scholarly journals Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Huifen Cao ◽  
Lorena Salazar-García ◽  
Fan Gao ◽  
Thor Wahlestedt ◽  
Chun-Lin Wu ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Single Strand ◽  
Dna Breaks ◽  
Strand Breaks ◽  
Template Strand ◽  
Naturally Occurring ◽  
Single Strand Breaks ◽  
Novel Approach ◽  
Genome Wide ◽  
Nucleotide Resolution

AbstractSingle-strand breaks (SSBs) represent the major form of DNA damage, yet techniques to map these lesions genome-wide with nucleotide-level precision are limited. Here, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realms of cellular biology, not obtainable with current approaches.

scholarly journals A novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells

2020 ◽  
Author(s):  
Fan Gao ◽  
Ye Cai ◽  
Lu Tang ◽  
Chun-Lin Wu ◽  
Huifen Cao ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Single Strand ◽  
Dna Breaks ◽  
Strand Breaks ◽  
Template Strand ◽  
Naturally Occurring ◽  
Single Strand Breaks ◽  
Novel Approach ◽  
Genome Wide ◽  
Nucleotide Resolution

Abstract Single strand breaks (SSBs) represent the major form of DNA damage, yet no technique exists to map these lesions genome-wide with nucleotide-level precision. Herein, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes of genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realm of cellular biology, not obtainable with current approaches.

scholarly journals A novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells

2020 ◽  
Author(s):  
Fan Gao ◽  
Ye Cai ◽  
Lu Tang ◽  
Chun-Lin Wu ◽  
Huifen Cao ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Single Strand ◽  
Dna Breaks ◽  
Strand Breaks ◽  
Template Strand ◽  
Naturally Occurring ◽  
Single Strand Breaks ◽  
Novel Approach ◽  
Genome Wide ◽  
Nucleotide Resolution

Abstract Abstract Single strand breaks (SSBs) represent the major form of DNA damage, yet no technique exists to map these lesions genome-wide with nucleotide-level precision. Herein, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes of genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realm of cellular biology, not obtainable with current approaches.

scholarly journals Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

2020 ◽  
Vol 78 (5) ◽  
pp. 975-985.e7 ◽  
Author(s):  
Annie M. Sriramachandran ◽  
Giuseppe Petrosino ◽  
María Méndez-Lago ◽  
Axel J. Schäfer ◽  
Liliana S. Batista-Nascimento ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Strand ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide ◽  
Resolution Mapping ◽  
Nucleotide Resolution

scholarly journals Emerging Technologies for Genome-Wide Profiling of DNA Breakage

2021 ◽  
Vol 11 ◽  
Author(s):  
Matthew J. Rybin ◽  
Melina Ramic ◽  
Natalie R. Ricciardi ◽  
Philipp Kapranov ◽  
Claes Wahlestedt ◽  
...  
Keyword(s):  
Genome Instability ◽  
Dna Double Strand Breaks ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Genomic Regions

Genome instability is associated with myriad human diseases and is a well-known feature of both cancer and neurodegenerative disease. Until recently, the ability to assess DNA damage—the principal driver of genome instability—was limited to relatively imprecise methods or restricted to studying predefined genomic regions. Recently, new techniques for detecting DNA double strand breaks (DSBs) and single strand breaks (SSBs) with next-generation sequencing on a genome-wide scale with single nucleotide resolution have emerged. With these new tools, efforts are underway to define the “breakome” in normal aging and disease. Here, we compare the relative strengths and weaknesses of these technologies and their potential application to studying neurodegenerative diseases.

scholarly journals A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
William H. Gittens ◽  
Dominic J. Johnson ◽  
Rachal M. Allison ◽  
Tim J. Cooper ◽  
Holly Thomas ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Genome Stability ◽  
Dna Double Strand Breaks ◽  
Dna Breaks ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Human Genomes ◽  
Nucleotide Resolution

Abstract DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

scholarly journals Preparation and Analysis of GLOE-Seq Libraries for Genome-Wide Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions

2020 ◽  
Vol 1 (2) ◽  
pp. 100076
Author(s):  
Giuseppe Petrosino ◽  
Nicola Zilio ◽  
Annie M. Sriramachandran ◽  
Helle D. Ulrich
Keyword(s):  
Dna Replication ◽  
Single Strand ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide

scholarly journals Manipulating chromosome structure and metaphase status with ultraviolet light and repair synthesis inhibitors

1985 ◽  
Vol 73 (1) ◽  
pp. 159-186
Author(s):  
A.M. Mullinger ◽  
R.T. Johnson
Keyword(s):  
Simian Virus 40 ◽  
Human Cells ◽  
Single Strand ◽  
Dna Breaks ◽  
Intact Cells ◽  
Repair Synthesis ◽  
Single Strand Break ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Chromosome Decondensation

DNA repair occurs in metaphase-arrested cells in response to ultraviolet irradiation. In the presence of the repair synthesis inhibitors hydroxyurea and 1-beta-D-arabinofuranosylcytosine the chromosomes of such cells, as seen in Carnoy-fixed preparations, are decondensed. The extent of decondensation is related to both the u.v. dose and the duration of incubation in the presence of inhibitors. For any particular cell type there is a reasonable correlation between the amount of decondensation and the number of single-strand DNA breaks generated by the repair process under the same inhibitory conditions, though the chromosome changes continue after the number of single-strand breaks has reached a plateau. The dose response of chromosome decondensation varies between different cell types but is in general correlated with differences in levels of single-strand breaks accumulated under comparable inhibitory conditions. Decondensation can be detected after 0.5 Jm-2 in repair-competent human cells. In human cells defective in excision repair there is much less chromosome decondensation in response to the same u.v. dose and time of repair inhibition. However, a simian virus 40-transformed muntjac cell displays pronounced chromosome decondensation but has limited incision ability. Both chromosome decondensation and single-strand break accumulation in the presence of inhibitors are reversed when DNA precursors are provided, but reversal after higher u.v. doses and longer periods of incubation leads to recondensed chromosomes that are fragmented. Elution of the DNA from such cells through polycarbonate filters under non-denaturing conditions reveals that double-strand DNA breaks are generated during the period of incubation with inhibitors. Although the chromosomes of repair-inhibited metaphase cells are decondensed in fixed preparations, their morphology appears normal in intact cells. The cells also retain a capacity to induce prematurely condensed chromosomes (PCC) when fused with interphase cells: compared with control mitotic cells, the speed of induction is sometimes reduced but the final amount of PCC produced is similar.

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