Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres

ABSTRACT Origins of DNA replication are key genetic elements, yet their identification remains elusive in most organisms. In previous work, we found that centromeres contain origins of replication (ORIs) that are determined epigenetically in the pathogenic yeast Candida albicans. In this study, we u...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hung-Ji Tsai, Joshua A. Baller, Ivan Liachko, Amnon Koren, Laura S. Burrack, Meleah A. Hickman, Mathuravani A. Thevandavakkam, Laura N. Rusche, Judith Berman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/70e68d4e98f34ef9b64f1dcf46320fb4
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:70e68d4e98f34ef9b64f1dcf46320fb4
record_format	dspace
spelling	oai:doaj.org-article:70e68d4e98f34ef9b64f1dcf46320fb42021-11-15T15:45:55ZOrigin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres10.1128/mBio.01703-142150-7511https://doaj.org/article/70e68d4e98f34ef9b64f1dcf46320fb42014-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01703-14https://doaj.org/toc/2150-7511ABSTRACT Origins of DNA replication are key genetic elements, yet their identification remains elusive in most organisms. In previous work, we found that centromeres contain origins of replication (ORIs) that are determined epigenetically in the pathogenic yeast Candida albicans. In this study, we used origin recognition complex (ORC) binding and nucleosome occupancy patterns in Saccharomyces cerevisiae and Kluyveromyces lactis to train a machine learning algorithm to predict the position of active arm (noncentromeric) origins in the C. albicans genome. The model identified bona fide active origins as determined by the presence of replication intermediates on nondenaturing two-dimensional (2D) gels. Importantly, these origins function at their native chromosomal loci and also as autonomously replicating sequences (ARSs) on a linear plasmid. A “mini-ARS screen” identified at least one and often two ARS regions of ≥100 bp within each bona fide origin. Furthermore, a 15-bp AC-rich consensus motif was associated with the predicted origins and conferred autonomous replicating activity to the mini-ARSs. Thus, while centromeres and the origins associated with them are epigenetic, arm origins are dependent upon critical DNA features, such as a binding site for ORC and a propensity for nucleosome exclusion. IMPORTANCE DNA replication machinery is highly conserved, yet the definition of exactly what specifies a replication origin differs in different species. Here, we utilized computational genomics to predict origin locations in Candida albicans by combining locations of binding sites for the conserved origin replication complex, necessary for replication initiation, together with chromatin organization patterns. We identified predicted sequences that exhibited bona fide origin function and developed a linear plasmid assay to delimit the DNA fragments necessary for origin function. Additionally, we found that a short AC-rich motif, which is enriched in predicted origins, is required for origin function. Thus, we demonstrated a new machine learning paradigm for identification of potential origins from a genome with no prior information. Furthermore, this work suggests that C. albicans has two different types of origins: “hard-wired” arm origins that rely upon specific sequence motifs and “epigenetic” centromeric origins that are recruited to kinetochores in a sequence-independent manner.Hung-Ji TsaiJoshua A. BallerIvan LiachkoAmnon KorenLaura S. BurrackMeleah A. HickmanMathuravani A. ThevandavakkamLaura N. RuscheJudith BermanAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 5 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Hung-Ji Tsai Joshua A. Baller Ivan Liachko Amnon Koren Laura S. Burrack Meleah A. Hickman Mathuravani A. Thevandavakkam Laura N. Rusche Judith Berman Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres
description	ABSTRACT Origins of DNA replication are key genetic elements, yet their identification remains elusive in most organisms. In previous work, we found that centromeres contain origins of replication (ORIs) that are determined epigenetically in the pathogenic yeast Candida albicans. In this study, we used origin recognition complex (ORC) binding and nucleosome occupancy patterns in Saccharomyces cerevisiae and Kluyveromyces lactis to train a machine learning algorithm to predict the position of active arm (noncentromeric) origins in the C. albicans genome. The model identified bona fide active origins as determined by the presence of replication intermediates on nondenaturing two-dimensional (2D) gels. Importantly, these origins function at their native chromosomal loci and also as autonomously replicating sequences (ARSs) on a linear plasmid. A “mini-ARS screen” identified at least one and often two ARS regions of ≥100 bp within each bona fide origin. Furthermore, a 15-bp AC-rich consensus motif was associated with the predicted origins and conferred autonomous replicating activity to the mini-ARSs. Thus, while centromeres and the origins associated with them are epigenetic, arm origins are dependent upon critical DNA features, such as a binding site for ORC and a propensity for nucleosome exclusion. IMPORTANCE DNA replication machinery is highly conserved, yet the definition of exactly what specifies a replication origin differs in different species. Here, we utilized computational genomics to predict origin locations in Candida albicans by combining locations of binding sites for the conserved origin replication complex, necessary for replication initiation, together with chromatin organization patterns. We identified predicted sequences that exhibited bona fide origin function and developed a linear plasmid assay to delimit the DNA fragments necessary for origin function. Additionally, we found that a short AC-rich motif, which is enriched in predicted origins, is required for origin function. Thus, we demonstrated a new machine learning paradigm for identification of potential origins from a genome with no prior information. Furthermore, this work suggests that C. albicans has two different types of origins: “hard-wired” arm origins that rely upon specific sequence motifs and “epigenetic” centromeric origins that are recruited to kinetochores in a sequence-independent manner.
format	article
author	Hung-Ji Tsai Joshua A. Baller Ivan Liachko Amnon Koren Laura S. Burrack Meleah A. Hickman Mathuravani A. Thevandavakkam Laura N. Rusche Judith Berman
author_facet	Hung-Ji Tsai Joshua A. Baller Ivan Liachko Amnon Koren Laura S. Burrack Meleah A. Hickman Mathuravani A. Thevandavakkam Laura N. Rusche Judith Berman
author_sort	Hung-Ji Tsai
title	Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres
title_short	Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres
title_full	Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres
title_fullStr	Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres
title_full_unstemmed	Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres
title_sort	origin replication complex binding, nucleosome depletion patterns, and a primary sequence motif can predict origins of replication in a genome with epigenetic centromeres
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/70e68d4e98f34ef9b64f1dcf46320fb4
work_keys_str_mv	AT hungjitsai originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT joshuaaballer originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT ivanliachko originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT amnonkoren originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT laurasburrack originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT meleahahickman originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT mathuravaniathevandavakkam originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT lauranrusche originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres AT judithberman originreplicationcomplexbindingnucleosomedepletionpatternsandaprimarysequencemotifcanpredictoriginsofreplicationinagenomewithepigeneticcentromeres
_version_	1718427524644470784

Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres

Ejemplares similares