Roche NimbleGen Webinar Series

Audio: Insights into the Evolutionary Significance of Whole Genome Duplications Provided by Populus Expression Arrays

Video: Insights into the Evolutionary Significance of Whole Genome Duplications Provided by Populus Expression Arrays

Audio: Duplicate gene expression evolution in cotton

Video: Duplicate gene expression evolution in cotton

Audio: Genome-Scale Targeted Sequencing and Expression Analysis in Duplicated Genomes

Video: Genome-Scale Targeted Sequencing and Expression Analysis in Duplicated Genomes

Genomic disorders are conditions that result from recurrent rearrangement of DNA caused by unequal crossing over between duplicated genomic sequences. Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model, we assessed 155 autopsy samples from fetuses with well-defined developmental pathologies in regions predisposed to recurrent rearrangement by array CGH. We found that 6% of fetal material showed evidence of microdeletion or microduplication, One of the microdeletions, identified in a fetus with multicystic dysplastic kidneys, encompasses the TCF2 gene on 17q12, previously shown to be mutated in maturity-onset diabetes as well as a subset of pediatric renal abnormalities. Fine-scale mapping with custom oligonucleotide arrays of the breakpoints in different patient cohorts reveals a recurrent 1.5 Mb de novo deletion in individuals with phenotypes ranging from congenital renal abnormalities to maturity-onset diabetes of the young type 5. Array analysis also reveals significant copy number and structural variation at the breakpoints. The 17q12 microdeletion is the first genomic disorder associated with diabetes and accounts for a significant proportion of previously unexplained pediatric renal disease.

Genomic disorders are conditions that result from recurrent rearrangement of DNA caused by unequal crossing over between duplicated genomic sequences. Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model, we assessed 155 autopsy samples from fetuses with well-defined developmental pathologies in regions predisposed to recurrent rearrangement by array CGH. We found that 6% of fetal material showed evidence of microdeletion or microduplication, One of the microdeletions, identified in a fetus with multicystic dysplastic kidneys, encompasses the TCF2 gene on 17q12, previously shown to be mutated in maturity-onset diabetes as well as a subset of pediatric renal abnormalities. Fine-scale mapping with custom oligonucleotide arrays of the breakpoints in different patient cohorts reveals a recurrent 1.5 Mb de novo deletion in individuals with phenotypes ranging from congenital renal abnormalities to maturity-onset diabetes of the young type 5. Array analysis also reveals significant copy number and structural variation at the breakpoints. The 17q12 microdeletion is the first genomic disorder associated with diabetes and accounts for a significant proportion of previously unexplained pediatric renal disease.

Methylation of lysine residues on histone H3 and H4 tails plays a key role in gene regulation, chromatin structure, and establishment and maintenance of epigenetic memory. In particular, methylation of lysines 9 or 27 of histone H3 (H3me3K9 and H3me3K27, respectively) have been associated with silenced chromatin. ChIP-chip analysis using human promoter arrays indicate that the two marks segregate differentially with the two most common types of transcription factors; H3me3K9 is highly enriched at zinc finger genes (ZNFs) and H3me3K27 is highly enriched at homeobox genes. Here we show that many promoters containing the H3me3K9 mark are also bound by the corepressor KAP1 (also known as TIF1B or TRIM28). We then performed a complete genomic analysis using a set of 38 tiling arrays, which identified ~7000 KAP1 binding sites in the entire human genome. KAP1 binding was specifically enriched at zinc finger genes. Although most KAP1 binding sites were within core promoter regions, a unique binding pattern was observed at ZNF target genes. Analysis of ChIP-chip data from promoter arrays as well as from whole genome tiling arrays will be discussed.

Methylation of lysine residues on histone H3 and H4 tails plays a key role in gene regulation, chromatin structure, and establishment and maintenance of epigenetic memory. In particular, methylation of lysines 9 or 27 of histone H3 (H3me3K9 and H3me3K27, respectively) have been associated with silenced chromatin. ChIP-chip analysis using human promoter arrays indicate that the two marks segregate differentially with the two most common types of transcription factors; H3me3K9 is highly enriched at zinc finger genes (ZNFs) and H3me3K27 is highly enriched at homeobox genes. Here we show that many promoters containing the H3me3K9 mark are also bound by the corepressor KAP1 (also known as TIF1B or TRIM28). We then performed a complete genomic analysis using a set of 38 tiling arrays, which identified ~7000 KAP1 binding sites in the entire human genome. KAP1 binding was specifically enriched at zinc finger genes. Although most KAP1 binding sites were within core promoter regions, a unique binding pattern was observed at ZNF target genes. Analysis of ChIP-chip data from promoter arrays as well as from whole genome tiling arrays will be discussed.

New methods for detecting changes in DNA copy number (CNVs) have begun to shed new light on genetic risk factors for Autism Spectrum Disorders. What these studies have shown is that large scale deletions and duplications of gene are a significant contributor to genetic risk, and furthermore that CNV risk factors are frequently the result of spontaneous germline mutation. Our findings raise the hypothesis that much the sporadic nature of autism due to spontaneous mutations. Spontaneous CNVs have been detected at many loci throughout the genome, and no single locus has been shown to account more than 1% of cases. These data are consistent with the notion that there are many genes in the genome that, when altered, can produce a similar disease phenotype. We hypothesize that the features of autism (impaired social interaction, difficulty with communication, and restricted interests and behaviors) owe there "commonality" to the fact that the diverse set of genes involved participate in a common biological network.

New methods for detecting changes in DNA copy number (CNVs) have begun to shed new light on genetic risk factors for Autism Spectrum Disorders. What these studies have shown is that large scale deletions and duplications of gene are a significant contributor to genetic risk, and furthermore that CNV risk factors are frequently the result of spontaneous germline mutation. Our findings raise the hypothesis that much the sporadic nature of autism due to spontaneous mutations. Spontaneous CNVs have been detected at many loci throughout the genome, and no single locus has been shown to account more than 1% of cases. These data are consistent with the notion that there are many genes in the genome that, when altered, can produce a similar disease phenotype. We hypothesize that the features of autism (impaired social interaction, difficulty with communication, and restricted interests and behaviors) owe there "commonality" to the fact that the diverse set of genes involved participate in a common biological network.

Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states.

Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states.

Large Noncoding RNAs (ncRNA) are becoming a distinguishing feature of the Metazoan genomes, but their functional roles are poorly understood. Here we describe a novel type of ncRNA termed HOTAIR that is 2.2. Kb RNA, has 5 spliced exons, a poly A tail and a 5’ meC cap, yet has no potential to code a sensible amino-acid sequence. HOTAIR is encoded antisense to the human HOXC cluster at the exact juncture of a 40 Kb domain of heterochromatin and a 60 Kb domain of euchromatin. However, HOTAIR doesn’t serve to regulate this boundary; Remarkably HOTAIR affects the global epigenetic state of the HOXD cluster located on a separate chromosome. HOTAIR binds the Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of large ncRNA may demarcate chromosomal domains of gene silencing from a distance. We further discuss RNA labeling optimizations, platform comparisons and the integration of ChIP-Chip and RNA expression on high-resolution DNA tiling arrays that were critical for our discovery of HOTAIR. Together, these results demonstrate the power of integrative genomics in elucidating the biological roles of large ncRNAs.