Identification, genome mapping, and CTCF binding of potential insulators within the FXYD5-COX7A1 locus of human Chromosome 19q13.12

Akopov, S. B.; Ruda, Vera M.; Batrak, Vera; Ветчинова, А. С.; Чернов, И. П.; Николаев, Л. Г.; Bode, Jürgen

doi:10.1007/s00335-006-0037-3

Cited by 14 publications

(21 citation statements)

References 40 publications

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“…This repeat serves as a boundary to block the influence of repressive chromatin modifications by generating short transcripts, which are necessary and sufficient to enable gene activation [134]. Mammalian LINE elements are frequently found within matrix attachment regions (MARs) [135,136]. Some Drosophila LTR retrotransposons have insulator activity and may block the activity of transcriptional enhancer elements when located between enhancer and promoter [137][138][139].…”

Section: Res As Insulator Elementsmentioning

confidence: 99%

Retroelements and their impact on genome evolution and functioning

Gogvadze

Buzdin

2009

Cell. Mol. Life Sci.

113

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Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.

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Section: Res As Insulator Elementsmentioning

confidence: 99%

Retroelements and their impact on genome evolution and functioning

Gogvadze

Buzdin

2009

Cell. Mol. Life Sci.

113

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“…Within this gene-rich human chromosome 19 region, we previously identified insulator-like sequences (24), CTCF transcription-factor binding sites (25), and nuclear matrix attachment regions (S/MARs) (18). These and other available data on human promoters (7) and transcribed sequences (26) make this locus one of the best characterized human genome regions regarding cis -regulatory elements.…”

Section: Discussionmentioning

confidence: 98%

A New Technique for Selective Identification and Mapping of Enhancers Within Long Genomic Sequences

Чернов

Stukacheva²,

Akopov³

et al. 2008

BioTechniques

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We report a new experimental method of direct selection, identification, and mapping of potential enhancer sequences within extended stretches of genomic DNA. The method allows simultaneous cloning of a quantity of sequences instead of tedious screening of the separate ones, thus providing a robust and high-throughput approach to the mapping of enhancers. The selection procedure is based on the ability of such sequences to activate a minimal promoter that drives expression of a selective gene. To this end a mixture of short DNA fragments derived from the segment of interest was cloned in a retroviral vector containing the neomycin phosphotransferase II gene under control of a cytomegalovirus (CMV) minimal promoter. The pool of retroviruses obtained was used to infect HeLa cells and then to select neomycin-resistant colonies containing constructs with enhancer-like sequences. The pool of the genomic fragments was rescued by PCR and cloned, forming a library of the potential enhancers. Fifteen enhancer-like fragments were selected from 1-Mb human genome locus, and enhancer activity of 13 of them was verified in a transient transfection reporter gene assay. The sequences selected were found to be predominantly located near 5' regions of genes or within gene introns.

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“…We have developed a function-based approach for direct selection of insulators from mixtures of genomic fragments [38] (Fig. 1).…”

Section: Iic) Mapping Of Loop-domain Chromatin Structure Elements -S/mentioning

confidence: 99%

“…(1). General scheme of selection and mapping of insulator sequences [38]. PGK-pr -the human phospho-glycerate kinase promoter, Neo R -the neomycin phosphotransferase gene, CMV-Enh -the cytomegalovirus enhancer, CMV-mPr -a cytomegalovirus minimal promoter, HSV-tk -the herpes simplex virus thymidine kinase gene.…”

Section: Iie) Protein Binding Sitesmentioning

confidence: 99%

“…A draft integrated map of a 160-kb human genome locus containing nine identified genes. Indicated are positions of protein target sites [51], putative insulators [38], nuclear matrix attachment regions (S/MARs) [33], open and closed chromatin regions as revealed by accessibility to Dam methylase [78], and CpG unmethylated sites [69; 71]. The map was prepared with the use of the Human Genome Browser at UCSC [92].…”

Section: V) Conclusionmentioning

confidence: 99%

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Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping

Николаев

Akopov²,

Чернов³

2007

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Abstract:The availability of complete human and other metazoan genome sequences has greatly facilitated positioning and analysis of various genomic functional elements, with initial emphasis on coding sequences. However, complete functional maps of sequenced eukaryotic genomes should include also positions of all non-coding regulatory elements. Unfortunately, experimental data on genomic positions of a multitude of regulatory sequences, such as enhancers, silencers, insulators, transcription terminators, and replication origins are very limited, especially at the whole genome level. Since most genomic regulatory elements (e.g. enhancers) are generally gene-, tissue-, or cell-specific, the prediction of these elements by computational methods is difficult and often ambiguous. Therefore, the development of high-throughput experimental approaches for identifying and mapping genomic functional elements is highly desirable. At the same time, the creation of whole-genome map of hundreds of thousands of regulatory elements in several hundreds of tissue/cell types is presently far beyond our capabilities. A possible alternative for the whole genome approach is to concentrate efforts on individual genomic segments and then to integrate the data obtained into a whole genome functional map. Moreover, the maps of polygenic fragments with functional cis-regulatory elements would provide valuable data on complex regulatory systems, including their variability and evolution. Here, we reviewed experimental approaches to the realization of these ideas, including our own developments of experimental techniques for selection of cis-acting functionally active DNA fragments from large (megabase-sized) segments of mammalian genomes.

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Identification, genome mapping, and CTCF binding of potential insulators within the FXYD5-COX7A1 locus of human Chromosome 19q13.12

Cited by 14 publications

References 40 publications

Retroelements and their impact on genome evolution and functioning

Retroelements and their impact on genome evolution and functioning

A New Technique for Selective Identification and Mapping of Enhancers Within Long Genomic Sequences

Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping

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