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3. Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

Author

Pugacheva, Elena M, Rivero-Hinojosa, Samuel, Espinoza, Celso A, Méndez-Catalá, Claudia Fabiola, Kang, Sungyun, Suzuki, Teruhiko, Kosaka-Suzuki, Natsuki, Robinson, Susan, Nagarajan, Vijayaraj, Ye, Zhen, Boukaba, Abdelhalim, Rasko, John EJ, Strunnikov, Alexander V, Loukinov, Dmitri, Ren, Bing, and Lobanenkov, Victor V

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Biological Sciences, Stem Cell Research, Biotechnology, Human Genome, Genetics, Stem Cell Research - Nonembryonic - Non-Human, Breast Cancer, Cancer, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Binding Sites, CCCTC-Binding Factor, Cell Line, Chromatin, DNA, DNA-Binding Proteins, Enhancer Elements, Genetic, Genome, Humans, K562 Cells, Male, Mice, Neoplasms, Nucleotide Motifs, Promoter Regions, Genetic, Protein Binding, Repressor Proteins, Spermatids, Spermatozoa, Transcription, Genetic, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundCTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.ResultsHere we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells.ConclusionsWe discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells.

Published
2015

5. Chromatin architecture reorganization during stem cell differentiation

Author

Dixon, Jesse R, Jung, Inkyung, Selvaraj, Siddarth, Shen, Yin, Antosiewicz-Bourget, Jessica E, Lee, Ah Young, Ye, Zhen, Kim, Audrey, Rajagopal, Nisha, Xie, Wei, Diao, Yarui, Liang, Jing, Zhao, Huimin, Lobanenkov, Victor V, Ecker, Joseph R, Thomson, James A, and Ren, Bing

Subjects
Biochemistry and Cell Biology, Genetics, Biological Sciences, Stem Cell Research, Stem Cell Research - Embryonic - Non-Human, Regenerative Medicine, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Alleles, Allelic Imbalance, Cell Differentiation, Cell Lineage, Chromatin, Chromatin Assembly and Disassembly, Embryonic Stem Cells, Enhancer Elements, Genetic, Epigenesis, Genetic, Epigenomics, Gene Regulatory Networks, Humans, Promoter Regions, Genetic, Reproducibility of Results, General Science & Technology
Abstract

Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.

Published
2015

6. A map of the cis-regulatory sequences in the mouse genome

Author

Shen, Yin, Yue, Feng, McCleary, David F, Ye, Zhen, Edsall, Lee, Kuan, Samantha, Wagner, Ulrich, Dixon, Jesse, Lee, Leonard, Lobanenkov, Victor V, and Ren, Bing

Subjects
Genetics, Vaccine Related, Biotechnology, Human Genome, Generic health relevance, Acetylation, Animals, Chromatin, Chromatin Immunoprecipitation, Conserved Sequence, Enhancer Elements, Genetic, Evolution, Molecular, Gene Expression Regulation, Genome, Male, Methylation, Mice, Mice, Inbred C57BL, Molecular Sequence Annotation, Nucleotide Motifs, Organ Specificity, Physical Chromosome Mapping, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Sequence Analysis, DNA, Transcription Factors, General Science & Technology
Abstract

The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 × 10(9) bases of the mouse genome possess a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. So far, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but on its own it cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including humans, Drosophila melanogaster and Caenorhabditis elegans. Here we apply the same experimental approach to a diverse set of 19 tissues and cell types in the mouse to produce a map of nearly 300,000 murine cis-regulatory sequences. The annotated sequences add up to 11% of the mouse genome, and include more than 70% of conserved non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we show that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and for the study of mechanisms regulating tissue-specific gene expression.

Published
2012

9. BORIS, A Novel Male Germ-Line-Specific Protein Associated with Epigenetic Reprogramming Events, Shares the Same 11-Zinc-Finger Domain with CTCF, The Insulator Protein Involved in Reading Imprinting Marks in the Soma

Author

Loukinov, Dmitri I., Pugacheva, Elena, Vatolin, Sergei, Pack, Svetlana D., Moon, Hanlim, Chernukhin, Igor, Mannan, Poonam, Larsson, Erik, Kanduri, Chandrasekhar, Vostrov, Alexander A., Cui, Hengmi, Niemitz, Emily L., Docquier, France M., Kistler, Malathi, Breen, Joseph J., Zhuang, Zhengping, Quitschke, Wolfgang W., Renkawitz, Rainer, Klenova, Elena M., Feinberg, Andrew P., Ohlsson, Rolf, Morse, Herbert C., and Lobanenkov, Victor V.

Published
2002

10. Supplementary Table 7 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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11. Supplementary Table 4 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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12. Supplementary Table 5 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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13. Supplemental Figure Legends 1-9 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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14. Supplementary Table 1 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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15. Supplementary Data from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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16. Supplementary Table 3 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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17. Data from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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18. Supplementary Table 2 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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19. Supplementary Table 6 from BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., primary, Barger, Carter J., primary, Sribenja, Sirinapa, primary, Rosario, Spencer, primary, Albahrani, Mustafa, primary, Truskinovsky, Alexander M., primary, Stablewski, Aimee, primary, Liu, Song, primary, Loukinov, Dmitri I., primary, Zentner, Gabriel E., primary, Lobanenkov, Victor V., primary, Karpf, Adam R., primary, and Higgins, Michael J., primary

Published
2023
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20. Supplementary Figure 2 from Conditional Expression of the CTCF-Paralogous Transcriptional Factor BORIS in Normal Cells Results in Demethylation and Derepression of MAGE-A1 and Reactivation of Other Cancer-Testis Genes

Author

Vatolin, Sergei, primary, Abdullaev, Ziedulla, primary, Pack, Svetlana D., primary, Flanagan, Patrick T., primary, Custer, Mary, primary, Loukinov, Dmitri I., primary, Pugacheva, Elena, primary, Hong, Julie A., primary, Morse, Herbert, primary, Schrump, David S., primary, Risinger, John I., primary, Barrett, J. Carl, primary, and Lobanenkov, Victor V., primary

Published
2023
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21. Supplementary Table 1 and Figure Legends from Conditional Expression of the CTCF-Paralogous Transcriptional Factor BORIS in Normal Cells Results in Demethylation and Derepression of MAGE-A1 and Reactivation of Other Cancer-Testis Genes

Author

Vatolin, Sergei, primary, Abdullaev, Ziedulla, primary, Pack, Svetlana D., primary, Flanagan, Patrick T., primary, Custer, Mary, primary, Loukinov, Dmitri I., primary, Pugacheva, Elena, primary, Hong, Julie A., primary, Morse, Herbert, primary, Schrump, David S., primary, Risinger, John I., primary, Barrett, J. Carl, primary, and Lobanenkov, Victor V., primary

Published
2023
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22. Supplementary Figures 1 and 3 from Conditional Expression of the CTCF-Paralogous Transcriptional Factor BORIS in Normal Cells Results in Demethylation and Derepression of MAGE-A1 and Reactivation of Other Cancer-Testis Genes

Author

Vatolin, Sergei, primary, Abdullaev, Ziedulla, primary, Pack, Svetlana D., primary, Flanagan, Patrick T., primary, Custer, Mary, primary, Loukinov, Dmitri I., primary, Pugacheva, Elena, primary, Hong, Julie A., primary, Morse, Herbert, primary, Schrump, David S., primary, Risinger, John I., primary, Barrett, J. Carl, primary, and Lobanenkov, Victor V., primary

Published
2023
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23. Histone modifications at human enhancers reflect global cell-type-specific gene expression

Author

Heintzman, Nathaniel D., Hon, Gary C., Hawkins, R. David, Kheradpour, Pouya, Stark, Alexander, Harp, Lindsey F., Ye, Zhen, Lee, Leonard K., Stuart, Rhona K., Ching, Christina W., Ching, Keith A., Antosiewicz-Bourget, Jessica E., Zhang, Xinmin, Green, Roland D., LObanenkov, Victor V., Stewart, Ron, Thomson, James A., Crawford, Gregory E., Kellis, Manolis, and Ren, Bing

Subjects
Post-translational modification -- Genetic aspects -- Research -- Physiological aspects -- Usage, DNA microarrays -- Usage -- Research -- Genetic aspects -- Physiological aspects, Gene expression -- Research -- Physiological aspects -- Genetic aspects -- Usage, Histones -- Physiological aspects -- Genetic aspects -- Research -- Usage, Environmental issues, Science and technology, Zoology and wildlife conservation, Physiological aspects, Usage, Research, Genetic aspects
Abstract

The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by [...]

Published
2009

28. BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14

Author

Hillman, Joanna C., primary, Pugacheva, Elena M., additional, Barger, Carter J., additional, Sribenja, Sirinapa, additional, Rosario, Spencer, additional, Albahrani, Mustafa, additional, Truskinovsky, Alexander M., additional, Stablewski, Aimee, additional, Liu, Song, additional, Loukinov, Dmitri I., additional, Zentner, Gabriel E., additional, Lobanenkov, Victor V., additional, Karpf, Adam R., additional, and Higgins, Michael J., additional

Published
2019
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33. Discovering a binary CTCF code with a little help from BORIS.

Author

Lobanenkov, Victor V. and Zentner, Gabriel E.

Subjects
*TRANSCRIPTIONAL repressor CTCF, *CHROMATIN, *DNA-binding proteins, *GENOMES, *EPIGENETICS
Abstract

CCCTC-binding factor (CTCF) is a conserved, essential regulator of chromatin architecture containing a unique array of 11 zinc fingers (ZFs). Gene duplication and sequence divergence during early amniote evolution generated the CTCF paralog Brother Of the Regulator of Imprinted Sites (BORIS), which has a DNA binding specificity identical to that of CTCF but divergent N- and C-termini. While healthy somatic tissues express only CTCF, CTCF and BORIS are normally co-expressed in meiotic and post-meiotic germ cells, and aberrant activation of BORIS occurs in tumors and some cancer cell lines. This has led to a model in which CTCF and BORIS compete for binding to some but not all genomic target sites; however, regulation of CTCF and BORIS genomic co-occupancy is not well understood. We recently addressed this issue, finding evidence for two major classes of CTCF target sequences, some of which contain single CTCF target sites (1xCTSes) and others containing two adjacent CTCF motifs (2xCTSes). The functional and chromatin structural features of 2xCTSes are distinct from those of 1xCTS-containing regions bound by a CTCF monomer. We suggest that these previously overlooked classes of CTCF binding regions may have different roles in regulating diverse chromatin-based phenomena, and may impact our understanding of heritable epigenetic regulation in cancer cells and normal germ cells. [ABSTRACT FROM AUTHOR]

Published
2018
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34. CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

Author

Kemp, Christopher J., primary, Moore, James M., additional, Moser, Russell, additional, Bernard, Brady, additional, Teater, Matt, additional, Smith, Leslie E., additional, Rabaia, Natalia A., additional, Gurley, Kay E., additional, Guinney, Justin, additional, Busch, Stephanie E., additional, Shaknovich, Rita, additional, Lobanenkov, Victor V., additional, Liggitt, Denny, additional, Shmulevich, Ilya, additional, Melnick, Ari, additional, and Filippova, Galina N., additional

Published
2014
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35. Histone Modifications at Human Enhancers Reflect Global Cell-Type-Specific Gene Expression

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Kellis, Manolis, Kheradpour, Pouya, Stark, Alexander, Heintzman, Nathaniel D., Hon, Gary C., Hawkins, R. David, Harp, Lindsey F., Ye, Zhen, Lee, Leonard K., Stuart, Rhona K., Ching, Christina W., Ching, Keith A., Antosiewicz-Bourget, Jessica E., Liu, Hui, Zhang, Xinmin, Green, Roland D., Lobanenkov, Victor V., Stewart, Ron, Thomson, James A., Crawford, Gregory E., Ren, Bing, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Kellis, Manolis, Kheradpour, Pouya, Stark, Alexander, Heintzman, Nathaniel D., Hon, Gary C., Hawkins, R. David, Harp, Lindsey F., Ye, Zhen, Lee, Leonard K., Stuart, Rhona K., Ching, Christina W., Ching, Keith A., Antosiewicz-Bourget, Jessica E., Liu, Hui, Zhang, Xinmin, Green, Roland D., Lobanenkov, Victor V., Stewart, Ron, Thomson, James A., Crawford, Gregory E., and Ren, Bing

Abstract

The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene1, 2, 3, the relative roles of these regulatory elements in this process are not clear. We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators in the human genome4, 5, 6. Here we use the same approach to identify these elements in multiple cell types and investigate their roles in cell-type-specific gene expression. We observed that the chromatin state at promoters and CTCF-binding at insulators is largely invariant across diverse cell types. In contrast, enhancers are marked with highly cell-type-specific histone modification patterns, strongly correlate to cell-type-specific gene expression programs on a global scale, and are functionally active in a cell-type-specific manner. Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.

Published
2012

36. A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and exhibits sequential epigenetic defects during Wilms' tumourigenesis

Author

Hancock, Anne L, Brown, Keith W, Moorwood, Kim, Moon, Hanlim, Holmgren, Claes, Mardikar, Sudhanshu H, Dallosso, Anthony R, Klenova, Elena, Loukinov, Dmitri, Ohlsson, Rolf, Lobanenkov, Victor V, Malik, Karim, Hancock, Anne L, Brown, Keith W, Moorwood, Kim, Moon, Hanlim, Holmgren, Claes, Mardikar, Sudhanshu H, Dallosso, Anthony R, Klenova, Elena, Loukinov, Dmitri, Ohlsson, Rolf, Lobanenkov, Victor V, and Malik, Karim

Abstract

We have shown previously that AWT1 and WT1-AS are functionally imprinted in human kidney. In the adult kidney, expression of both transcripts is restricted to the paternal allele, with the silent maternal allele retaining methylation at the WT1 antisense regulatory region (WT1 ARR). Here, we report characterization of the WT1 ARR differentially methylated region and show that it contains a transcriptional silencer element acting on both the AWT1 and WT1-AS promoters. DNA methylation of the silencer results in increased transcriptional repression, and the silencer is also shown to be an in vitro and in vivo target site for the imprinting regulator protein CTCF. Binding of CTCF is methylation-sensitive and limited to the unmethylated silencer. Potentiation of the silencer activity is demonstrated after CTCF protein is knocked down, suggesting a novel silencer-blocking activity for CTCF. We also report assessment of WT1 ARR methylation in developmental and tumour tissues, including the first analysis of Wilms' tumour precursor lesions, nephrogenic rests. Nephrogenic rests show increases in methylation levels relative to foetal kidney and reductions relative to the adult kidney, together with biallelic expression of AWT1 and WT1-AS. Notably, the methylation status of CpG residues within the CTCF target site appears to distinguish monoallelic and biallelic expression states. Our data suggest that failure of methylation spreading at the WT1 ARR early in renal development, followed by imprint erasure, occurs during Wilms' tumourigenesis. We propose a model wherein imprinting defects at chromosome 11p13 may contribute to Wilms' tumourigenesis.

Published
2007
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39. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

Author

Hawkins, R David, primary, Hon, Gary C, additional, Yang, Chuhu, additional, Antosiewicz-Bourget, Jessica E, additional, Lee, Leonard K, additional, Ngo, Que-Minh, additional, Klugman, Sarit, additional, Ching, Keith A, additional, Edsall, Lee E, additional, Ye, Zhen, additional, Kuan, Samantha, additional, Yu, Pengzhi, additional, Liu, Hui, additional, Zhang, Xinmin, additional, Green, Roland D, additional, Lobanenkov, Victor V, additional, Stewart, Ron, additional, Thomson, James A, additional, and Ren, Bing, additional

Published
2011
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41. BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma.

Author

Loukinov, Dmitri I, Pugacheva, Elena, Vatolin, Sergei, Pack, Svetlana D, Moon, Hanlim, Chernukhin, Igor, Mannan, Poonam, Larsson, Erik, Kanduri, Chandrasekhar, Vostrov, Alexander A, Cui, Hengmi, Niemitz, Emily L, Rasko, John E J, Docquier, France M, Kistler, Malathi, Breen, Joseph J, Zhuang, Zhengping, Quitschke, Wolfgang W, Renkawitz, Rainer, Klenova, Elena M, Feinberg, Andrew P, Ohlsson, Rolf, Morse, Herbert C, Lobanenkov, Victor V, Loukinov, Dmitri I, Pugacheva, Elena, Vatolin, Sergei, Pack, Svetlana D, Moon, Hanlim, Chernukhin, Igor, Mannan, Poonam, Larsson, Erik, Kanduri, Chandrasekhar, Vostrov, Alexander A, Cui, Hengmi, Niemitz, Emily L, Rasko, John E J, Docquier, France M, Kistler, Malathi, Breen, Joseph J, Zhuang, Zhengping, Quitschke, Wolfgang W, Renkawitz, Rainer, Klenova, Elena M, Feinberg, Andrew P, Ohlsson, Rolf, Morse, Herbert C, and Lobanenkov, Victor V

Published
2002

43. Interspecies Comparative Genomic Hybridization (I-CGH): A New Twist to Study Animal Tumor Models

Author

Jaikumar, Sivakumar, primary, Zhuang, Zhengping, additional, Mannan, Poonam, additional, Vortmeyer, Alexander O., additional, Furuta, Makoto, additional, Dickerman, Rob, additional, Bedanova, Julia, additional, Lonser, Russell R., additional, Walbridge, Stuart, additional, Weil, Robert J., additional, Lobanenkov, Victor V., additional, Oldfield, Edward H., additional, and Pack, Svetlana D., additional

Published
2007
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45. Elicitation of T Cell Responses to Histologically Unrelated Tumors by Immunization with the Novel Cancer-Testis Antigen, Brother of the Regulator of Imprinted Sites

Author

Ghochikyan, Anahit, primary, Mkrtichyan, Mikayel, additional, Loukinov, Dmitri, additional, Mamikonyan, Gregory, additional, Pack, Svetlana D., additional, Movsesyan, Nina, additional, Ichim, Thomas E., additional, Cribbs, David H., additional, Lobanenkov, Victor V., additional, and Agadjanyan, Michael G., additional

Published
2007
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46. Cloning and characterization of zebrafish CTCF: Developmental expression patterns, regulation of the promoter region, and evolutionary aspects of gene organization

Author

Pugacheva, Elena M., primary, Kwon, Yoo-Wook, additional, Hukriede, Neil A., additional, Pack, Svetlana, additional, Flanagan, Patrick T., additional, Ahn, Jong-Chan, additional, Park, Jeong Ae, additional, Choi, Kyu-Sil, additional, Kim, Kyu-Won, additional, Loukinov, Dmitri, additional, Dawid, Igor B., additional, and Lobanenkov, Victor V., additional

Published
2006
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48. Rasgrf1 Imprinting Is Regulated by a CTCF-Dependent Methylation-Sensitive Enhancer Blocker

Author

Yoon, Bongjune, primary, Herman, Herry, additional, Hu, Benjamin, additional, Park, Yoon Jung, additional, Lindroth, Anders, additional, Bell, Adam, additional, West, Adam G., additional, Chang, Yanjie, additional, Stablewski, Aimee, additional, Piel, Jessica C., additional, Loukinov, Dmitri I., additional, Lobanenkov, Victor V., additional, and Soloway, Paul D., additional

Published
2005
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49. Reciprocal Binding of CTCF and BORIS to the NY-ESO-1 Promoter Coincides with Derepression of this Cancer-Testis Gene in Lung Cancer Cells

Author

Hong, Julie A., primary, Kang, Yang, additional, Abdullaev, Ziedulla, additional, Flanagan, Patrick T., additional, Pack, Svetlana D., additional, Fischette, Maria R., additional, Adnani, Mina T., additional, Loukinov, Dmitri I., additional, Vatolin, Sergei, additional, Risinger, John I., additional, Custer, Mary, additional, Chen, G. Aaron, additional, Zhao, Ming, additional, Nguyen, Dao M., additional, Barrett, J. Carl, additional, Lobanenkov, Victor V., additional, and Schrump, David S., additional

Published
2005
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50. Conditional Expression of the CTCF-Paralogous Transcriptional Factor BORIS in Normal Cells Results in Demethylation and Derepression of MAGE-A1 and Reactivation of Other Cancer-Testis Genes

Author

Vatolin, Sergei, primary, Abdullaev, Ziedulla, additional, Pack, Svetlana D., additional, Flanagan, Patrick T., additional, Custer, Mary, additional, Loukinov, Dmitri I., additional, Pugacheva, Elena, additional, Hong, Julie A., additional, Morse, Herbert, additional, Schrump, David S., additional, Risinger, John I., additional, Barrett, J. Carl, additional, and Lobanenkov, Victor V., additional

Published
2005
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