ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing.
Transposon-insertion sequencing (TIS) is a powerful approach for deciphering genetic requirements for bacterial growth in different conditions, as it enables simultaneous genome-wide analysis of the fitness of thousands of mutants. However, current methods for comparative analysis of TIS data do not adjust for stochastic experimental variation between datasets and are limited to interrogation of annotated genomic elements. Here, we present ARTIST, an accessible TIS analysis pipeline for identifying essential regions that are required for growth under optimal conditions as well as conditionally essential loci that participate in survival only under specific conditions. ARTIST uses simulation-based normalization to model and compensate for experimental noise, and thereby enhances the statistical power in conditional TIS analyses. ARTIST also employs a novel adaptation of the hidden Markov model to generate statistically robust, high-resolution, annotation-independent maps of fitness-linked loci across the entire genome. Using ARTIST, we sensitively and comprehensively define Mycobacterium tuberculosis and Vibrio cholerae loci required for host infection while limiting inclusion of false positive loci. ARTIST is applicable to a broad range of organisms and will facilitate TIS-based dissection of pathways required for microbial growth and survival under a multitude of conditions.
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts, United States of America.
Justin R
JR
Pritchard
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts, United States of America; Howard Hughes Medical Institute, Boston, Massachusetts, United States of America.
Michael C
MC
Chao
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts, United States of America; Howard Hughes Medical Institute, Boston, Massachusetts, United States of America.
Sören
S
Abel
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts, United States of America; Howard Hughes Medical Institute, Boston, Massachusetts, United States of America.
Brigid M
BM
Davis
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts, United States of America.
Catherine
C
Baranowski
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts, United States of America.
Yanjia J
YJ
Zhang
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts, United States of America.
Eric J
EJ
Rubin
Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America; Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts, United States of America; Howard Hughes Medical Institute, Boston, Massachusetts, United States of America.
Matthew K
MK
Waldor
D003198:Computer Simulation; D004251:DNA Transposable Elements / Q000235:genetics*; D040961:Genetic Drift; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics*; D008390:Markov Chains; D016254:Mutagenesis, Insertional / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000472:pathogenicity; D012984:Software; D014734:Vibrio cholerae / Q000235:genetics / Q000472:pathogenicity
D004251:DNA Transposable Elements