Structural Basis for SRY-dependent 46-X,Y Sex Reversal: Modulation of DNA Bending by a Naturally Occurring Point Mutation

Murphy, Elizabeth C.; Zhurkin, Victor B.; Louis, John M.; Cornilescu, Gabriel; Clore, G. Marius

doi:10.1006/jmbi.2001.4977

Cited by 135 publications

(300 citation statements)

References 87 publications

(131 reference statements)

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“…We have shown that chick FNP extracts interacting with the Sox binding site in DNase I footprinting assays create a prominent hypersensitive site. Such hypersensitive sites often result from protein-DNA interactions that dramatically alter the structure of DNA, as when Sox factors introduce significant bends into DNA (van Houte et al, 1995;Werner et al, 1995;Murphy et al, 2001). Additionally, several Sox family members, including Sox6, can bind to the enhancer in EMSAs, and we have shown that Sox6 is present in mouse head extracts and can interact with the enhancer.…”

Section: Sox Proteins Interact With the Tcfap2a Enhancer Elementmentioning

confidence: 72%

Frontal nasal prominence expression driven by Tcfap2a relies on a conserved binding site for STAT proteins

Donner

Williams

2006

Developmental Dynamics

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The AP-2 transcription factor family is linked with development of the head and limbs in both vertebrate and invertebrate species. Recent evidence has also implicated this gene family in the evolution of the neural crest in chordates, a critical step that allowed the development and elaboration of the vertebrate craniofacial skeleton. In mice, the inappropriate embryonic expression of one particular AP-2 gene, Tcfap2a, encoding AP-2␣, results in multiple developmental abnormalities, including craniofacial and limb defects. Thus, Tcfap2a provides a valuable genetic resource to analyze the regulatory hierarchy responsible for the evolution and development of the face and limbs. Previous studies have identified a 2-kilobase intronic region of both the mouse and human AP-2␣ locus that directs expression of a linked LacZ transgene to the facial processes and the distal mesenchyme of the limb bud in transgenic mice. Further analysis identified two highly conserved regions of ϳ200 -400 bp within this tissue-specific enhancer. We have now initiated a transgenic and biochemical analysis of the most important of these highly conserved regions. Our analysis indicates that although the sequences regulating face and limb expression have been integrated into a single enhancer, different cis-acting sequences ultimately control these two expression domains. Moreover, these studies demonstrate that a conserved STAT binding site provides a major contribution to the expression of Tcfap2a in the facial prominences. Developmental Dynamics 235: 1358 -1370, 2006.

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Section: Sox Proteins Interact With the Tcfap2a Enhancer Elementmentioning

confidence: 72%

Frontal nasal prominence expression driven by Tcfap2a relies on a conserved binding site for STAT proteins

Donner

Williams

2006

Developmental Dynamics

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“…The Fe(II)-CO WT and Fe(II)-CO H103G structure ensembles were refined with NMR-derived geometric restraints (37). An equivalent number of restraints of similar types (e.g., NOEs, RDCs, etc.)…”

Section: Discussionmentioning

confidence: 99%

A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation

Erbil¹,

Price

Wemmer

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

112

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“…Base pair hydrogen bond distance restraints were employed as in ref 13. Base pair planarity restraints were used to prevent undue buckling while allowing propeller twisting to occur (13,46). Two multidimensional knowledge-based potentials of mean force were employed.…”

Section: Methods and Theorymentioning

confidence: 99%

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

2007

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The structure and dynamics of the Dickerson DNA dodecamer [5′d(CGCGAATTCGCG) 2 ] in solution have been investigated by joint simulated annealing refinement against NMR and large-angle X-ray scattering data (extending from 0.25 to 3 Å -1 ). The NMR data comprise an extensive set of heteroand homonuclear residual dipolar coupling and 31 P chemical shift anisotropy restraints in two alignment media, supplemented by NOE and 3 J coupling data. The NMR and X-ray scattering data cannot be fully ascribed to a single structure representation, indicating the presence of anisotropic motions that impact the experimental observables in different ways. Refinement with ensemble sizes (N e ) of g2 to represent the atomic motions reconciles all the experimental data within measurement error. Cross validation against both the dipolar coupling and X-ray scattering data suggests that the optimal ensemble size required to account for the current data is 4. The resulting ensembles permit one to obtain a detailed view of the conformational space sampled by the dodecamer in solution and permit one to analyze fluctuations in helicoidal parameters, sugar puckers, and BI-BII backbone transitions and to obtain quantitative metrics of atomic motion such as generalized order parameters and thermal B factors. The calculated order parameters are in good agreement with experimental order parameters obtained from 13 C relaxation measurements. Although DNA behaves as a relatively rigid rod with a persistence length of ∼150 bp, dynamic conformational heterogeneity at the base pair level is functionally important since it readily permits optimization of intermolecular protein-DNA interactions.

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Structural Basis for SRY-dependent 46-X,Y Sex Reversal: Modulation of DNA Bending by a Naturally Occurring Point Mutation

Cited by 135 publications

References 87 publications

Frontal nasal prominence expression driven by Tcfap2a relies on a conserved binding site for STAT proteins

Frontal nasal prominence expression driven by Tcfap2a relies on a conserved binding site for STAT proteins

A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

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