3D genomics imposes evolution of the domain model of eukaryotic genome organization

Razin, Sergey V.; Vassetzky, Yegor S.

doi:10.1007/s00412-016-0604-7

Cited by 14 publications

(9 citation statements)

References 152 publications

(190 reference statements)

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“…Interestingly, both kinases and helicases were identified among barley TBPs (Bielskiene et al, 2012). The formation of tight complexes by GQs in the regulatory regions of genes can contribute to the maintenance of the 3D network which is believed to be the form of genome folding (Razin & Vassetzky, 2017;Razin & Gavrilov, 2018). GQs could also determine the high affinity of DNA isolated from complexes with TBPs to proteins, as complexes can be reconstituted in vitro (Bielskiene et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

“…The traditional concept of chromatin domains attached to the nuclear matrix is being revisited. The nucleus is described as a set of topologically associating domains, and DNA-protein interactions develop within these domains (Razin & Vassetzky, 2017;Razin & Ulianov, 2017;Razin, Iarovaia & Vassetzky, 2014). The very existence of the nuclear matrix and specific matrixattachment regions in DNA is denied (Hancock, 2004;Hancock, 2014;Razin, Iarovaia & Vassetzky, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences

Sjakste

Ļeonova

Petrovs

et al. 2020

PeerJ

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Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. Discussion The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences

Sjakste

Ļeonova

Petrovs

et al. 2020

PeerJ

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“…In addition, our understanding of the levels of DNA packaging has undergone significant changes. With the emergence of 3D genomics it became possible to revisit some long-standing models, such as the domain model of eukaryotic genome organization [ 55 ]. Analysis of interaction frequencies of the remote genomic elements allowed to identify self-interacting chromatin domains,TADs [ 39 ] which appear to represent structural-functional domains of eukaryotic genome [ 71 , 127 ].…”

Section: Discussionmentioning

confidence: 99%

“…The question of whether structural organization of the genome coincides with its functional organization has been debated in the literature over many years (for a review, see [ 55 ]). The problem is difficult to solve because both functional and structural domains of the genome still lack a clear definition.…”

Section: Tads Are Structural and Functional Domains Of The Genomementioning

confidence: 99%

Gene functioning and storage within a folded genome

Razin

Ulianov

2017

Cell Mol Biol Lett

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In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity. For many years the hierarchical model of DNA folding was the most popular. It was assumed that nucleosome fiber (10-nm fiber) is folded into 30-nm fiber and further on into chromatin loops attached to a nuclear/chromosome scaffold. Recent studies have demonstrated that there is much less regularity in chromatin folding within the cell nucleus. The very existence of 30-nm chromatin fibers in living cells was questioned. On the other hand, it was found that chromosomes are partitioned into self-interacting spatial domains that restrict the area of enhancers action. Thus, TADs can be considered as structural-functional domains of the chromosomes. Here we discuss the modern view of DNA packaging within the cell nucleus in relation to the regulation of gene expression. Special attention is paid to the possible mechanisms of the chromatin fiber self-assembly into TADs. We discuss the model postulating that partitioning of the chromosome into TADs is determined by the distribution of active and inactive chromatin segments along the chromosome.This article was specially invited by the editors and represents work by leading researchers.

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“…Nucleus is divided into transcriptionally active and repressive compartments (reviewed in [1]). Transcriptional activation is associated with the euchromatic regions of the nucleus and transcriptional factories (reviewed in [2]).…”

Section: Introdutionmentioning

confidence: 99%

Intranuclear localization of transcription factories and immunoglobulin heavy chain gene alleles during human B-cell maturation

et al. 2016

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Immunoglobulin heavy chain (IGH) gene locus is expressed monoallelically in human B cells. Aim. To study the role of nuclear organization in regulation of the IGH expression during B-cell differentiation. Methods. Immunofluorescence in situ hybridization on 3D-preserved nuclei (3D immuno-FISH). Results. Active RNA polymerase II (Pol II) molecules and the IGH locus were detected in the periphery of the nucleoli at some stages of B-cell differentiation. Conclusions. We observed significant changes in the pattern of distribution of RNA polymerase II in the nucleus during B-cell differentiation, but no preferential co-localization of the productive IGH allele with the transcription factories in the vicinity of the nucleolus and in the nucleoplasm was observed. K e y w o r d s: Immunoglobulin heavy chain gene, transcription, nucleolus, B-cell maturation IntrodutionNucleus is divided into transcriptionally active and repressive compartments (reviewed in [1]). Transcriptional activation is associated with the euchromatic regions of the nucleus and transcriptional factories (reviewed in [2]). A functional immunoglobulin heavy chain is produced monoallelically (Rajewsky 1996); it undergoes regulated transcription during the B lymphocyte development. Transcription might be controlled by localized al-terations in the chromatin structure. Whether such a mechanism is sufficient to account for the allele-specific transcription of the IGH locus is currently unknown. In mice, the localization of productive and non-productive IGH alleles changes during B-cell maturation. A non-productive IGH allele is located close to the nuclear periphery whereas the productive IGH allele is associated with euchromatin [5-7]; much less is known about the role of nuclear organization in the human IGH allelic transcription. We have recently found that the IGH locus was located

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3D genomics imposes evolution of the domain model of eukaryotic genome organization

Cited by 14 publications

References 152 publications

Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences

Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences

Gene functioning and storage within a folded genome

Intranuclear localization of transcription factories and immunoglobulin heavy chain gene alleles during human B-cell maturation

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