Oda, Mayumi, Glass, Jacob L., Thompson, Reid F., Mo, Yongkai, Olivier, Emmanuel N., Figueroa, Maria E., ...
Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows...
Thompson, Reid F., Suzuki, Masako, Lau, Kevin W., Greally, John M.
Motivation: DNA cytosine methylation is an important epigenetic regulator, critical for mammalian development and the control of gene expression. Numerous techniques using either restriction enzyme...
Reduced-representation methylation mapping (2008)
Jeddeloh, Jeffrey A, Greally, John M, Rando, Oliver J
Abstract The power of massively parallel sequencing has been harnessed to map cytosine methylation patterns in the mouse genome, allowing insights into the relationship of methylation with DNA...
An analytical pipeline for genomic representations used for cytosine methylation studies (2008)
Thompson, Reid F., Reimers, Mark, Khulan, Batbayar, Gissot, Mathieu, Richmond, Todd A., Chen, Quan, ...
Motivation: Representations of the genome can be generated by the selection of a subpopulation of restriction fragments using ligation-mediated PCR. Such representations form the basis for a number...
Epigenomic Modifications Predict Active Promoters and Gene Structure in Toxoplasma gondii (2007)
Mathieu Gissot, Krystyna A. Kelly, James W. Ajioka, John M. Greally, Kami Kim
Mechanisms of gene regulation are poorly understood in Apicomplexa, a phylum that encompasses deadly human pathogens like Plasmodium and Toxoplasma. Initial studies suggest that epigenetic phenomena,...
Comparative isoschizomer profiling of cytosine methylation: The HELP assay (2006)
Khulan, Batbayar, Thompson, Reid F., Ye, Kenny, Fazzari, Melissa J., Suzuki, Masako, Stasiek, Edyta, ...
The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its...
Comparative isoschizomer profiling of cytosine methylation: The HELP assay (2006)
Khulan, Batbayar, Thompson, Reid F., Ye, Kenny, Fazzari, Melissa J., Suzuki, Masako, Stasiek, Edyta, ...
The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its...
Stefan, Mihaela, Claiborn, Kathryn C, Stasiek, Edyta, Chai, Jing-Hua, Ohta, Tohru, Longnecker, Richard, ...
Abstract Background Prader-Willi and Angelman syndrome (PWS and AS) patients typically have an ~5 Mb deletion of human chromosome 15q11-q13, of opposite parental origin. A mouse model of PWS and AS...
Tsuchiya, Karen D., Greally, John M., Yi, Yajun, Noel, Kevin P., Truong, Jean-Pierre, Disteche, Christine M.
We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared...
Tsuchiya, Karen D., Greally, John M., Yi, Yajun, Noel, Kevin P., Truong, Jean-Pierre, Disteche, Christine M.
We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared...
Alami, Raouf, Greally, John M., Tanimoto, Keiji, Hwang, Steven, Feng, Yong-Qing, Engel, James D., ...
Expression of a construct integrated at different genomic locations often varies because of position effects that have been subcategorized as stable (decreased level of expression) and variegating...
Conserved characteristics of heterochromatin-forming DNA at the 15q11-q13 imprinting center. (1999)
Greally, John M., Gray, Todd A., Gabriel, James M., Song, Li Qun, Zemel, Sharon, Nicholls, Robert D.
Nuclear matrix binding assays (NMBAs) define certain DNA sequences as matrix attachment regions (MARs), which often have cis-acting epigenetic regulatory functions. We used NMBAs to analyze the...
Conserved characteristics of heterochromatin-forming DNA at the 15q11-q13 imprinting center
Greally, John M., Gray, Todd A., Gabriel, James M., Song, Li Qun, Zemel, Sharon, Nicholls, Robert D.
Nuclear matrix binding assays (NMBAs) define certain DNA sequences as matrix attachment regions (MARs), which often have cis-acting epigenetic regulatory functions. We used NMBAs to analyze the...
Position Effects Are Influenced by the Orientation of a Transgene with Respect to Flanking Chromatin
Feng, Yong-Qing, Lorincz, Matthew C., Fiering, Steve, Greally, John M., Bouhassira, Eric E.
We have inserted two expression cassettes at tagged reference chromosomal sites by using recombinase-mediated cassette exchange in mammalian cells. The three sites of integration displayed either...
To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally...
State, Matthew W., Greally, John M., Cuker, Adam, Bowers, Peter N., Henegariu, Octavian, Morgan, Thomas M., ...
Gilles de la Tourette syndrome (GTS) is a potentially debilitating neuropsychiatric disorder defined by the presence of both vocal and motor tics. Despite evidence that this and a related phenotypic...
Mammalian linker-histone subtypes differentially affect gene expression in vivo
Alami, Raouf, Fan, Yuhong, Pack, Stephanie, Sonbuchner, Timothy M., Besse, Arnaud, Lin, Qingcong, ...
Posttranslational modifications and remodeling of nucleosomes are critical factors in the regulation of transcription. Higher-order folding of chromatin also is likely to contribute to the control of...
Homez, a homeobox leucine zipper gene specific to the vertebrate lineage
Bayarsaihan, Dashzeveg, Enkhmandakh, Badam, Makeyev, Aleksandr, Greally, John M., Leckman, James F., Ruddle, Frank H.
This work describes a vertebrate homeobox gene, designated Homez (homeodomain leucine zipper-encoding gene), that encodes a protein with an unusual structural organization. There are several regions...
Tsuchiya, Karen D., Greally, John M., Yi, Yajun, Noel, Kevin P., Truong, Jean-Pierre, Disteche, Christine M.
We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared...
Stefan, Mihaela, Claiborn, Kathryn C, Stasiek, Edyta, Chai, Jing-Hua, Ohta, Tohru, Longnecker, Richard, ...
Conserved characteristics of heterochromatin-forming DNA at the 15q11-q13 imprinting center
Greally, John M., Gray, Todd A., Gabriel, James M., Song, Li Qun, Zemel, Sharon, Nicholls, Robert D.
Nuclear matrix binding assays (NMBAs) define certain DNA sequences as matrix attachment regions (MARs), which often have cis-acting epigenetic regulatory functions. We used NMBAs to analyze the...
Position Effects Are Influenced by the Orientation of a Transgene with Respect to Flanking Chromatin
Feng, Yong-Qing, Lorincz, Matthew C., Fiering, Steve, Greally, John M., Bouhassira, Eric E.
We have inserted two expression cassettes at tagged reference chromosomal sites by using recombinase-mediated cassette exchange in mammalian cells. The three sites of integration displayed either...
To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally...
State, Matthew W., Greally, John M., Cuker, Adam, Bowers, Peter N., Henegariu, Octavian, Morgan, Thomas M., ...
Gilles de la Tourette syndrome (GTS) is a potentially debilitating neuropsychiatric disorder defined by the presence of both vocal and motor tics. Despite evidence that this and a related phenotypic...
Mammalian linker-histone subtypes differentially affect gene expression in vivo
Alami, Raouf, Fan, Yuhong, Pack, Stephanie, Sonbuchner, Timothy M., Besse, Arnaud, Lin, Qingcong, ...
Posttranslational modifications and remodeling of nucleosomes are critical factors in the regulation of transcription. Higher-order folding of chromatin also is likely to contribute to the control of...
Homez, a homeobox leucine zipper gene specific to the vertebrate lineage
Bayarsaihan, Dashzeveg, Enkhmandakh, Badam, Makeyev, Aleksandr, Greally, John M., Leckman, James F., Ruddle, Frank H.
This work describes a vertebrate homeobox gene, designated Homez (homeodomain leucine zipper-encoding gene), that encodes a protein with an unusual structural organization. There are several regions...
Tsuchiya, Karen D., Greally, John M., Yi, Yajun, Noel, Kevin P., Truong, Jean-Pierre, Disteche, Christine M.
We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared...
Stefan, Mihaela, Claiborn, Kathryn C, Stasiek, Edyta, Chai, Jing-Hua, Ohta, Tohru, Longnecker, Richard, ...
Comparative isoschizomer profiling of cytosine methylation: The HELP assay
Khulan, Batbayar, Thompson, Reid F., Ye, Kenny, Fazzari, Melissa J., Suzuki, Masako, Stasiek, Edyta, ...
The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its...
Epigenomic Modifications Predict Active Promoters and Gene Structure in Toxoplasma gondii
Gissot, Mathieu, Kelly, Krystyna A, Ajioka, James W, Greally, John M, Kim, Kami
Mechanisms of gene regulation are poorly understood in Apicomplexa, a phylum that encompasses deadly human pathogens like Plasmodium and Toxoplasma. Initial studies suggest that epigenetic phenomena,...
Polo, Jose M., Juszczynski, Przemyslaw, Monti, Stefano, Cerchietti, Leandro, Ye, Kenny, Greally, John M., ...
Diffuse large B cell lymphomas (DLBCLs) often express BCL6, a transcriptional repressor required for the formation of normal germinal centers. In a subset of DLBCLs, BCL6 is deregulated by...
CG dinucleotide clustering is a species-specific property of the genome
Glass, Jacob L., Thompson, Reid F., Khulan, Batbayar, Figueroa, Maria E., Olivier, Emmanuel N., Oakley, Erin J., ...
Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated...
An Integrative Genomic and Epigenomic Approach for the Study of Transcriptional Regulation
Figueroa, Maria E., Reimers, Mark, Thompson, Reid F., Ye, Kenny, Li, Yushan, Selzer, Rebecca R., ...
The molecular heterogeneity of acute leukemias and other tumors constitutes a major obstacle towards understanding disease pathogenesis and developing new targeted-therapies. Aberrant gene regulation...
Toxoplasma gondii and Cryptosporidium parvum Lack Detectable DNA Cytosine Methylationâ–ż
Gissot, Mathieu, Choi, Sang-Woon, Thompson, Reid F., Greally, John M., Kim, Kami
Epigenetic factors play a role in the expression of virulence traits in Apicomplexa. Apicomplexan genomes encode putative DNA cytosine methylation enzymes. To assess the presence of cytosine...
Reduced-representation methylation mapping
Jeddeloh, Jeffrey A, Greally, John M, Rando, Oliver J
Massively parallel sequencing has been harnessed to map DNA methylation patterns in the mouse genome.
Oda, Mayumi, Glass, Jacob L., Thompson, Reid F., Mo, Yongkai, Olivier, Emmanuel N., Figueroa, Maria E., ...
Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows...