.
MeSH term(s)	Humans ; Cell Cycle Proteins/metabolism ; Chromatids/metabolism ; Chromatin/metabolism ; Cohesins/metabolism ; DNA/genetics ; DNA/metabolism ; Sister Chromatid Exchange ; Cell Line, Tumor
Chemical Substances	Cell Cycle Proteins ; Chromatin ; Cohesins ; DNA (9007-49-2) ; CDCA5 protein, human
Language	English
Publishing date	2024-03-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adl4606
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: A CpG island-encoded mechanism protects genes from premature transcription termination.

Hughes, Amy L / Szczurek, Aleksander T / Kelley, Jessica R / Lastuvkova, Anna / Turberfield, Anne H / Dimitrova, Emilia / Blackledge, Neil P / Klose, Robert J

Nature communications

2023 Volume 14, Issue 1, Page(s) 726

Abstract: Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains ... ...

Abstract	Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
MeSH term(s)	CpG Islands/genetics ; Transcription, Genetic ; Histones/metabolism ; Chromatin/genetics ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; DNA Methylation/genetics
Chemical Substances	Histones ; Chromatin ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36236-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A CpG island-encoded mechanism protects genes from premature transcription termination

Amy L. Hughes / Aleksander T. Szczurek / Jessica R. Kelley / Anna Lastuvkova / Anne H. Turberfield / Emilia Dimitrova / Neil P. Blackledge / Robert J. Klose

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 19

Abstract: Here the authors discover that SET1 complexes function as transcription anti-termination factors that bind to CpG islands and protect low to moderately transcribed genes from the pervasive termination activity of the ZC3H4 complex. ...

Abstract	Here the authors discover that SET1 complexes function as transcription anti-termination factors that bind to CpG islands and protect low to moderately transcribed genes from the pervasive termination activity of the ZC3H4 complex.
Keywords	Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Aqueous mounting media increasing tissue translucence improve image quality in Structured Illumination Microscopy of thick biological specimen.

Szczurek, Aleksander / Contu, Fabio / Hoang, Agnieszka / Dobrucki, Jurek / Mai, Sabine

Scientific reports

2018 Volume 8, Issue 1, Page(s) 13971

Abstract: Structured Illumination Microscopy (SIM) is a super-resolution microscopy method that has significantly advanced studies of cellular structures. It relies on projection of illumination patterns onto a fluorescently labelled biological sample. The ... ...

Abstract	Structured Illumination Microscopy (SIM) is a super-resolution microscopy method that has significantly advanced studies of cellular structures. It relies on projection of illumination patterns onto a fluorescently labelled biological sample. The information derived from the sample is then shifted to a detectable band, and in the process of image calculation in Fourier space the resolution is doubled. Refractive index homogeneity along the optical path is crucial to maintain a highly modulated illumination pattern necessary for high-quality SIM. This applies in particular to thick samples consisting of large cells and tissues. Surprisingly, sample mounting media for SIM have not undergone a significant evolution for almost a decade. Through identification and systematic evaluation of a number of non-hazardous, water-soluble chemical components of mounting media, we demonstrate an unprecedented improvement in SIM-image quality. Mounting solutions presented in this research are capable of reducing abundant light scattering which constitutes the limiting factor in 3D-SIM imaging of large Hodgkin's lymphoma and embryonic stem cells as well as 10 µm tissue sections. Moreover, we demonstrate usefulness of some of the media in single molecule localisation microscopy. The results presented here are of importance for standardisation of 3D-SIM data acquisition pipelines for an expanding community of users.
MeSH term(s)	Animals ; Hodgkin Disease/pathology ; Humans ; Image Processing, Computer-Assisted/methods ; Imaging, Three-Dimensional/methods ; Lighting/instrumentation ; Lymphocytes/ultrastructure ; Mice ; Microscopy, Fluorescence/instrumentation ; Microscopy, Fluorescence/methods ; Quality Improvement ; Spleen/ultrastructure ; Tumor Cells, Cultured
Language	English
Publishing date	2018-09-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-32191-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Super-resolution binding activated localization microscopy through reversible change of DNA conformation

Szczurek, Aleksander / Birk, Udo / Knecht, Hans / Dobrucki, Jurek / Mai, Sabine / Cremer, Christoph

Nucleus. 2018 Dec. 31, v. 9, no. 1

2018

Abstract: Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type ...

Abstract	Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.
Keywords	DNA ; DNA conformation ; chromatin ; fluorescence ; light microscopy ; medicine
Language	English
Dates of publication	2018-1231
Size	p. 182-189.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2017.1419846
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Aqueous mounting media increasing tissue translucence improve image quality in Structured Illumination Microscopy of thick biological specimen

Aleksander Szczurek / Fabio Contu / Agnieszka Hoang / Jurek Dobrucki / Sabine Mai

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 12

Abstract: Abstract Structured Illumination Microscopy (SIM) is a super-resolution microscopy method that has significantly advanced studies of cellular structures. It relies on projection of illumination patterns onto a fluorescently labelled biological sample. ... ...

Abstract	Abstract Structured Illumination Microscopy (SIM) is a super-resolution microscopy method that has significantly advanced studies of cellular structures. It relies on projection of illumination patterns onto a fluorescently labelled biological sample. The information derived from the sample is then shifted to a detectable band, and in the process of image calculation in Fourier space the resolution is doubled. Refractive index homogeneity along the optical path is crucial to maintain a highly modulated illumination pattern necessary for high-quality SIM. This applies in particular to thick samples consisting of large cells and tissues. Surprisingly, sample mounting media for SIM have not undergone a significant evolution for almost a decade. Through identification and systematic evaluation of a number of non-hazardous, water-soluble chemical components of mounting media, we demonstrate an unprecedented improvement in SIM-image quality. Mounting solutions presented in this research are capable of reducing abundant light scattering which constitutes the limiting factor in 3D-SIM imaging of large Hodgkin’s lymphoma and embryonic stem cells as well as 10 µm tissue sections. Moreover, we demonstrate usefulness of some of the media in single molecule localisation microscopy. The results presented here are of importance for standardisation of 3D-SIM data acquisition pipelines for an expanding community of users.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-09-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Super-resolution microscopy approaches to nuclear nanostructure imaging.

Cremer, Christoph / Szczurek, Aleksander / Schock, Florian / Gourram, Amine / Birk, Udo

Methods (San Diego, Calif.)

2017 Volume 123, Page(s) 11–32

Abstract: The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has ... ...

Abstract	The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
Language	English
Publishing date	2017-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2017.03.019
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Article ; Online: Super-resolution binding activated localization microscopy through reversible change of DNA conformation.

Szczurek, Aleksander / Birk, Udo / Knecht, Hans / Dobrucki, Jurek / Mai, Sabine / Cremer, Christoph

Nucleus (Austin, Tex.)

2018 Volume 9, Issue 1, Page(s) 182–189

Abstract	Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.
MeSH term(s)	Binding Sites ; Cell Nucleus/chemistry ; Cell Nucleus/metabolism ; DNA/chemistry ; DNA/metabolism ; Nucleic Acid Conformation ; Single Molecule Imaging
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2018-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2017.1419846
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