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Article: The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways.

Chen, Zulong / Tyler, Jessica K

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 909696

Abstract: DNA double-strand breaks (DSBs), the most deleterious DNA lesions, are primarily repaired by two pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ), the choice of which is largely dependent on cell cycle phase and the ... ...

Abstract	DNA double-strand breaks (DSBs), the most deleterious DNA lesions, are primarily repaired by two pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ), the choice of which is largely dependent on cell cycle phase and the local chromatin landscape. Recent studies have revealed that post-translational modifications on histones play pivotal roles in regulating DSB repair pathways including repair pathway choice. In this review, we present our current understanding of how these DSB repair pathways are employed in various chromatin landscapes to safeguard genomic integrity. We place an emphasis on the impact of different histone post-translational modifications, characteristic of euchromatin or heterochromatin regions, on DSB repair pathway choice. We discuss the potential roles of damage-induced chromatin modifications in the maintenance of genome and epigenome integrity. Finally, we discuss how RNA transcripts from the vicinity of DSBs at actively transcribed regions also regulate DSB repair pathway choice.
Language	English
Publishing date	2022-06-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.909696
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Article ; Online: A new era for research into aging.

Kaeberlein, Matt / Tyler, Jessica K

eLife

2021 Volume 10

Abstract: eLife is publishing a special issue on aging, geroscience and longevity to mark the rapid progress made in this field over the past decade, both in terms of mechanistic understanding and translational approaches that are poised to have clinical impact on ...

Abstract	eLife is publishing a special issue on aging, geroscience and longevity to mark the rapid progress made in this field over the past decade, both in terms of mechanistic understanding and translational approaches that are poised to have clinical impact on age-related diseases.
MeSH term(s)	Aging ; Geroscience ; Humans ; Longevity
Language	English
Publishing date	2021-01-28
Publishing country	England
Document type	Editorial ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.65286
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Article ; Online: A Proximity Ligation Method to Detect Proteins Bound to Single-Stranded DNA after DNA End Resection at DNA Double-Strand Breaks.

Fowler, Faith C / Tyler, Jessica K

Methods and protocols

2021 Volume 5, Issue 1

Abstract: After a DNA double-strand break, cells utilize either non-homologous end joining or homologous recombination to repair the broken DNA ends. Homologous recombination requires extensive nucleolytic processing of one of the DNA strands, resulting in long ... ...

Abstract	After a DNA double-strand break, cells utilize either non-homologous end joining or homologous recombination to repair the broken DNA ends. Homologous recombination requires extensive nucleolytic processing of one of the DNA strands, resulting in long stretches of 3' single-strand DNA overhangs. Typically, single-stranded DNA is measured using immunofluorescence microscopy to image the foci of replication protein A, a single-stranded DNA-binding protein. Microscopy analysis of bromodeoxyuridine foci under nondenaturing conditions has also been used to measure single-stranded DNA. Here, we describe a proximity ligation assay which uses genome-wide bromodeoxyuridine incorporation to label single-stranded DNA in order to measure the association of a protein of interest with single-stranded DNA. This method is advantageous over traditional foci analysis because it is more direct and specific than traditional foci co-localization microscopy methods, uses only one color channel, and can reveal protein-single-stranded DNA interactions that are rare and potentially undetectable using traditional microscopy methods. We show here the association of replication protein A and bromodeoxyuridine as proof-of-concept.
Language	English
Publishing date	2021-12-29
Publishing country	Switzerland
Document type	Journal Article
ISSN	2409-9279
ISSN (online)	2409-9279
DOI	10.3390/mps5010003
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Article ; Online: A Flow Cytometry-Based Method for Analyzing DNA End Resection in G

Chen, Bo-Ruei / Tyler, Jessica K / Sleckman, Barry P

Bio-protocol

2022 Volume 12, Issue 10, Page(s) e4413

Abstract: DNA double strand breaks (DSBs) constantly arise in cells during normal cellular processes or upon exposure to genotoxic agents, and are repaired mostly by homologous recombination (HR) and non-homologous end joining (NHEJ). One key determinant of DNA ... ...

Abstract	DNA double strand breaks (DSBs) constantly arise in cells during normal cellular processes or upon exposure to genotoxic agents, and are repaired mostly by homologous recombination (HR) and non-homologous end joining (NHEJ). One key determinant of DNA DSB repair pathway choice is the processing of broken DNA ends to generate single strand DNA (ssDNA) overhangs, a process termed DNA resection. The generation of ssDNA overhangs commits DSB repair through HR and inhibits NHEJ. Therefore, DNA resection must be carefully regulated to avoid mis-repaired or persistent DSBs. Accordingly, many approaches have been developed to monitor ssDNA generation in cells to investigate genes and pathways that regulate DNA resection. Here we describe a flow cytometric approach measuring the levels of replication protein A (RPA) complex, a high affinity ssDNA binding complex composed of three subunits (RPA70, RPA32, and RPA14 in mammals), on chromatin after DNA DSB induction to assay DNA resection. This flow cytometric assay requires only conventional flow cytometers and can easily be scaled up to analyze a large number of samples or even for genetic screens of pooled mutants on a genome-wide scale. We adopt this assay in G
Language	English
Publishing date	2022-05-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.4413
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Article ; Online: A Simple, Improved Method for Scarless Genome Editing of Budding Yeast Using CRISPR-Cas9.

Aguilar, Rhiannon R / Shen, Zih-Jie / Tyler, Jessica K

Methods and protocols

2022 Volume 5, Issue 5

Abstract: Until recently, the favored method for making directed modifications to the budding yeast genome involved the introduction of a DNA template carrying the desired genetic changes along with a selectable marker, flanked by homology arms. This approach both ...

Abstract	Until recently, the favored method for making directed modifications to the budding yeast genome involved the introduction of a DNA template carrying the desired genetic changes along with a selectable marker, flanked by homology arms. This approach both limited the ability to make changes within genes due to disruption by the introduced selectable marker and prevented the use of that selectable marker for subsequent genomic manipulations. Following the discovery of CRISPR-Cas9-mediated genome editing, protocols were developed for modifying any DNA region of interest in a similar single transformation step without the need for a permanent selectable marker. This approach involves the generation of a DNA double-strand break (DSB) at the desired genomic location by the Cas9 nuclease, expressed on a plasmid which also expresses the guide RNA (gRNA) sequence directing the location of the DSB. The DSB is subsequently repaired via homologous recombination using a PCR-derived DNA repair template. Here, we describe in detail an improved method for incorporation of the gRNA-encoding DNA sequences into the Cas9 expression plasmid. Using Golden Gate cloning, annealed oligonucleotides bearing unique single-strand DNA overhangs are ligated into directional restriction enzyme sites. We describe the use of this CRISPR-Cas9 genome editing protocol to introduce multiple types of directed genetic changes into the yeast genome.
Language	English
Publishing date	2022-10-04
Publishing country	Switzerland
Document type	Journal Article
ISSN	2409-9279
ISSN (online)	2409-9279
DOI	10.3390/mps5050079
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Article: Nucleosomes Find Their Place in Life.

Tyler, Jessica K

Trends in genetics : TIG

2016 Volume 32, Issue 11, Page(s) 689–690

Abstract: To carry epigenetic information, the chromatin structure must be accurately rebuilt after its deconstruction during genomic replication. Using an elegant, novel approach, Vasseur et al.[1] reveal that transcription plays a key role in sculpting the ... ...

Abstract	To carry epigenetic information, the chromatin structure must be accurately rebuilt after its deconstruction during genomic replication. Using an elegant, novel approach, Vasseur et al.[1] reveal that transcription plays a key role in sculpting the chromatin after DNA replication.
MeSH term(s)	Chromatin/genetics ; DNA Replication/genetics ; Epigenesis, Genetic/genetics ; Genome/genetics ; Histones/genetics ; Humans ; Nucleosomes/genetics ; Transcription, Genetic
Chemical Substances	Chromatin ; Histones ; Nucleosomes
Language	English
Publishing date	2016-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2016.09.001
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Article ; Online: The role of autophagy in the regulation of yeast life span.

Tyler, Jessica K / Johnson, Jay E

Annals of the New York Academy of Sciences

2018 Volume 1418, Issue 1, Page(s) 31–43

Abstract: The goal of the aging field is to develop novel therapeutic interventions that extend human health span and reduce the burden of age-related disease. While organismal aging is a complex, multifactorial process, a popular theory is that cellular aging is ... ...

Abstract	The goal of the aging field is to develop novel therapeutic interventions that extend human health span and reduce the burden of age-related disease. While organismal aging is a complex, multifactorial process, a popular theory is that cellular aging is a significant contributor to the progressive decline inherent to all multicellular organisms. To explore the molecular determinants that drive cellular aging, as well as how to retard them, researchers have utilized the highly genetically tractable budding yeast Saccharomyces cerevisiae. Indeed, every intervention known to extend both cellular and organismal health span was identified in yeast, underlining the power of this approach. Importantly, a growing body of work has implicated the process of autophagy as playing a critical role in the delay of aging. This review summarizes recent reports that have identified a role for autophagy, or autophagy factors in the extension of yeast life span. These studies demonstrate (1) that yeast remains an invaluable tool for the identification and characterization of conserved mechanisms that promote cellular longevity and are likely to be relevant to humans, and (2) that the process of autophagy has been implicated in nearly all known longevity-promoting manipulations and thus represents an ideal target for interventions aimed at improving human health span.
MeSH term(s)	Autophagy ; Endoplasmic Reticulum/metabolism ; Epigenesis, Genetic ; Golgi Apparatus/metabolism ; Homeostasis ; Hormesis ; Humans ; Lipids/physiology ; Longevity ; Methionine/administration & dosage ; Models, Biological ; Parkinson Disease/pathology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/physiology
Chemical Substances	Lipids ; Methionine (AE28F7PNPL)
Language	English
Publishing date	2018-01-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	211003-9
ISSN	1749-6632 ; 0077-8923
ISSN (online)	1749-6632
ISSN	0077-8923
DOI	10.1111/nyas.13549
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Article ; Online: Selenium supplementation inhibits IGF-1 signaling and confers methionine restriction-like healthspan benefits to mice.

Plummer, Jason D / Postnikoff, Spike Dl / Tyler, Jessica K / Johnson, Jay E

eLife

2021 Volume 10

Abstract: Methionine restriction (MR) dramatically extends the healthspan of several organisms. Methionine-restricted rodents have less age-related pathology and increased longevity as compared with controls, and recent studies suggest that humans might benefit ... ...

Abstract	Methionine restriction (MR) dramatically extends the healthspan of several organisms. Methionine-restricted rodents have less age-related pathology and increased longevity as compared with controls, and recent studies suggest that humans might benefit similarly. Mechanistically, it is likely that the decreased IGF-1 signaling that results from MR underlies the benefits of this regimen. Thus, we hypothesized that interventions that decrease IGF-1 signaling would also produce MR-like healthspan benefits. Selenium supplementation inhibits IGF-1 signaling in rats and has been studied for its putative healthspan benefits. Indeed, we show that feeding mice a diet supplemented with sodium selenite results in an MR-like phenotype, marked by protection against diet-induced obesity, as well as altered plasma levels of IGF-1, FGF-21, adiponectin, and leptin. Selenomethionine supplementation results in a similar, albeit less robust response, and also extends budding yeast lifespan. Our results indicate that selenium supplementation is sufficient to produce MR-like healthspan benefits for yeast and mammals.
MeSH term(s)	Animal Feed/analysis ; Animals ; Diet ; Dietary Supplements/analysis ; Dose-Response Relationship, Drug ; Female ; Insulin-Like Growth Factor I/genetics ; Insulin-Like Growth Factor I/metabolism ; Male ; Methionine/administration & dosage ; Mice/physiology ; Mice, Inbred C57BL ; Random Allocation ; Selenium/administration & dosage ; Selenium/metabolism ; Selenomethionine/administration & dosage ; Selenomethionine/metabolism ; Sodium Selenite/administration & dosage ; Sodium Selenite/metabolism
Chemical Substances	insulin-like growth factor-1, mouse ; Insulin-Like Growth Factor I (67763-96-6) ; Selenomethionine (964MRK2PEL) ; Methionine (AE28F7PNPL) ; Selenium (H6241UJ22B) ; Sodium Selenite (HIW548RQ3W)
Language	English
Publishing date	2021-03-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.62483
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Article: Reprogramming Carbohydrate Metabolism in Cancer and Its Role in Regulating the Tumor Microenvironment.

Adhikari, Swagata / Guha, Deblina / Mohan, Chitra / Mukherjee, Shravanti / Tyler, Jessica K / Das, Chandrima

Sub-cellular biochemistry

2022 Volume 100, Page(s) 3–65

Abstract: Altered metabolism has become an emerging feature of cancer cells impacting their proliferation and metastatic potential in myriad ways. Proliferating heterogeneous tumor cells are surrounded by other resident or infiltrating cells, along with ... ...

Abstract	Altered metabolism has become an emerging feature of cancer cells impacting their proliferation and metastatic potential in myriad ways. Proliferating heterogeneous tumor cells are surrounded by other resident or infiltrating cells, along with extracellular matrix proteins, and other secretory factors constituting the tumor microenvironment. The diverse cell types of the tumor microenvironment exhibit different molecular signatures that are regulated at their genetic and epigenetic levels. The cancer cells elicit intricate crosstalks with these supporting cells, exchanging essential metabolites which support their anabolic processes and can promote their survival, proliferation, EMT, angiogenesis, metastasis and even therapeutic resistance. In this context, carbohydrate metabolism ensures constant energy supply being a central axis from which other metabolic and biosynthetic pathways including amino acid and lipid metabolism and pentose phosphate pathway are diverged. In contrast to normal cells, increased glycolytic flux is a distinguishing feature of the highly proliferative cancer cells, which supports them to adapt to a hypoxic environment and also protects them from oxidative stress. Such rewired metabolic properties are often a result of epigenetic alterations in the cancer cells, which are mediated by several factors including, DNA, histone and non-histone protein modifications and non-coding RNAs. Conversely, epigenetic landscapes of the cancer cells are also dictated by their diverse metabolomes. Altogether, this metabolic and epigenetic interplay has immense potential for the development of efficient anti-cancer therapeutic strategies. In this book chapter we emphasize upon the significance of reprogrammed carbohydrate metabolism in regulating the tumor microenvironment and cancer progression, with an aim to explore the different metabolic and epigenetic targets for better cancer treatment.
MeSH term(s)	Humans ; Tumor Microenvironment ; Neoplasms/drug therapy ; Glycolysis/physiology ; Carbohydrate Metabolism ; Histones/metabolism
Chemical Substances	Histones
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article
ISSN	0306-0225 ; 0096-8757
ISSN	0306-0225 ; 0096-8757
DOI	10.1007/978-3-031-07634-3_1
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Article ; Online: A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function.

Rosas, Ruben / Aguilar, Rhiannon R / Arslanovic, Nina / Seck, Anna / Smith, Duncan J / Tyler, Jessica K / Churchill, Mair E A

eLife

2023 Volume 12

Abstract: The histone chaperone chromatin assembly factor 1 (CAF-1) deposits two nascent histone H3/H4 dimers onto newly replicated DNA forming the central core of the nucleosome known as the tetrasome. How CAF-1 ensures there is sufficient space for the assembly ... ...

Abstract	The histone chaperone chromatin assembly factor 1 (CAF-1) deposits two nascent histone H3/H4 dimers onto newly replicated DNA forming the central core of the nucleosome known as the tetrasome. How CAF-1 ensures there is sufficient space for the assembly of tetrasomes remains unknown. Structural and biophysical characterization of the lysine/glutamic acid/arginine-rich (KER) region of CAF-1 revealed a 128-Å single alpha-helix (SAH) motif with unprecedented DNA-binding properties. Distinct KER sequence features and length of the SAH drive the selectivity of CAF-1 for tetrasome-length DNA and facilitate function in budding yeast. In vivo, the KER cooperates with the DNA-binding winged helix domain in CAF-1 to overcome DNA damage sensitivity and maintain silencing of gene expression. We propose that the KER SAH links functional domains within CAF-1 with structural precision, acting as a DNA-binding spacer element during chromatin assembly.
MeSH term(s)	Chromatin Assembly Factor-1 ; Protein Conformation, alpha-Helical ; DNA ; DNA Damage ; Molecular Chaperones ; Gene Silencing ; Histones/genetics
Chemical Substances	Chromatin Assembly Factor-1 ; DNA (9007-49-2) ; Molecular Chaperones ; Histones
Language	English
Publishing date	2023-07-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.83538
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