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Article ; Online: Shaping chromatin with DICER.

Chitale, Shalaka / Richly, Holger

2017 Volume 8, Issue 25, Page(s) 39937–39938

Language	English
Publishing date	2017-07-05
Publishing country	United States
Document type	Editorial
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.17773
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online ; Thesis: Nucleotide excision repair: interplay between nuclear compartmentalization, histone modifications and signaling

Chitale, Shalaka [Verfasser]

2017

Author's details	Shalaka Chitale
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: H4K20me2: Orchestrating the recruitment of DNA repair factors in nucleotide excision repair.

Chitale, Shalaka / Richly, Holger

Nucleus (Austin, Tex.)

2018 Volume 9, Issue 1, Page(s) 212–215

Abstract: The integrity of the genome is maintained by specific DNA repair pathways. The main pathway removing DNA lesions induced by exposure to UV light is nucleotide excision repair (NER). The DNA damage response at chromatin is accompanied by the recruitment ... ...

Abstract	The integrity of the genome is maintained by specific DNA repair pathways. The main pathway removing DNA lesions induced by exposure to UV light is nucleotide excision repair (NER). The DNA damage response at chromatin is accompanied by the recruitment of DNA repair factors to the lesion site and the deposition of specific histone marks. The function of these histone marks in NER stays for the most part elusive. We have recently reported that the methyltransferase MMSET catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2) at the lesion site. The deposition of H4K20me2 at DNA damage sites elicits the recruitment of the NER factor XPA providing evidence for an H4K20me2-dependent DNA repair factor recruitment mechanism during lesion recognition in the global-genomic branch of NER. Here we discuss how H4K20me2 might impact on the chromatin conformation and the DNA damage response.
MeSH term(s)	DNA/metabolism ; DNA Damage ; DNA Repair ; Histones/metabolism ; Humans ; Lysine/metabolism ; Methyltransferases/metabolism ; Nucleotides/metabolism
Chemical Substances	Histones ; Nucleotides ; DNA (9007-49-2) ; Methyltransferases (EC 2.1.1.-) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2018-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2018.1444327
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: H4K20me2: Orchestrating the recruitment of DNA repair factors in nucleotide excision repair

Chitale, Shalaka / Richly, Holger

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

2018

Abstract	The integrity of the genome is maintained by specific DNA repair pathways. The main pathway removing DNA lesions induced by exposure to UV light is nucleotide excision repair (NER). The DNA damage response at chromatin is accompanied by the recruitment of DNA repair factors to the lesion site and the deposition of specific histone marks. The function of these histone marks in NER stays for the most part elusive. We have recently reported that the methyltransferase MMSET catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2) at the lesion site. The deposition of H4K20me2 at DNA damage sites elicits the recruitment of the NER factor XPA providing evidence for an H4K20me2-dependent DNA repair factor recruitment mechanism during lesion recognition in the global-genomic branch of NER. Here we discuss how H4K20me2 might impact on the chromatin conformation and the DNA damage response.
Keywords	DNA ; DNA damage ; DNA repair ; chromatin ; genome ; histones ; lysine ; methyltransferases ; ultraviolet radiation
Language	English
Dates of publication	2018-1231
Size	p. 212-215.
Publishing place	Taylor & Francis
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2018.1444327
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Article ; Online: Nuclear organization of nucleotide excision repair is mediated by RING1B dependent H2A-ubiquitylation.

Chitale, Shalaka / Richly, Holger

Oncotarget

2017 Volume 8, Issue 19, Page(s) 30870–30887

Abstract: One of the major cellular DNA repair pathways is nucleotide excision repair (NER). It is the primary pathway for repair of various DNA lesions caused by exposure to ultraviolet (UV) light, such as cyclobutane pyrimidine dimers (CPDs) and 6-4 ... ...

Abstract	One of the major cellular DNA repair pathways is nucleotide excision repair (NER). It is the primary pathway for repair of various DNA lesions caused by exposure to ultraviolet (UV) light, such as cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts. Although lesion-containing DNA associates with the nuclear matrix after UV irradiation it is still not understood how nuclear organization affects NER. Analyzing unscheduled DNA synthesis (UDS) indicates that NER preferentially occurs in specific nuclear areas, viz the nucleolus. Upon inducing localized damage, we observe migration of damaged DNA towards the nucleolus. Employing a LacR-based tethering system we demonstrate that H2A-ubiquitylation via the UV-RING1B complex localizes chromatin close to the nucleolus. We further show that the H2A-ubiquitin binding protein ZRF1 resides in the nucleolus, and that it anchors ubiquitylated chromatin along with XPC. Our data thus provide insight into the sub-nuclear organization of NER and reveal a novel role for histone H2A-ubiquitylation.
Language	English
Publishing date	2017-05-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.16142
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DICER- and MMSET-catalyzed H4K20me2 recruits the nucleotide excision repair factor XPA to DNA damage sites.

Chitale, Shalaka / Richly, Holger

The Journal of cell biology

2017 Volume 217, Issue 2, Page(s) 527–540

Abstract: Ultraviolet (UV) irradiation triggers the recruitment of DNA repair factors to the lesion sites and the deposition of histone marks as part of the DNA damage response. The major DNA repair pathway removing DNA lesions caused by exposure to UV light is ... ...

Abstract	Ultraviolet (UV) irradiation triggers the recruitment of DNA repair factors to the lesion sites and the deposition of histone marks as part of the DNA damage response. The major DNA repair pathway removing DNA lesions caused by exposure to UV light is nucleotide excision repair (NER). We have previously demonstrated that the endoribonuclease DICER facilitates chromatin decondensation during lesion recognition in the global-genomic branch of NER. Here, we report that DICER mediates the recruitment of the methyltransferase MMSET to the DNA damage site. We show that MMSET is required for efficient NER and that it catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2). H4K20me2 at DNA damage sites facilitates the recruitment of the NER factor XPA. Our work thus provides evidence for an H4K20me2-dependent mechanism of XPA recruitment during lesion recognition in the global-genomic branch of NER.
MeSH term(s)	Biocatalysis ; Cell Line, Tumor ; DEAD-box RNA Helicases/metabolism ; DNA Damage ; DNA Repair ; HEK293 Cells ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/metabolism ; Humans ; Lysine/metabolism ; Repressor Proteins/metabolism ; Ribonuclease III/metabolism ; Ultraviolet Rays ; Xeroderma Pigmentosum Group A Protein/metabolism
Chemical Substances	Histones ; Repressor Proteins ; XPA protein, human ; Xeroderma Pigmentosum Group A Protein ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; NSD2 protein, human (EC 2.1.1.43) ; DICER1 protein, human (EC 3.1.26.3) ; Ribonuclease III (EC 3.1.26.3) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2017-12-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201704028
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Ub I Zs.190: Show issues

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Article ; Online: DICER and ZRF1 contribute to chromatin decondensation during nucleotide excision repair.

Chitale, Shalaka / Richly, Holger

Nucleic acids research

2017 Volume 45, Issue 10, Page(s) 5901–5912

Abstract: Repair of damaged DNA relies on the recruitment of DNA repair factors in a well orchestrated manner. As a prerequisite, the chromatin needs to be decondensed by chromatin remodelers to allow for binding of repair factors and for DNA repair to occur. ... ...

Abstract	Repair of damaged DNA relies on the recruitment of DNA repair factors in a well orchestrated manner. As a prerequisite, the chromatin needs to be decondensed by chromatin remodelers to allow for binding of repair factors and for DNA repair to occur. Recent studies have implicated members of the SWI/SNF and INO80 families as well as PARP1 in nucleotide excision repair (NER). In this study, we report that the endonuclease DICER is implicated in chromatin decondensation during NER. In response to UV irradiation, DICER is recruited to chromatin in a ZRF1-mediated manner. The H2A-ubiquitin binding protein ZRF1 and DICER together impact on the chromatin conformation via PARP1. Moreover, DICER-mediated chromatin decondensation is independent of its catalytic activity. Taken together, we describe a novel function of DICER at chromatin and its interaction with the ubiquitin signalling cascade during GG-NER.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/growth & development ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans/radiation effects ; Cell Line ; Cell Line, Tumor ; Chromatin/chemistry ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; DNA Damage ; DNA Repair ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Fibroblasts/radiation effects ; HEK293 Cells ; Histones/genetics ; Histones/metabolism ; Humans ; Oncogene Proteins/genetics ; Oncogene Proteins/metabolism ; Osteoblasts/cytology ; Osteoblasts/metabolism ; Osteoblasts/radiation effects ; Poly (ADP-Ribose) Polymerase-1/genetics ; Poly (ADP-Ribose) Polymerase-1/metabolism ; Ribonuclease III/genetics ; Ribonuclease III/metabolism ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ultraviolet Rays
Chemical Substances	Chromatin ; DNA-Binding Proteins ; DNAJC2 protein, human ; Histones ; Oncogene Proteins ; Ubiquitin ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; DICER1 protein, human (EC 3.1.26.3) ; Ribonuclease III (EC 3.1.26.3) ; DEAD-box RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2017-06-02
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx261
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Zs.A 1067: Show issues

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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Timing of DNA lesion recognition: Ubiquitin signaling in the NER pathway.

Chitale, Shalaka / Richly, Holger

Cell cycle (Georgetown, Tex.)

2016 Volume 16, Issue 2, Page(s) 163–171

Abstract: Damaged DNA is repaired by specialized repair factors that are recruited in a well-orchestrated manner to the damage site. The DNA damage response at UV inflicted DNA lesions is accompanied by posttranslational modifications of DNA repair factors and the ...

Abstract	Damaged DNA is repaired by specialized repair factors that are recruited in a well-orchestrated manner to the damage site. The DNA damage response at UV inflicted DNA lesions is accompanied by posttranslational modifications of DNA repair factors and the chromatin environment sourrounding the lesion. In particular, mono- and poly-ubiquitylation events are an integral part of the DNA damage signaling. Whereas ubiquitin signaling at DNA doublestrand breaks has been subject to intensive studies comparatively little is known about the intricacies of ubiquitylation events occurring during nucleotide excision repair (NER), the major pathway to remove bulky helix lesions. Both, the global genomic (GG-NER) and the transcription-coupled (TC-NER) branches of NER are subject to ubiquitylation and deubiquitylation processes.Here we summarize our current knowledge of the ubiquitylation network that drives DNA repair in the NER pathway and we discuss the crosstalk of ubiquitin signaling with other prominent post-translational modfications that might be essential to time the DNA damage recognition step.
MeSH term(s)	Animals ; DNA Damage ; DNA Repair ; Humans ; Signal Transduction ; Time Factors ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Ubiquitin
Language	English
Publishing date	2016-12-08
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.1080/15384101.2016.1261227
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Zs.A 5881: Show issues

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Jg. 1995 - 2021: Lesesall (2.OG)
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Article ; Online: A semiconductor 96-microplate platform for electrical-imaging based high-throughput phenotypic screening.

Nature communications

2023 Volume 14, Issue 1, Page(s) 7576

Abstract: High-content imaging for compound and genetic profiling is popular for drug discovery but limited to endpoint images of fixed cells. Conversely, electronic-based devices offer label-free, live cell functional information but suffer from limited spatial ... ...

Abstract	High-content imaging for compound and genetic profiling is popular for drug discovery but limited to endpoint images of fixed cells. Conversely, electronic-based devices offer label-free, live cell functional information but suffer from limited spatial resolution or throughput. Here, we introduce a semiconductor 96-microplate platform for high-resolution, real-time impedance imaging. Each well features 4096 electrodes at 25 µm spatial resolution and a miniaturized data interface allows 8× parallel plate operation (768 total wells) for increased throughput. Electric field impedance measurements capture >20 parameter images including cell barrier, attachment, flatness, and motility every 15 min during experiments. We apply this technology to characterize 16 cell types, from primary epithelial to suspension cells, and quantify heterogeneity in mixed co-cultures. Screening 904 compounds across 13 semiconductor microplates reveals 25 distinct responses, demonstrating the platform's potential for mechanism of action profiling. The scalability and translatability of this semiconductor platform expands high-throughput mechanism of action profiling and phenotypic drug discovery applications.
MeSH term(s)	High-Throughput Screening Assays/methods ; Drug Discovery ; Diagnostic Imaging ; Electric Impedance ; Electrodes
Language	English
Publishing date	2023-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43333-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A semiconductor 96-microplate platform for electrical-imaging based high-throughput phenotypic screening.

bioRxiv : the preprint server for biology

2023

Abstract: Profiling compounds and genetic perturbations via high-content imaging has become increasingly popular for drug discovery, but the technique is limited to endpoint images of fixed cells. In contrast, electronic-based devices offer label-free, functional ... ...

Abstract	Profiling compounds and genetic perturbations via high-content imaging has become increasingly popular for drug discovery, but the technique is limited to endpoint images of fixed cells. In contrast, electronic-based devices offer label-free, functional information of live cells, yet current approaches suffer from low-spatial resolution or single-well throughput. Here, we report a semiconductor 96-microplate platform designed for high-resolution real-time impedance "imaging" at scale. Each well features 4,096 electrodes at 25 µm spatial resolution while a miniaturized data interface allows 8× parallel plate operation (768 total wells) within each incubator for enhanced throughputs. New electric field-based, multi-frequency measurement techniques capture >20 parameter images including tissue barrier, cell-surface attachment, cell flatness, and motility every 15 min throughout experiments. Using these real-time readouts, we characterized 16 cell types, ranging from primary epithelial to suspension, and quantified heterogeneity in mixed epithelial and mesenchymal co-cultures. A proof-of-concept screen of 904 diverse compounds using 13 semiconductor microplates demonstrates the platform's capability for mechanism of action (MOA) profiling with 25 distinct responses identified. The scalability of the semiconductor platform combined with the translatability of the high dimensional live-cell functional parameters expands high-throughput MOA profiling and phenotypic drug discovery applications.
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.01.543281
Database	MEDical Literature Analysis and Retrieval System OnLINE

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