scholarly journals CRISPR-Cas-mediated tethering recruits the yeast HMR mating-type locus to the nuclear periphery but fails to silence gene expression

2021 ◽  
Author(s):  
Emily R Cliff ◽  
Robin L Kirkpatrick ◽  
Daniel Cunningham-Bryant ◽  
Brianna Fernandez ◽  
Jesse G Zalatan
Keyword(s):  
Gene Expression ◽  
Genome Structure ◽  
Nuclear Periphery ◽  
Model Systems ◽  
Type Locus ◽  
Synthetic Genome ◽  
Structural Differences ◽  
And Function ◽  
The Relationship ◽  
Silence Gene

To investigate the relationship between genome structure and function, we have developed a programmable CRISPR-Cas system for nuclear peripheral recruitment in yeast. We benchmarked this system at the HMR and GAL2 loci, both well-characterized model systems for localization to the nuclear periphery. Using microscopy and gene silencing assays, we demonstrate that CRISPR-Cas-mediated tethering can recruit the HMR locus but does not silence reporter gene expression. A previously reported Gal4-mediated tethering system does silence gene expression, and we demonstrate that the silencing phenotype has an unexpected dependence on the structure of the protein tether. The CRISPR-Cas system was unable to recruit GAL2 to the nuclear periphery. Our results reveal potential challenges for synthetic genome structure perturbations and suggest that distinct functional effects can arise from subtle structural differences in how genes are recruited to the periphery.

scholarly journals CRISPR-Cas-Mediated Tethering Recruits the Yeast HMR Mating-Type Locus to the Nuclear Periphery but Fails to Silence Gene Expression

2021 ◽  
Author(s):  
Emily R. Cliff ◽  
Robin L. Kirkpatrick ◽  
Daniel Cunningham-Bryant ◽  
Brianna Fernandez ◽  
Joseph L. Harman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mating Type ◽  
Nuclear Periphery ◽  
Type Locus ◽  
Mating Type Locus ◽  
Silence Gene

Skeletal muscle bioenergetic health and function in people living with HIV: association with glucose tolerance and alcohol use

2021 ◽  
Author(s):  
Danielle E. Levitt ◽  
Tekeda F Ferguson ◽  
Stefany DePrato Primeaux ◽  
Jeanette A Zavala ◽  
Jameel Ahmed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alcohol Use ◽  
Glucose Tolerance ◽  
Mitochondrial Gene ◽  
Proton Leak ◽  
Mitochondrial Gene Expression ◽  
Mitochondrial Volume ◽  
And Function ◽  
The Relationship

At-risk alcohol use is prevalent and increases dysglycemia among people living with human immunodeficiency virus (PLWH). Skeletal muscle (SKM) bioenergetic dysregulation is implicated in dysglycemia and type 2 diabetes. The objective of this study was to determine the relationship between at-risk alcohol, glucose tolerance, and SKM bioenergetic function in PLWH. Thirty-five PLWH (11 females, 24 males, age: 53±9 yrs, body mass index: 29.0±6.6 kg/m2) with elevated fasting glucose enrolled in the ALIVE-Ex study provided medical history and alcohol use information (Alcohol Use Disorders Identification Test, AUDIT), then underwent an oral glucose tolerance test (OGTT) and SKM biopsy. Bioenergetic health and function and mitochondrial volume were measured in isolated myoblasts. Mitochondrial gene expression was measured in SKM. Linear regression adjusting for age, sex, and smoking was performed to examine the relationship between glucose tolerance (2-h glucose post-OGTT), AUDIT, and their interaction with each outcome measure. Negative indicators of bioenergetic health were significantly (p<0.05) greater with higher 2-h glucose (proton leak) and AUDIT (proton leak, non-mitochondrial oxygen consumption, and bioenergetic health index). Mitochondrial volume was increased with the interaction of higher 2-h glucose and AUDIT. Mitochondrial gene expression decreased with higher 2-h glucose (TFAM, PGC1B, PPARG, MFN1), AUDIT (MFN1, DRP1, MFF), and their interaction (PPARG, PPARD, MFF). Decreased expression of mitochondrial genes were coupled with increased mitochondrial volume and decreased bioenergetic health in SKM of PLWH with higher AUDIT and 2-h glucose. We hypothesize these mechanisms reflect poorer mitochondrial health and may precede overt SKM bioenergetic dysregulation observed in type 2 diabetes.

scholarly journals Nup93 and CTCF co-modulate spatiotemporal dynamics and function of the HOXA gene cluster during differentiation

2019 ◽  
Author(s):  
Ajay S. Labade ◽  
Adwait Salvi ◽  
Krishanpal Karmodiya ◽  
Kundan Sengupta
Keyword(s):  
Gene Expression ◽  
Gene Locus ◽  
Nuclear Periphery ◽  
Spatiotemporal Dynamics ◽  
Differentiated Cells ◽  
Undifferentiated Cells ◽  
Dynamics And Function ◽  
Hoxa Gene Expression ◽  
And Function ◽  
Hoxa Gene

ABSTRACTNucleoporins regulate nuclear transport. In addition, nucleoporins also modulate chromatin organization and gene expression. Here we investigated the role of nucleoporin Nup93, in regulating HOXA gene expression during differentiation. ChIP-Seq analysis revealed that Nup93 associates with genes involved in development and differentiation. Furthermore, Nup93 occupancy significantly overlaps with CTCF. Interestingly, Nup93 and CTCF show antagonistic roles in regulating 3’ and 5’ end HOXA genes in undifferentiated cells. The HOXA gene locus untethered from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. Remarkably, occupancy of Nup93 and CTCF on HOXA gene locus progressively declined during differentiation but was restored in differentiated cells, consistent with the rerepression and re-localization of the HOXA gene locus with the nuclear periphery upon differentiation. In summary, Nup93 is a key modulator of the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.

scholarly journals Placental genomic risk scores and early neurodevelopmental outcomes

2021 ◽  
Vol 118 (7) ◽  
pp. e2019789118
Author(s):  
Gianluca Ursini ◽  
Giovanna Punzi ◽  
Benjamin W. Langworthy ◽  
Qiang Chen ◽  
Kai Xia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Disorders ◽  
Brain Volume ◽  
Risk Scores ◽  
Neurodevelopmental Outcomes ◽  
History Of ◽  
And Function ◽  
Relationship Of ◽  
The Relationship ◽  
Genomic Risk

Tracing the early paths leading to developmental disorders is critical for prevention. In previous work, we detected an interaction between genomic risk scores for schizophrenia (GRSs) and early-life complications (ELCs), so that the liability of the disorder explained by genomic risk was higher in the presence of a history of ELCs, compared with its absence. This interaction was specifically driven by loci harboring genes highly expressed in placentae from normal and complicated pregnancies [G. Ursini et al., Nat. Med. 24, 792–801 (2018)]. Here, we analyze whether fractionated genomic risk scores for schizophrenia and other developmental disorders and traits, based on placental gene-expression loci (PlacGRSs), are linked with early neurodevelopmental outcomes in individuals with a history of ELCs. We found that schizophrenia’s PlacGRSs are negatively associated with neonatal brain volume in singletons and offspring of multiple pregnancies and, in singletons, with cognitive development at 1 y and, less strongly, at 2 y, when cognitive scores become more sensitive to other factors. These negative associations are stronger in males, found only with GRSs fractionated by placental gene expression, and not found in PlacGRSs for other developmental disorders and traits. The relationship of PlacGRSs with brain volume persists as an anlage of placenta biology in adults with schizophrenia, again selectively in males. Higher placental genomic risk for schizophrenia, in the presence of ELCs and particularly in males, alters early brain growth and function, defining a potentially reversible neurodevelopmental path of risk that may be unique to schizophrenia.

Centromere identity and function put to use: construction and transfer of mammalian artificial chromosomes to animal models

2020 ◽  
Vol 64 (2) ◽  
pp. 185-192
Author(s):  
Ye Yang ◽  
Michael A. Lampson ◽  
Ben E. Black
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Animal Model ◽  
Synthetic Biology ◽  
Animal Models ◽  
Model Systems ◽  
Expression Vectors ◽  
Artificial Chromosomes ◽  
Conventional Expression ◽  
And Function

Abstract Mammalian artificial chromosomes (MACs) are widely used as gene expression vectors and have various advantages over conventional expression vectors. We review and discuss breakthroughs in MAC construction, initiation of functional centromeres allowing their faithful inheritance, and transfer from cell culture to animal model systems. These advances have contributed to advancements in synthetic biology, biomedical research, and applications in industry and in the clinic.

scholarly journals Cognitive Reserve in Model Systems for Mechanistic Discovery: The Importance of Longitudinal Studies

2021 ◽  
Vol 12 ◽  
Author(s):  
Joseph A. McQuail ◽  
Amy R. Dunn ◽  
Yaakov Stern ◽  
Carol A. Barnes ◽  
Gerd Kempermann ◽  
...  
Keyword(s):  
Longitudinal Studies ◽  
Cognitive Reserve ◽  
Structure And Function ◽  
Review Article ◽  
Model Systems ◽  
Cross Sectional ◽  
Early Predictors ◽  
Brain Structure And Function ◽  
And Function ◽  
The Relationship

The goal of this review article is to provide a resource for longitudinal studies, using animal models, directed at understanding and modifying the relationship between cognition and brain structure and function throughout life. We propose that forthcoming longitudinal studies will build upon a wealth of knowledge gleaned from prior cross-sectional designs to identify early predictors of variability in cognitive function during aging, and characterize fundamental neurobiological mechanisms that underlie the vulnerability to, and the trajectory of, cognitive decline. Finally, we present examples of biological measures that may differentiate mechanisms of the cognitive reserve at the molecular, cellular, and network level.

scholarly journals Regulatory Mechanisms at the MouseIgf2/H19 Locus

2001 ◽  
Vol 21 (23) ◽  
pp. 8189-8196 ◽  
Author(s):  
Christopher R. Kaffer ◽  
Alex Grinberg ◽  
Karl Pfeifer
Keyword(s):  
Gene Expression ◽  
Developmental Disorders ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Normal Function ◽  
Model Systems ◽  
Monoallelic Expression ◽  
Enhancer Element ◽  
And Function

ABSTRACT The closely linked H19 and Igf2 genes show highly similar patterns of gene expression but are reciprocally imprinted. H19 is expressed almost exclusively from the maternally inherited chromosome, while Igf2 expression is mostly from the paternal chromosome. In humans, loss of imprinting at this locus is associated with tumors and with developmental disorders. Monoallelic expression at the imprinted Igf2/H19 locus occurs by at least two distinct mechanisms: a developmentally regulated silencing of the paternal H19 promoter, and transcriptional insulation of the maternal Igf2 promoters. Both mechanisms of allele-specific silencing are ultimately dependent on a commoncis-acting element located just upstream of theH19 promoter. The coordinated expression patterns and some experimental data support the idea that positive regulatory elements are also shared by the two genes. To clarify the organization and function of positive and negative regulatory elements at theH19/Igf2 locus, we analyzed two mouse mutations. First, we generated a deletion allele to localize enhancers used in vivo for expression of both H19 and Igf2 in mesodermal tissues to sequences downstream of the H19 gene. Coincidentally, we demonstrated that some expression ofIgf2 is independent of the shared enhancer element. Second, we used this new information to further characterize an ectopicH19 differentially regulated region and the associated insulator. We demonstrated that its activity is parent-of-origin dependent. In contrast to recent results from Drosophilamodel systems; we showed that this duplication of a mammalian insulator does not interfere with its normal function. Implications of these findings for current models for monoallelic gene expression at this locus are discussed.

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