Zinc Finger Proteins and the 3D Organization of Chromosomes

Feinauer, Christoph; Hofmann, Andreas; Goldt, Sebastian; Liu, Lei; Máté, Gabriell; Heermann, Dieter W.

doi:10.1016/b978-0-12-410523-2.00003-1

Cited by 11 publications

(12 citation statements)

References 59 publications

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“…CTCF has a DNA binding motif consisting of eleven zinc finger domains, recognizing tens of thousands DNA sites across the mammalian genome16. Binding of CTCF to DNA has been shown to contribute to the formation of three-dimensional DNA loops, mediating long-range chromatin interactions between different regulatory sequences in somatic cells1517.…”

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confidence: 99%

CTCF contributes in a critical way to spermatogenesis and male fertility

Hernández‐Hernández

Lilienthal

Fukuda

et al. 2016

Sci Rep

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The CCCTC-binding factor (CTCF) is an architectural protein that governs chromatin organization and gene expression in somatic cells. Here, we show that CTCF regulates chromatin compaction necessary for packaging of the paternal genome into mature sperm. Inactivation of Ctcf in male germ cells in mice (Ctcf-cKO mice) resulted in impaired spermiogenesis and infertility. Residual spermatozoa in Ctcf-cKO mice displayed abnormal head morphology, aberrant chromatin compaction, impaired protamine 1 incorporation into chromatin and accelerated histone depletion. Thus, CTCF regulates chromatin organization during spermiogenesis, contributing to the functional organization of mature sperm.

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mentioning

confidence: 99%

CTCF contributes in a critical way to spermatogenesis and male fertility

Hernández‐Hernández

Lilienthal

Fukuda

et al. 2016

Sci Rep

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“…In the case of SP1, the head may interact with nucleotides between positions −11 and −1. The behavior for EGR1 is more elusive because HOMO and LUMO are completely dispersed over the nucleotides [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]. Despite the description emphasizing the similarity between the ZF and nucleotide interaction in the literature over the consensus nucleotides [5], the mechanisms of protein attachment in EGR 1 and SP1 are not the same [67,68].…”

Section: ) the Orange Lines In Figures 3cd And The Red Lines Inmentioning

confidence: 82%

“…These ZF proteins could mediate long-range chromosomal interactions in eukaryotic cells, >100 thousand base pair (bp) [7][8][9][10]. However, the exact relation between the long-ranged correlation in genomic scale nucleotide sequences (>20 thousand bp) and the chromosomal three-dimensional organization is still not clear [10][11][12][13][14][15] and subject to intense research. Furthermore, since transcription factors spot specific sequences without the opening of the double helix, we expect some biological mechanism for probing nucleotide based on local properties [16].…”

Section: Introductionmentioning

confidence: 99%

“…They are responsible for the genome special structure in the DNA loops too, exposing or hiding the genes, and work as an insulator, avoiding the spread of heterochromatin [6]. These ZF proteins could mediate long-range chromosomal interactions in eukaryotic cells, >100 thousand base pair (bp) [7][8][9][10]. However, the exact relation between the long-ranged correlation in genomic scale nucleotide sequences (>20 thousand bp) and the chromosomal three-dimensional organization is still not clear [10][11][12][13][14][15] and subject to intense research.…”

Section: Introductionmentioning

confidence: 99%

“…The most common polymeric description considers DNA as a single one-dimensional strand, explaining the DNA denaturation semi-analytically [17][18][19]. The literature also report the mechanical properties of chromosomal fibers and the long-range nucleotide interaction due to DNA loops, histones and zinc finger proteins, using Monte Carlo simulation [10,[20][21][22]. Since electrons play a crucial role in the DNA-protein interaction, we must consider the DNA from the electric charge distribution too.…”

Section: Introductionmentioning

confidence: 99%

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The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model

2016

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Instead of ATCG letter alignments, typically used in bioinformatics, we propose a new alignment method using the probability distribution function of the bottom of the occupied molecular orbital (BOMO), highest occupied molecular orbital (HOMO), and lowest unoccupied orbital (LUMO). We apply the technique to transcription factors with Cys 2 His 2 zinc fingers. These transcription factors search for binding sites, probing for the electronic patterns at the minor and major DNA groves. The eukaryotic Cys 2 His 2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains. They are responsible for gene regulation and the spatial organization of DNA. To study and understand these zinc finger DNA-protein interactions, we use the extended ladder in the DNA model proposed by Zhu et al. [1]. Considering one single spinless electron in each nucleotide π -orbital along a double DNA chain (dDNA), we find a typical pattern for the bottom of BOMO, HOMO, and LUMO along the binding sites. We specifically looked at two members of zinc finger protein family: specificity protein 1 (SP1) and early grown response 1 transcription factors (EGR1). When the valence band is filled, we find electrons in the purines along the nucleotide sequence, compatible with the electric charges of the binding amino acids in SP1 and EGR1 zinc finger.

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