Next-generation analysis of trypanosomatid genome stability and instability

Emma M. Briggs; Catarina A. Marques; Joao Reis-Cunha; Jennifer Black; Samantha Campbell; Jeziel Damasceno; Daniella Bartholomeu; Kathryn Crouch; Richard McCulloch

doi:10.1007/978-1-0716-0294-2_15

Next-generation analysis of trypanosomatid genome stability and instability

Emma M. Briggs, Catarina A. Marques, Joao Reis-Cunha, Jennifer Black, Samantha Campbell, Jeziel Damasceno, Daniella Bartholomeu, Kathryn Crouch, Richard McCulloch^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract / Description of output

Understanding the rate and patterns of genome variation is becoming ever more amenable to whole-genome analysis through advances in DNA sequencing, which may, at least in some circumstances, have supplanted more localized analyses by cellular and genetic approaches. Whole-genome analyses can utilize both short- and long-read sequence technologies. Here we describe how sequence generated by these approaches has been used in trypanosomatids to examine DNA replication dynamics, the accumulation of modified histone H2A due to genome damage, and evaluation of genome variation, focusing on ploidy change.

Original language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press
Pages	225-262
Number of pages	38
ISBN (Electronic)	978-1-0716-0294-2
ISBN (Print)	978-1-0716-0293-5
DOIs	https://doi.org/10.1007/978-1-0716-0294-2_15
Publication status	E-pub ahead of print - 28 Mar 2020

Publication series

Name	Methods in Molecular Biology
Volume	2116
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords / Materials (for Non-textual outputs)

ChIP-seq
copy number variation
DNA damage
DNA replication
MFA-seq
next-generation sequencing
ploidy
single nucleotide polymorphisms

Access to Document

10.1007/978-1-0716-0294-2_15Licence: Creative Commons: Attribution (CC-BY)

Briggs2020_Protocol_Next-GenerationAnalysisOfTrypaFinal published version, 1.12 MBLicence: Creative Commons: Attribution (CC-BY)

Deciphering developmental commitment in African trypanosomes using single-cell transcriptomics
Briggs, E.
UK-based charities
20/01/20 → 19/01/24
Project: Research

Cite this

Briggs, E. M., Marques, C. A., Reis-Cunha, J., Black, J., Campbell, S., Damasceno, J., Bartholomeu, D., Crouch, K., & McCulloch, R. (2020). Next-generation analysis of trypanosomatid genome stability and instability. In Methods in Molecular Biology (pp. 225-262). (Methods in Molecular Biology; Vol. 2116). Humana Press. Advance online publication. https://doi.org/10.1007/978-1-0716-0294-2_15

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title = "Next-generation analysis of trypanosomatid genome stability and instability",

abstract = "Understanding the rate and patterns of genome variation is becoming ever more amenable to whole-genome analysis through advances in DNA sequencing, which may, at least in some circumstances, have supplanted more localized analyses by cellular and genetic approaches. Whole-genome analyses can utilize both short- and long-read sequence technologies. Here we describe how sequence generated by these approaches has been used in trypanosomatids to examine DNA replication dynamics, the accumulation of modified histone H2A due to genome damage, and evaluation of genome variation, focusing on ploidy change.",

keywords = "ChIP-seq, copy number variation, DNA damage, DNA replication, MFA-seq, next-generation sequencing, ploidy, single nucleotide polymorphisms",

author = "Briggs, {Emma M.} and Marques, {Catarina A.} and Joao Reis-Cunha and Jennifer Black and Samantha Campbell and Jeziel Damasceno and Daniella Bartholomeu and Kathryn Crouch and Richard McCulloch",

note = "Funding Information: This work was supported by the BBSRC [BB/K006495/1, BB/M028909/1, BB/N016165/1], the European Commission [RECREPEMLE], and the Wellcome Trust [206815, 083485, 089172]. The Wellcome Centre for Integrative Parasitology is supported by core funding from the Wellcome Trust [104111]. Publisher Copyright: {\textcopyright} The Author(s) 2020.",

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doi = "10.1007/978-1-0716-0294-2_15",

language = "English",

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AU - Marques, Catarina A.

AU - Reis-Cunha, Joao

AU - Black, Jennifer

AU - Campbell, Samantha

AU - Damasceno, Jeziel

AU - Bartholomeu, Daniella

AU - Crouch, Kathryn

AU - McCulloch, Richard

N1 - Funding Information: This work was supported by the BBSRC [BB/K006495/1, BB/M028909/1, BB/N016165/1], the European Commission [RECREPEMLE], and the Wellcome Trust [206815, 083485, 089172]. The Wellcome Centre for Integrative Parasitology is supported by core funding from the Wellcome Trust [104111]. Publisher Copyright: © The Author(s) 2020.

PY - 2020/3/28

Y1 - 2020/3/28

N2 - Understanding the rate and patterns of genome variation is becoming ever more amenable to whole-genome analysis through advances in DNA sequencing, which may, at least in some circumstances, have supplanted more localized analyses by cellular and genetic approaches. Whole-genome analyses can utilize both short- and long-read sequence technologies. Here we describe how sequence generated by these approaches has been used in trypanosomatids to examine DNA replication dynamics, the accumulation of modified histone H2A due to genome damage, and evaluation of genome variation, focusing on ploidy change.

AB - Understanding the rate and patterns of genome variation is becoming ever more amenable to whole-genome analysis through advances in DNA sequencing, which may, at least in some circumstances, have supplanted more localized analyses by cellular and genetic approaches. Whole-genome analyses can utilize both short- and long-read sequence technologies. Here we describe how sequence generated by these approaches has been used in trypanosomatids to examine DNA replication dynamics, the accumulation of modified histone H2A due to genome damage, and evaluation of genome variation, focusing on ploidy change.

KW - ChIP-seq

KW - copy number variation

KW - DNA damage

KW - DNA replication

KW - MFA-seq

KW - next-generation sequencing

KW - ploidy

KW - single nucleotide polymorphisms

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DO - 10.1007/978-1-0716-0294-2_15

M3 - Chapter

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AN - SCOPUS:85082513019

SN - 978-1-0716-0293-5

T3 - Methods in Molecular Biology

SP - 225

EP - 262

BT - Methods in Molecular Biology

PB - Humana Press

ER -

Next-generation analysis of trypanosomatid genome stability and instability

Abstract / Description of output

Publication series

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

Deciphering developmental commitment in African trypanosomes using single-cell transcriptomics

Cite this