REX1 and YY2 bind RE/ERV elements in both ES and TS cells.

<p>(A) REX1 association to RE in TS cells. Binding was assessed in chromatin immunoprecipitation assays using αREX1 serum followed by quantification of precipitated DNA using real-time qPCR amplification. The figure shows analysis of non-binding reference sites as controls (CGR-A, CGR-B), and <i>Gapdh</i>, several sequences present in the genome as multiple copies (MLV36, γ-satellite) and the ERV elements indicated. Association is represented as percentage bound (relative to purified chromatin extract from the same lysate). Enrichment was calculated as percentage association relative to control chromatin, and is represented as fold binding or enrichment relative to a non-binding reference gene <i>Gapdh</i>. Error bars indicate SEM. (B) As A except for YY2 binding in ES cells. Data on CGR-A, CGR-B and <i>musD</i> are from a single experiment. (C) YY2 binding to Class III elements. Binding of YY2 in ES cells to class III ERV sequences present in the genome as multiple copies (<i>Orr1</i> and <i>MalR</i>) was assessed by qPCR analysis as described in <b>A</b>. The figure shows fold enrichment relative to a non-binding reference gene <i>Gapdh</i>. Data on CGR-C, <i>musD</i>, <i>Tsix</i> and <i>Spata</i> are from a single experiment.</p

Data_Sheet_4_Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia.PDF

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.</p

Image_1_Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia.TIFF

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.</p

Image_3_Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia.TIFF

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.</p

Association of YY1 and YY2 to chromatin.

<p>(A) A motif enriched in the genome wide YY2 ChIP-seq peaks is depicted as a sequence logo. Data from the top 20 peaks were analyzed as described in M&M. (B) Association of YY1 (in ES cells) or YY2 (in TS cells) to genomic targets was assessed as described in the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154268#pone.0154268.g003" target="_blank">Fig 3B</a>, using either αYY1 (left panel) or αYY2 serum (right panel). Codes for genomic targets analyzed refer to a YY1 genomic target (<i>YY1T1</i>) and several YY2 target genes (<i>T5T1</i>, <i>T18T1</i>) from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154268#pone.0154268.t002" target="_blank">Table 2</a> (see text for <i>S5T1</i>). The data in the left panel represent the average of three independent experiments ± SEM. The right panel shows the results of a typical experiment out of several performed, except for <i>T18T1</i>, multiple replicates performed.</p

Data_Sheet_2_Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia.PDF

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.</p

Image_9_Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia.tiff

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.</p

YY2 binding to genomic targets.

<p>(A) Semiquantitative PCR and (B) qPCR to validate YY2 association in TS cells to peaks identified by sequencing (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154268#pone.0154268.t002" target="_blank">Table 2</a>). (A) EtBr stained gel shows PCR products of the genomic regions immunoprecipitated by YY2 (αYY2). Preimmune serum (PreI) was used as a control. Purified chromatin extract from the lysate was used to confirm amplicons. MQ, reactions without input DNA served as a negative control. <i>Gapdh</i> promoter was used as a reference gene. (B) Association of YY2 in TS cells to potential genomic targets (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154268#pone.0154268.t002" target="_blank">Table 2</a>) was assessed by <i>locus</i>-specific qPCR analysis after chromatin immunoprecipitation using αYY2, or preimmune serum (PreI) as a control. The <i>Gapdh</i> promoter is included as a negative control. The amount of immunoprecipitated DNA as a percentage of input DNA was recalculated as fold association normalized to the <i>Gapdh</i> promoter. Error bars represent SEM. (C) As B, data is represented directly as a percentage of input DNA. Each panel represents an independent experiment.</p

Data_Sheet_5_Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia.PDF

Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.</p

Sequencing data.

<p>Sequencing data.</p