1998 — 2000 |
Lasalle, Janine M |
R21Activity Code Description: To encourage the development of new research activities in categorical program areas. (Support generally is restricted in level of support and in time.) |
Lsc Analysis of Cell Cycle Regulated Chromosome Dynamics @ University of California Davis
DESCRIPTION: (Applicant's Description) In multicellular eukaryotes chromosomal DNA is functionally dynamic in different cells, tissues, or stages of development. Therefore, an important aspect of investigating epigenetic mechanisms of gene expression is an understanding of the functional organization of chromosomes within their native cellular environment. Although metaphase chromosomes have been the standard subject of cytogenetic studies, interphase chromosomes are in a much more dynamic state as they undergo replication, transcription, methylation and chromatin organization during the cell cycle. The recent demonstration of a temporal and spatial association of chromosome 15q 11-13 regions that occurs in the late S phase of the cell cycle in human somatic lymphocytes was found to be deficient in cell, from patients with the parental imprinting disorders Angelman and Prader-Willi's syndromes. Homologous association was also observed at the Beckwith-Wiedemann syndrome locus at 11p15, a different imprinted locus implicated in tumorigenesis. These results demonstrate that chromosomal alteration such a uniparental disomy, deletion, or translocation can alter the normal dynamics of chromosome; during the cell cycle. However, a large scale human genome-wide search has not been performed to determine if other chromosomal domains exhibit transient interactions during the cell cycle. The existing method for examining transient chromosome interactions requires a large number of cultured primary lymphocytes, two very expensive instruments and long hours of data analysis. Cells are first fractionated on the basis of DNA content by flow cytometry, then analyzed for fluorescence in situ hybridization (FISH) signals in three- dimensionally intact nuclei by confocal laser cytometry (CLSM), then measured for 3D intersignal distance, then the data are statistically analyzed. In this proposal, a potentially more efficient and cost-effective method for the analysis of cell cycle-specific chromosome dynamics by laser scanning cytometry (LSC) is outlined so that a large-scale investigation chromosomes may be performed.
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0.958 |
2002 — 2016 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
The Role of Mecp2 in Rett Syndrome @ University of California At Davis
DESCRIPTION (provided by applicant): Rett syndrome is caused by mutation in the gene MECP2, encoding an epigenetic factor that binds to methylated DNA throughout the mammalian genome. MeCP2 had multiple described functional domains, but the majority of the molecule is an inherently disordered protein, meaning that is does not encode a defined secondary structure. At least two alternatively spliced isoforms and multiple phosphorylation sites of MeCP2 have been described. In addition, multiple interacting proteins of MeCP2 have been observed that are beginning to explain how MeCP2 may have such a diverse array of functions, including global chromatin structures, transcriptional repression, and transcriptional activation. Multiple gene targets of MeCP2 have emerged and help to explain how MeCP2 modulates neuronal activity and maturation, but MeCP2 is also an abundant nuclear protein that binds and acts globally on chromatin dynamics in neurons. The molecular complexities of MeCP2 appear to be consistent with a role as a master epigenetic regulator that both regulates and is regulated by multiple signal transduction and epigenetic pathways in the developing and mature mammalian brain. Therefore, understanding the post-translational modifications, isoforms and different interacting partners of MeCP2 as well as their binding sites genome-wide are expected to be critical for understanding its functions and their relevance to RTT and related neurodevelopmental disorders. This application focuses on the most abundant yet understudied MeCP2 isoform, MeCP2e1. Preliminary results demonstrate that mice selectively deficient in MeCP2e1 exhibit several features common to other Rett mouse models, including a delayed postnatal onset of neurological symptoms, reduced sociability, deficiencies in the elevated plus maze, and early lethality. The overall objective is to understand the structural and biochemical bases of MeC2e1 versus MeCP2e2 functions in pre- and postnatal brain development and their relevance to behavior. Aim 1 will investigate the structural and functional differences between MeCP2e1 and MeCP2e2 in vitro and in vivo. Aim 2 will investigate developmental roles for MeCP2e1 in recognizing the dynamic DNA methylome of developing neurons through combined genomic approaches. Aim 3 will investigate the social, behavioral, and metabolic effects of MeCP2e1 deficiency. The results of these studies are expected to be significant for understanding neurodevelopmental epigenetic pathways relevant for Rett syndrome and other more common neurodevelopmental disorders, including autism.
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0.958 |
2005 — 2009 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Epigenetic Etiologies of Autism-Spectrum Disorders @ University of California At Davis
DESCRIPTION (provided by applicant): Autism is an increasingly common disorder of complex etiology, affected by both genetic and environmental influences. Autism has several phenotypic features in common with the neurodevelopmental disorders Rett syndrome and Angelman syndrome. Rett syndrome (RTT) is an X-linked dominant disorder caused by mutations in MECP2, which encodes methyl-CpG-binding protein 2 (MeCP2). Methylation of CpG dinucleotides and methyl-specific binding proteins are part of an epigenetic pathway essential for parental imprinting and chromatin dynamics during normal brain development. Angelman syndrome (AS) is an imprinted disorder caused by maternal deficiency of chromosome 15q11-13. In addition, MECP2 mutations have been found in a few patients diagnosed with AS and autism and 15q11-13 duplications are the most common cytogenetic abnormality found in autism. Together these findings support the broad premise that these three distinct genetic syndromes share overlap in their pathogenic mechanisms. This research proposal will focus on the hypothesis that MECP2 regulates gene expression in the 15q11-13 region, and that aberrations in this regulatory pathway may contribute to phenotypic features of autism-spectrum disorders. The first aim of the proposal is to determine the effect of MeCP2 deficiency on gene expression in the imprinted 15q11-13 locus by several quantitative approaches. The second aim of the proposal is to determine the mechanism by which MeCP2 regulates gene expression within 15q11-13. The third aim is to investigate expression defects in MeCP2 and target genes in the 15q11-13 region in multiple autism brain samples. These studies aim to uncover important mechanistic similarities between the overlapping neurodevelopmental disorders RTT, AS, and autism. The successful completion of these studies should yield findings to help develop better diagnostic and treatment modalities for autism-spectrum disorders.
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0.958 |
2006 — 2009 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Epigenetic Interaction of Mecp2 and Organic Pollutants in Neurodevelopment @ University of California At Davis
DESCRIPTION (provided by applicant): Epigenetic mechanisms act at the interface between genetics and environment and are an important determinant in disease risk to complex human diseases such as cancer or autism. This proposal employs a combination of systems and approaches that focus on the central question of the impact of persistent environmental pollutants (POPs) on precise epigenetic changes that occur in neurodevelopmental disorders. The widespread prevalence of POPs such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in the environment and their detection in human milk has prompted concern about in utero and early infant exposure to these compounds. Perinatal exposure to PCBs and PBDEs in rats results in long-lasting defects in learning, memory, behavior, and seizure susceptibility in adulthood. Epigenetic changes to the genome as a result of PCB and PBDE exposures have not been previously explored but are a plausible explanation for the long-lasting effects on neuropsychological function. This proposal will focus specifically on two compounds, PCB 95 and PBDE 47, with high levels in humans and known effects on neurodevelopment. The genetically controlled component of the proposed studies will be to use a genetically engineered Mecp2 mutant mouse model of Rett syndrome and autism. In additional to animal studies, human blood and post-mortem brain samples from individuals with autism, mental retardation, and controls will be tested for precise epigenetic changes in three neurodevelopmentally important genes (MECP2, GABRB3, UBE3A). Since PCB and PBDE levels will be determined in these human samples, correlations of exposures to epigenetic changes can be performed. Several public health relevant questions will be addressed by these studies: What specific epigenetic changes to neurodevelopmentally important genes occur as a result of POP exposure? What is the compounding effect of known genetic and environmental factors in the etiology of autism and mental retardation? Can specific epigenetic changes be diagnostic for autism and mental retardation of unknown genetic etiology? Are epigenetic changes affecting neurodevelopment heritable?
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0.958 |
2008 |
Lasalle, Janine M |
S10Activity Code Description: To make available to institutions with a high concentration of NIH extramural research awards, research instruments which will be used on a shared basis. |
Icys Laser Scanning Cytometer For Uc Davis Core @ University of California Davis
[unreadable] DESCRIPTION (provided by applicant): The CompuCyte iCys Laser Scanning Cytometer is a versatile research imaging microscope that combines elements of flow cytometry, automated fluorescent microscopy, and image analysis. A first generation Compucyte Laser Scanning Cytometer (LSC) was purchased by the UC Davis School of Medicine in 1997 for shared use within the Optical Biology Core facility. In the last 10 years, the LSC has been actively used at UC Davis, resulting in more than 15 publications and 12 new grants using the technology. Currently, 9 funded NIH grants from 6 investigators are dependent on an operational LSC. Starting in mid-2007, the older model LSC will no longer be supported by CompuCyte, so the purchase of a new iCys LSC is essential to the completion of these funded projects. In addition, the new iCys LSC not only has an updated software and computer system, but is in an inverted microscope format, allowing new applications to include live cell imaging, 96-well plate high throughput assays, and multi-slide processing. Institutional support is provided for an extended service contract and a confocal module on the iCys LSC to allow the high-throughput quantitative analyses of small intra-nuclear spots in fluorescence in situ hybridization, sub-nuclear protein dynamics, intra-cellular inclusions, and organelle studies in primary neurons. There is no equivalent equipment on the UC Davis campus or surrounding area that would serve the quantitative imaging needs of these NIH-funded programs. The iCys LSC with confocal module will strongly impact inter-disciplinary biomedical research on the common pediatric disorders of autism and mental retardation, as well as the common age-related disorders of dementia, ataxia, blindness, cancer, and diabetes. These are common goals of the UC Davis Health System and the NIH. The placement of a shared iCys LSC imaging system in a core facility with a strong track record of support is a cost effective way of supporting NIH funded researchers at UC Davis. [unreadable] [unreadable] [unreadable]
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0.958 |
2011 — 2017 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. R56Activity Code Description: To provide limited interim research support based on the merit of a pending R01 application while applicant gathers additional data to revise a new or competing renewal application. This grant will underwrite highly meritorious applications that if given the opportunity to revise their application could meet IC recommended standards and would be missed opportunities if not funded. Interim funded ends when the applicant succeeds in obtaining an R01 or other competing award built on the R56 grant. These awards are not renewable. |
Noncoding Rnas At the Heart of the Prader-Willi Locus @ University of California At Davis
DESCRIPTION (provided by applicant): Prader-Willi syndrome (PWS) is a neurodevelopmental disorder with a known genetic etiology, but a complex epigenetic basis. PWS is an imprinted disorder, meaning that genes expressed only on the paternal but not the maternal chromosome 15q11-13 region are responsible. Furthermore, unlike genetic mutations that affect protein-coding genes, the smallest genetic deletions causing PWS only affect noncoding transcripts of RNA. At the heart of the minimally deleted region in PWS are two types of noncoding RNAs. First, the HBII-85/SNORD116 small nucleolar RNAs (snoRNAs) localize to the nucleolus in maturing neurons and impact rRNA and nucleolar maturation. Second, the host gene exons surrounding the HBII-85/SNORD116 snoRNAs are spliced and nuclear retained as a long noncoding RNA (lncRNA), forming a large RNA cloud-like structure that increases in size with neuronal maturity. While most of the focus in the PWS field has been on understanding the function of the snoRNAs and protein coding genes, the host snoRNA-lncRNA may be of equal if not greater importance to understanding and treating the underlying neurodevelopmental defect in PWS. In this proposal, we seek to answer three major unanswered questions regarding the molecular pathogenesis of PWS. 1) What is the mechanistic basis for chromatin decondensation specifically in mature neurons? 2) Which ncRNA is responsible for the PWS phenotype, the snoRNAs or the host lncRNA? 3) What are the genetic and mechanistic bases of the mouse/human phenotypic differences associated with the PWS locus deficiency and duplication? The approaches include novel fluorescence in situ methods for combined detection of R-loops, ncRNAs, and chromatin decondensation in mouse and human brain and novel mouse-human hybrid neuronal cell lines and human PWS induced pluripotent cell derived neurons. The results of these experiments are expected to improve understanding of functional role of the lncRNAs at the heart of the PWS locus and potentially enable future epigenetic therapies for PWS.
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0.958 |
2012 — 2017 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. R56Activity Code Description: To provide limited interim research support based on the merit of a pending R01 application while applicant gathers additional data to revise a new or competing renewal application. This grant will underwrite highly meritorious applications that if given the opportunity to revise their application could meet IC recommended standards and would be missed opportunities if not funded. Interim funded ends when the applicant succeeds in obtaining an R01 or other competing award built on the R56 grant. These awards are not renewable. |
Methylomic and Genomic Impacts of Organic Pollutants in Dup15q Syndrome @ University of California At Davis
DESCRIPTION (provided by applicant): This study is designed to test a novel paradigm that the human genome dynamically interacts with the environment and that epigenetic mechanisms are at the interface of genome- environment interactions. The human genome is marked by structural variations including large copy number variations and differences in repetitive sequences. Environmental toxins such as polychlorinated biphenyls (PCBs) can induce DNA hypomethylation. DNA hypomethylation is a known contributor to genomic instability of CpG-rich Alu repeats in the primate lineage. Chromosome 15q11-13 duplication syndrome (Dup15q), is the most common copy number variation observed in neurodevelopmental disorders, and is responsible for 1-3% of autism cases. This proposal is based on the serendipitous finding that human brain samples with Dup15q syndrome showed significantly higher levels of the persistent organic pollutant PCB-95 than controls or idiopathic autism cases. Furthermore, a genetically susceptible mouse perinatally exposed to the related flame retardant BDE-47 exhibited hypomethylation in brain and reduced sociability compared to controls. This study is designed to experimentally determine if PCB-95 and/or BDE-47 play a causal or compounding role in structural rearrangements of 15q using combined genomic and epigenomic approaches. In addition, this study will directly investigate the effect of combined genomic and environmental insults on the integrity of the methylome and transcriptome in human brain samples. The first aim seeks to experimentally model chromosome 15 duplication in a novel human cell line system to examine effects of PCB-95 or BDE-47 exposures on genomic stability (DNA-seq) and DNA methylation (MethylC-seq) using next generation sequencing technology. In the second aim, the effect of genetic and epigenetic changes on long-range chromatin loop structure within 15q11-q13 will be examined by chromatin conformation capture sequencing (4C-seq) and correlated to specific transcriptional alterations. The third aim seeks to directly investigate specific 15q gene targets for epigenetic and transcriptional changes in human brain samples with and without chromosome 15 duplication and high PCB-95 levels. The results of these studies are expected to formally test the hypothesis that DNA methylation levels reduced by specific environmental pollutants may result in genomic rearrangements and alterations in long-range chromatin, leading to transcriptional changes. In addition, epigenetic alterations of autism candidate genes involved in synaptogenesis in human brain samples are expected to be uncovered by this approach. Finally, the results of these studies are expected to be broadly relevant to understanding the relationship between the genome, environmental exposures, and the epigenome in human health and disease.
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0.958 |
2013 — 2017 |
Lasalle, Janine M |
P01Activity Code Description: For the support of a broadly based, multidisciplinary, often long-term research program which has a specific major objective or a basic theme. A program project generally involves the organized efforts of relatively large groups, members of which are conducting research projects designed to elucidate the various aspects or components of this objective. Each research project is usually under the leadership of an established investigator. The grant can provide support for certain basic resources used by these groups in the program, including clinical components, the sharing of which facilitates the total research effort. A program project is directed toward a range of problems having a central research focus, in contrast to the usually narrower thrust of the traditional research project. Each project supported through this mechanism should contribute or be directly related to the common theme of the total research effort. These scientifically meritorious projects should demonstrate an essential element of unity and interdependence, i.e., a system of research activities and projects directed toward a well-defined research program goal. |
Project 2: Perinatal Epigenetic Signature of Environmental Exposure @ University of California At Davis
Epigenetic mechanisms act at the interface of genetic and environmental risk factors in autism. Project 2 is designed to investigate to focus on the epigenetic mark of DNA niethylation, as environmental toxins have been demonstrated to reduce global DNA methylation levels while methyl-donor nutrients can be protective. This project will make use primarily of human cord blood samples from the MARBLES study in order to test the hypothesis that epigenetic patterns laid down in eariy life that regulate synapse maturation and immune responses will be impaired in autism through interactions between genetic and environmental factors. The first aim is designed to perform a genome-wide analysis of DNA methylation and copy number variation and to study the association of differences in genetics and epigenetics with environmental exposures (from Project 1 and Core C) and nutrients. The second aim will investigate methylation of a specific gene locus, FOXP3, as an epigenetic marker of regulatory T cells and will make use of immunology expertise and existing participant samples from both MARBLES and CHARGE from Project 3. The third aim will test a multifactorial mechanistic model of transcription-induced epigenetic memory of perinatal gene x environment interactions at two specific loci, F0XP3 and FMR1, through interactions with Projects 3 and 4. Together these studies will increase understanding of the epigenetic interface between genetic and environmental risk factors in autism, leading to improved diagnosis, prevention, and therapies.
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0.958 |
2018 — 2021 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Neuroimmune Interactions in Rett Syndrome @ University of California At Davis
Neuroimmune interactions and epigenetic mechanisms act at the interface of genetic and environmental risk factors that determine the severity and progression of both common and rare brain disorders. A prime example of a complex monogenic disease is Rett syndrome, an X-linked dominant neurodevelopmental disorder caused by mutations in MECP2. Rett syndrome is epigenetic at two levels: first in the regulation of MECP2 by X chromosome inactivation, and second because MECP2 encodes a known epigenetic regulator, methyl CpG binding protein 2. Girls with Rett syndrome are heterozygous for MECP2 mutations that are primarily germ-line paternal de novo events. Rett babies are born apparently normal, and then experience a regression in cognitive and motor functions in late infancy. Mouse models of Rett syndrome also recapitulate the delay in the onset of detectable neurological symptoms and motor deficits. While the MeCP2 protein is most highly expressed in neurons, both human Rett patients and mouse models exhibit system-wide immune, mitochondrial, and metabolic manifestations that are likely secondary to the causal mutation?s disruption of neuronal homeostasis. What is lacking in the Rett field is a temporal understanding of how the molecular signatures of disease progression in distinct cell types within the brain interact with the immune system?s responses inside and outside of the brain. We propose to investigate the molecular signatures of critical time points of neuroimmune pathogenesis in a novel Rett syndrome mouse model based on a human mutation. Epigenomic investigation of specific cell types in cortex, including microglia, excitatory neurons, and inhibitory neurons will be integrated with 1) single cell transcriptomics from hippocampus and hypothalamus, 2) measurements of immune dysfunction, and 3) metabolite and gut microbiota profiles. The objective of the first aim will be to characterize the time course of neuroimmune interactions in the context of symptom progression in Rett syndrome. Results from the first aim will reveal the molecular dynamics of how immune responses exacerbate neuronal dysfunction and vice versa. In the second aim, we propose to modulate the microglia prior to the onset of disease progression to directly test the role of microglia in the timing and severity of symptoms in this Rett mouse model. LPS injections in pre-symptomatic mice will be performed to activate microglia so as to test the hypothesis that microglia activated by a ?second hit? will increase the severity and speed of onset of neurologic and motor symptoms in the Rett syndrome model. As a reciprocal experiment, microglia will be depleted in adolescent mice using the drug PLX5622 and either allowed to replenish after short term drug treatment or continuously depleted through adulthood to test the hypothesis that microglia are critical mediators of symptom progression. From these experiments, we expect to obtain an integrated molecular time course of events explaining how Mecp2 mutation interacts with immune responses in brain and periphery. We will also determine if activated microglia in Rett syndrome may accelerate the disease severity and be an important therapeutic target for future pre-clinical investigations.
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0.958 |
2018 — 2021 |
Lasalle, Janine M Lein, Pamela (co-PI) [⬀] Schmidt, Rebecca Jean (co-PI) [⬀] |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Pcb Epigenomic Brain & Behavior Lasting Effects Study (Pebbles) @ University of California At Davis
Placental tissue is normally discarded at birth, but is essentially a molecular time capsule for gene by environmental interactions and dysregulated molecular and cellular pathways that can be revealed at the level of the epigenome. Identifying epigenetic biomarkers at birth that reflect in utero exposures or predict adverse neurodevelopmental outcomes is an important goal that has been limited by prior technologies or lack of relevant tissue availability. Our team of currently collaborating interdisciplinary scientists within the Children?s Center for Environmental Health plans to use existing placental samples from a prospective high-risk cohort study (MARBLES) to identify epigenetic biomarkers at birth for in utero exposure to polychlorinated biphenyls (PCB) and neurodevelopmental outcomes by age three. Using unbiased whole genome bisulfite sequencing (WGBS), we have previously demonstrated that placental tissues retain the distinctive DNA methylation patterns of the preimplantation embryo and so can capture the molecular state in very early development, a feature that is conserved across mammalian species, including mouse. The new hypothesis to be tested in this proposal is that perinatal exposures to PCB adversely impact neurodevelopment and leave a lasting molecular signature over genes relevant to neurodevelopment that can be detected in placenta. The proposed PCB Epigenomic Brain & Behavior Lasting Effects Study (PEBBLES) will combine the analysis of human placental samples from the high-risk MARBLES cohort with the analysis of placenta and brain tissues and sorted cell types derived from a mouse model of perinatal exposure to the same mixture of PCB congeners detected in MARBLES mothers. This study will leverage existing neurological and behavioral analyses and samples to examine the relationship between PCB-induced perturbations of DNA methylation marks with adverse neurotoxic outcomes. Epigenomic analyses of placenta and brain as well as sorted cellular subtypes from each of these tissues will include WGBS for methylome, RNA-seq for transcriptome, and ATAC-seq for chromatin accessibility. Bioinformatic and statistical analyses will integrate the genomic data sets with behavioral and molecular outcome measures and determine whether similar epigenetic marks are observed in placenta that could be used to predict long-lasting adverse brain and behavioral outcomes in humans. !
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0.958 |
2019 |
Lasalle, Janine M Lein, Pamela (co-PI) [⬀] Schmidt, Rebecca Jean (co-PI) [⬀] |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Epigenomic Brain & Behavior Lasting Effects Study (Pebbles) Admin Supplement @ University of California At Davis
Placental tissue, which is normally discarded at birth, is a molecular time capsule that captures gene by environmental interactions and dysregulated molecular and cellular pathways that can be revealed at the level of the epigenome. Identifying epigenetic biomarkers at birth that reflect in utero exposures or predict adverse neurodevelopmental outcomes is an important goal that has been limited by prior technologies or lack of relevant tissue availability. Our team of currently collaborating interdisciplinary scientists within the Children?s Center for Environmental Health plans to use existing placental samples from a prospective high-risk cohort study (MARBLES) to identify epigenetic biomarkers at birth for in utero exposure to polychlorinated biphenyls (PCBs) and neurodevelopmental outcomes at age three years. In the MARBLES cohort, we have shown that taking folic acid in the form of prenatal vitamins specifically in the first month of pregnancy was associated with a 50% reduction in the risk for autism. Our human studies and the work of others also show evidence that folic acid supplementation can counter epigenetic and neurodevelopmental effects of environmental contaminants. Furthermore, using unbiased whole genome bisulfite sequencing (WGBS), we have previously demonstrated that placental tissues retain the distinctive DNA methylation patterns of the preimplantation embryo and so can capture the molecular state in very early development, a feature that is conserved across mammalian species, including mouse. The proposed PCB Epigenomic Brain & Behavior Lasting Effects Study (PEBBLES) combines WGBS analysis of human placental samples from the high-risk MARBLES cohort with a more extensive epigenomic analysis of placenta and brain tissues and sorted cell types derived from a mouse model of perinatal exposure to the same mixture of PCB congeners detected in MARBLES mothers. The hypothesis to be tested in the parent PEBBLES grant is that perinatal PCB exposures adversely impact neurodevelopment and leave a lasting molecular signature over genes relevant to neurodevelopment that can be detected in placenta. The hypothesis to be tested in the nutritional supplement to PEBBLES is that dietary folic acid supplementation will be protective against the adverse effects of PCB exposures at the level of the epigenome in an experimental animal model and human placenta. Bioinformatic and statistical analyses will integrate the genomic data sets with behavioral and molecular outcome measures and determine whether similar epigenetic marks are observed in placenta that could be used to predict long-lasting brain and behavioral outcomes in humans. !
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0.958 |
2019 — 2021 |
Lasalle, Janine M |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Imprinted Snorna Loci and Circadian Entrainment @ University of California At Davis
Sufficient sleep is essential for optimal metabolic, cognitive, and mental health. Circadian rhythms affecting sleep behavior are genetically determined, but environmentally entrained by external cues such as light exposure. Circadian entrainment is predicted to be established by poorly understood epigenetic mechanisms that allow mammals to adapt their metabolism to the environment. Distinct patterns of sleep and diurnal metabolism have evolved within mammals, coinciding with the acquisition of SNORD116 small nucleolar RNA (snoRNA) repeats in the Prader-Willi syndrome (PWS) locus. The PWS locus is imprinted, meaning that genes expressed only on the paternal but not the maternal chromosome 15q11-q13 region are causative. PWS is caused by the loss of two types of noncoding RNAs encoded by SNORD116. First, SNORD116 snoRNAs localize to the nucleolus in maturing neurons and impact rRNA and nucleolar maturation. Second, the host gene exons flanking the SNORD116 snoRNAs are spliced and retained in the nucleus as a long noncoding RNA, forming a large RNA cloud structure that regulates transcription of circadian transcription factors, DNA methylation, and metabolism. The intronic sequences of SNORD116 exhibit high GC skew, promoting the formation of DNA:RNA hybrid structures called R-loops. R-loops promote chromatin decondensation, slow transcriptional progression, and protect from DNA methylation. Interestingly, maternal overexpression of a similarly structured large imprinted snoRNA cluster on chromosome 14 causes PWS-related Temple syndrome, and published evidence supports the cross-regulation of these two imprinted loci. In our recent analyses of epigenetic changes associated with circadian rhythmicity and the Snord116 locus, >23,000 rhythmic methylated CpGs were observed in wild-type mouse cortex, of which 97% were lost or time-shifted in Snord116+/- littermates. These Snord116-impacted methylation enhancers and promoters regulated genes with functions highly enriched for circadian entrainment and body weight, including genes within the Temple syndrome locus. In this proposal, we seek to understand the role of Snord116 in circadian entrainment and the epigenetic mechanisms underlying Snord116 regulation of rhythmic circadian cycles of gene expression genome-wide, with a focus on imprinted snoRNA loci. The results of these experiments are expected to expand functional knowledge of imprinted noncoding RNAs and potentially enable future epigenetic therapies for imprinting disorders. In addition, determining how noncoding RNAs regulate circadian epigenetic rhythms and metabolism during sleep/wake cycles to modify phenotypes is an emerging basic science field. These studies may therefore have profound future impacts on improving sleep, mental health, and weight problems that affect almost all humans.
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0.958 |