DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti.

Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool / Christopher Riccardi,Iacopo Passeri,Lisa Cangioli,Camilla Fagorzi,Marco Fondi,Alessio Mengoni. - In: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. - ISSN 1422-0067. - ELETTRONICO. - 24:(2023), pp. 159.0-159.0. [10.3390/ijms24010159]

Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool

Christopher Riccardi;Iacopo Passeri;Lisa Cangioli;Camilla Fagorzi;Marco Fondi
;
Alessio Mengoni
2023

Abstract

DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti.
2023
24
0
0
Goal 12: Responsible consumption and production
Goal 15: Life on land
Christopher Riccardi,Iacopo Passeri,Lisa Cangioli,Camilla Fagorzi,Marco Fondi,Alessio Mengoni
File in questo prodotto:
File Dimensione Formato  
Riccardi and Passeri et al 2022 IJMS.pdf

accesso aperto

Descrizione: Riccardi, Passeri et al
Tipologia: Pdf editoriale (Version of record)
Licenza: Open Access
Dimensione 2.49 MB
Formato Adobe PDF
2.49 MB Adobe PDF

I documenti in FLORE sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/1294539
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 0
  • ???jsp.display-item.citation.isi??? 1
social impact