Enhancers promote transcription by providing a binding platform for transcription factors [ 12 ] that can act on (distal) target genes through three-dimensional chromatin looping [ 13 - 15 ]. (biomedcentral.com)
Hybrids2
We used the hyperthermophilic crenarchaeon Sulfolobus solfataricus as a model archaeal species to investigate the formation of RNA:DNA hybrids. (wsu.edu)
Our molecular characterization of RNA:DNA hybrids in S. solfataricus indicates they are strongly associated with transcriptionally active regions and likely represent R-loop structures. (wsu.edu)
Genome3
Transcriptionally active regions of the genome are particularly susceptible to DNA damage through the production of R-loop regions, consisting of an RNA:DNA hybrid along with a displaced ssDNA non-template strand, which is particularly susceptible to damage. (wsu.edu)
Additionally, variation of production and persistence of these R-loops in strain backgrounds with differential DNA damage responses implicates DSB repair processes in maintaining genome stability during transcriptional activities in S. solfataricus. (wsu.edu)
R-loop formation has to be strictly regulated by the cell to ensure genome integrity, for example, the exposed ssDNA on R-loops is more vulnerable to breakage, deamination, and nuclease cleavage, resulting in DNA damage, mutations, and chromosome rearrangements ( Constantino and Koshland 2015 ). (bioradiations.com)
Complexes2
SUMMARY: Recent studies suggest that the loop extrusion activity of StructuralMaintenance of Chromosomes complexes is central to proper organization of genomesin vivo. (ens-lyon.fr)
The crystal structures reveal important differences in the conformations of the CDR-H2 loops in the complexes that propagate into other regions of the antigen-antibody interface, and suggest that both neutralization properties and affinity for the target can be attributed, at least in part, to the differences in the interactions of the CDR-H2 loops with the antigen. (nih.gov)
Vivo1
Immunostaining of mouse mammary epithelium was performed to quantify R-loops and DNA damage in vivo . (nih.gov)
Molecular1
Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. (biomedcentral.com)
Strand5
A ) Addition of crude extract to λ-phage DNA molecules leads to the generation of multiple highly-enriched DNA clusters, suggestive of nucleosomal formation along the strand. (elifesciences.org)
Kymographs of nucleosomal cluster formation in both metaphase (upper) and interphase (lower) along a strand upon addition of crude extract. (elifesciences.org)
C ) Examples of completely stretched loops in metaphase (left and middle) and a partially extended interphase loop (right) upon hydrodynamic stretching with buffer flow perpendicular to strand orientation. (elifesciences.org)
D ) Kymograph of a looping event on a strand upon treatment with crude extract. (elifesciences.org)
R-loops are cellular three-stranded nucleic acid structures comprised of a DNA:RNA hybrid and a displaced DNA strand. (bioradiations.com)
Structures2
Based on their importance, it is no surprise that dysregulation of R-loop structures is associated with several human diseases, including neurodegenerative syndromes and cancer ( Groh and Gromak 2014 ). (bioradiations.com)
Additional data support the conflicting nature of R loops - they can be detrimental structures, which when uncontrolled result in disease, but they can also have a positive effect by regulating essential cellular processes. (bioradiations.com)
Interactions1
Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. (biomedcentral.com)
Addition1
Kymograph of DNA signal over time displaying a looping event upon addition of H3-H4-depleted extract (middle). (elifesciences.org)
Search1
The required capabilities for Darwin's first goal -- the search for and subsequent characterization of earth-like planets orbiting nearby stars -- are such that for its second goal -- high resolution astrophysical imaging -- the sensitivity will be similar to JWST and the angular resolution 1-2 orders better. (spie.org)
Active1
iii ) Side and top view schematics visualizing how soluble active loop-extruding factors extrude loops in H3-H4-depleted extract. (elifesciences.org)
Simulation1
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. (ens-lyon.fr)
Lower2
R-loops at concentrations 10-fold lower than those required for transactivation. (nih.gov)
B ) Dynamics of the formation of DNA loops induced by H3-H4-depleted extract in metaphase (upper) and interphase (lower). (elifesciences.org)
Damage1
R-loops and DNA damage were also detected in mammary epithelial cells of mice treated with BP-3 and PP. (nih.gov)
Study1
In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. (biomedcentral.com)
Human1
In previous studies we reported a series of broadly neutralizing mini-antibodies derived from a synthetic naïve human combinatorial antibody library by panning against a mimetic of the trimeric N-HR coiled coil, followed by affinity maturation using targeted diversification of the CDR-H2 loop. (nih.gov)