Carolyn J. Brown
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Impact of somatic <i>XIST</i> deletions on ongoing XIST expression and inactive X silencing and heterochromatin Open
The long non-coding RNA XIST is critical for establishing X-chromosome inactivation early in development. XIST remains expressed from the inactive X throughout female life; yet in somatic cells silencing of most genes continues in the abse…
Human XIST: Origin and Divergence of a cis-Acting Silencing RNA Open
Dimorphism of sex chromosomes often leads to a need for dosage compensation. In eutherian mammals, XIST, a long non-coding RNA, is expressed from the X chromosome that will be silenced, triggering X-chromosome inactivation (XCI). XIST orig…
View article: Escape from X-chromosome inactivation at <i>KDM5C</i> is driven by promoter-proximal DNA elements and enhanced by domain context
Escape from X-chromosome inactivation at <i>KDM5C</i> is driven by promoter-proximal DNA elements and enhanced by domain context Open
Over 20% of human X-linked genes escape from X-chromosome inactivation (XCI), and are important contributors to sex differences in gene expression. Candidate factors involved in escape have been identified through enrichment analyses and i…
View article: Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta
Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta Open
Background The human placenta is distinct from most organs due to its uniquely low-methylated genome. DNA methylation (DNAme) is particularly depleted in the placenta at partially methylated domains and on the inactive X chromosome (Xi) in…
Recruitment of chromatin remodelers by XIST B-repeat region is variably dependent on HNRNPK Open
X-chromosome inactivation is triggered by the long non-coding RNA XIST, whose structure is characterized by tandem repeats that modularly recruit different proteins and chromatin remodelers. Previously, we reported that the addition of the…
Novel Ameloblastin Variants, Contrasting Amelogenesis Imperfecta Phenotypes Open
Amelogenesis imperfecta (AI) comprises a group of rare, inherited disorders with abnormal enamel formation. Ameloblastin (AMBN), the second most abundant enamel matrix protein (EMP), plays a critical role in amelogenesis. Pathogenic bialle…
Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation Open
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes…
View article: Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data
Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data Open
Background Many human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into analyses vital. Unfortunately, X and Y chromosome data are frequently excluded from larg…
Derivation of a minimal functional XIST by combining human and mouse interaction domains Open
X-inactive specific transcript (XIST) is a 17–19 kb long non-coding ribonucleic acid (RNA) critical for X-chromosome inactivation. Tandem repeats within the RNA serve as functional domains involved in the cis-limited recruitment of heteroc…
Derivation of a minimal functional XIST by combining human and mouse interaction domains Open
XIST is a 17-19 kb long non-coding RNA critical for X-chromosome inactivation. Tandem repeats within the RNA serve as functional domains involved in the cis-limited recruitment of heterochromatic changes and silencing. To explore the suffi…
Refining the genomic determinants underlying escape from X-chromosome inactivation Open
X-chromosome inactivation (XCI) epigenetically silences one X chromosome in every cell in female mammals. Although the majority of X-linked genes are silenced, in humans 20% or more are able to escape inactivation and continue to be expres…
Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation Open
Background Mammalian dosage compensation is achieved by the inactivation of one X chromosome in XX individuals. In eutheria this process is initiated early in development by the long non-coding RNA XIST. Studies of the initiation of silenc…
Additional file 3 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation Open
Additional file3: Table S2. Comparison of histone marks between sex and XCI status. See additional files. The first sheet shows BH adjusted p-values comparing female vs male and escape genes vs those subject to XCI per mark in CEMT with ou…
Additional file 7 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation Open
Additional file7: Table S18. DNAmeQTL analysis for the loci significantly associated with DNAme-based XCI status calls. See additional files. These loci were independently tested as DNAmeQTLs in females and males, with some columns color c…
Additional file 5 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation Open
Additional file5: Table S16. Top 100 results from an analysis associating XCI status with genotype. See additional files. There are separate sheets for association with Xi/Xa and 450k based XCI status calls, and for comparing to all chromo…
Additional file 4 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation Open
Additional file4: Table S4. All XCI status calls made here. See additional files. The first sheet contains a single XCI status call per gene per method. Published calls are from Balaton, et al. 2015. Other sheets contain all calls per samp…
Additional file 2 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation Open
Additional file2: Table S1. List of samples used. See additional files. For CEMT samples, tissue was annotated to combine samples from related areas. Columns D through L refer to the availability of the dataset for each sample. Patient hea…
Additional file 6 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation Open
Additional file6: Table S17. The number of loci associated with each gene and genes associated with each locus. See additional files. These are for the association between DNAme based XCI status and genetic polymorphisms.
Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation Open
Background Mammalian dosage compensation is achieved by the inactivation of one X chromosome in XX individuals. In eutheria this process is initiated early in development by the long non-coding RNA XIST. Studies of the initiation of silenc…
Independent domains for recruitment of PRC1 and PRC2 by human XIST Open
XIST establishes inactivation across its chromosome of origin, even when expressed from autosomal transgenes. To identify the regions of human XIST essential for recruiting heterochromatic marks we generated a series of overlapping deletio…
View article: A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta
A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta Open
Background Human placental DNA methylation (DNAme) data is a valuable resource for studying sex differences during gestation, as DNAme profiles after delivery reflect the cumulative effects of gene expression patterns and exposures across …
Contribution of epigenetic changes to escape from X-chromosome inactivation Open
Background X-chromosome inactivation (XCI) is the epigenetic inactivation of one of two X chromosomes in XX eutherian mammals. The facultatively heterochromatic inactive X chromosome acquires many chromatin changes including DNA methylatio…
View article: Additional file 2 of A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta
Additional file 2 of A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta Open
Additional file 2: Supplementary Table 1. Title: Results of linear modelling for all 324,104 autosomal CpGs tested. Description: Linear modelling statistics for sex differential methylation analysis at all 324,104 autosomal CpG sites in th…
View article: Additional file 3 of A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta
Additional file 3 of A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta Open
Additional file 3: Supplementary Table 2. Title: Table of significant placental autosomal sex-associated DMRs. Description: Summary statistics and genomic locations of all signficant sex-associated DMRs identified.
Additional file 2 of Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing Open
Additional file 2: Table S1. All XCI status calls made in this study compared to human.Table S1. All XCI status calls made in this study compared to human.
Additional file 3 of Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing Open
Additional file 3: Table S2. Individual XCI status calls per dataset. Each sheet is a separate dataset analyzed.