Post-primary education in West Ham, 1918-39.

This thesis is concerned with post-primary education in West Ham 1918-39, with particular reference to secondary education. The realities of local educational experience are set against a background of educational acts an economies. The economic difficulties of the 1920s and the Depression of the 1930s were keenly felt in West Ham despite the efforts of the predominantly Labour council to mitigate poverty. A gap sometimes existed between the educational opportunities Labour councillors wished to provide and those they were able to provide. Generally a pragmatic approach was taken and certainly a secondary education was not seen as essential for all. Chapter One outlines West Ham's pre-1918 history and growth with reference to local politics and immigrant and religious groupings. West Ham's interwar history is told in greater detail. Chapter Two relates the difficulties encountered by the West Ham Education Committee in its decision to establish compulsory continuation schools, not least from the parents of West Ham. West Ham was one of the few areas in the country which succeeded in implementing compulsory continuation education albeit for a limited period. A section on technical education is also included in this chapter, although detailed treatment is hampered by a scarcity of records. Chapter Three examines West Ham's secondary school scholarships in the context of the national situation. West Ham's higher elementary/central school scholarships are subjected to the same scrutiny. Each of West Ham's secondary schools shared a broadly similar curriculum and ethos. Chapter Four highlights these similarities but also points out differences. Of the five interwar secondary schools, two catered for girls, one for boys and two were mixed. Two of the secondary schools were Catholic institutions, although both accepted non-Catholic pupils. Three of the schools were aided and two municipal. A section is included on West Ham's higher elementary/central schools but records are less full than those for the secondary schools. Chapter Five compares and contrasts West Ham's interwar secondary school system with that in East Ham, its sister borough. Chapter Six discusses both the economic and cultural factors underlying local attitudes to post-compulsory schooling. The main conclusions drawn relate to these attitudes which militated against any easy acceptance of such education as necessarily beneficial

Evolutionary model of sex chromosome dosage compensation compared to the basal compensation response of an autosome after a deletion.

<p>After the proto-Y chromosome evolved a gene with a male-determining function (green bar), it became subject to gradual gene loss on a gene-by-gene or segment-by-segment basis due to lack of recombination between the proto-sex chromosomes. If the lost region on the proto-Y chromosome contained dosage sensitive genes such as those that encode transcriptional factors (yellow bars), this would have triggered a basal dosage compensation response (yellow faucet) on the proto-X chromosome and led to a partial (1.5-fold) increase of expression (small arrows). The same basal dosage compensation process would also modify a deleted region on an autosome (A) in an abnormal cell. Dosage-insensitive genes (black bars) may escape this process. When broader regions were lost on the proto-Y chromosome, the collective imbalance effects of multiple aneuploid genes would have become highly deleterious and the increased load of aneuploidy could have stressed the basal mechanism of dosage compensation. Survival was achieved by recruiting regulatory complexes such as the MSL complex (red faucet) to aneuploid X segments (red regions), to further increase gene expression (big arrows) and rescue the X monosomy. This feed-forward sex chromosome–specific regulation would provide 1.35-fold increase in expression, which together with the basal dosage compensation (1.5-fold increase) would achieve the approximate two-fold upregulation of most genes on the present day X chromosome. In contrast, large-scale deleterious autosomal aneuploidy would be lost due to lack of a specific sex-driven compensatory mechanism.</p

Expression levels change in response to altered gene dose in aneuploidy.

<p>The transcript output from a given pair of chromosomes in normal WT diploid cells is set as a value of 2. In case of aneuploidy (monosomy or trisomy), the amount of transcript would be strictly correlated with gene dose in the absence of a dosage compensation mechanism (No DC). In the presence of partial DC, the expression level per copy would be partially increased in monosomy or partially decreased in trisomy, relative to the diploid level. In the presence of complete DC, expression levels would be adjusted so that the amount of transcripts is the same in monosomic or trisomic cells compared to diploid cells.</p

KDM6A is preferentially recruited to <i>Rhox6</i> and <i>9</i> in female ES cells.

<p>(A) ChIP-qPCR analysis of KDM6A occupancy at the 5′ end of <i>Rhox6</i> and <i>9</i> is higher in female (PGK12.1 and E8) than male (WD44 and E14) undifferentiated ES cells (*p<0.05). (B) H3K4me3 enrichment during differentiation of female PGK12.1 and male WD44 ES cells shows lower levels in male ES cells and a decrease of between day 0 and 15 in agreement with gene silencing after differentiation of these ES cells (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003489#pgen-1003489-g001" target="_blank">Figure 1</a>). (C) KDM6A occupancy at the 5′ end of <i>Rhox6</i> and <i>9</i> during differentiation of female PGK12.1 ES cells and male WD44 ES cells. (D) H3K27me3 levels at the 5′ end of <i>Rhox6</i> and <i>9</i> mirror KDM6A occupancy changes. The increase at day 15 is due to X inactivation in female PGK12.1 ES cells (see also Figures S2B, S4, and S6). Average enrichment/occupancy for two separate ChIP experiments is shown as ChIP/input (A, B, C).</p

<i>Rhox6</i> and <i>9</i> are bivalent and preferentially occupied by KDM6A in female ES cells.

<p>H3K27me3, H3K4me3 and KDM6A enrichment profiles in undifferentiated female PGK12.1 (pink) and male WD44 ES (blue) cells at representative genes from each <i>Rhox</i> subcluster (α, β, and γ) demonstrate that only <i>Rhox6</i> and <i>9</i> are highly enriched with both histone modifications and are bound by KDM6A (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003489#pgen.1003489.s006" target="_blank">Figure S6</a>). <i>Rhox3e</i> (α cluster) is enriched in H3K27me3 but not H3K4me3 or KDM6A, and <i>Rhox12</i> (γ cluster) shows little enrichment for the proteins analyzed. Significant enrichment peaks based on Nimblescan analysis (FDR score <.05) are shown. Data uploaded to UCSC genome browser (NCBI36/mm8).</p

Female Bias in <i>Rhox6</i> and <i>9</i> Regulation by the Histone Demethylase KDM6A

<div><p>The <i>Rho</i>x cluster on the mouse X chromosome contains reproduction-related homeobox genes expressed in a sexually dimorphic manner. We report that two members of the <i>Rhox</i> cluster, <i>Rhox6</i> and <i>9</i>, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Consistent with other homeobox genes, <i>Rhox6</i> and <i>9</i> are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells, KDM6A is specifically recruited to <i>Rhox6</i> and <i>9</i> for gene activation, a process inhibited by <i>Kdm6a</i> knockdown in a dose-dependent manner. In contrast, KDM6A occupancy at <i>Rhox6</i> and <i>9</i> is low in male ES cells and knockdown has no effect on expression. In mouse ovary where <i>Rhox6</i> and <i>9</i> remain highly expressed, KDM6A occupancy strongly correlates with expression. Our study implicates <i>Kdm6a</i>, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies.</p></div

<i>Rhox6</i> and <i>9</i> expression and KDM6A occupancy are high in ovary where the genes are imprinted.

<p>(A) <i>Rhox6</i> and <i>9</i> have significantly higher expression in mouse ovary than in testis, based on re-analyses of published expression array data for 14 testis and 12 ovary specimens (*p<0.05, **p<0.001). Expression normalized to array mean (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003489#pgen-1003489-g001" target="_blank">Figure 1C</a>). (B) KDM6A occupancy measured by ChIP-qPCR at the 5′end of <i>Rhox6</i> and <i>9</i> is higher in ovary than in testis, and is very low to undetectable in brain where these genes are not expressed <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003489#pgen.1003489-Maclean1" target="_blank">[19]</a>. Occupancy levels were normalized to input fractions. (C) <i>Kdm6a</i> has high expression in female tissues especially ovary based on analyses of published expression array data (***p<0.0001) (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003489#pgen-1003489-g001" target="_blank">Figure 1F</a>). (D) <i>Rhox6</i> and <i>9</i> are expressed from the maternal allele only in ovary because of imprinting. DNA sequence chromatograms of gDNA and RT-PCR (cDNA) products derived from ovary from female F1 mice obtained by mating <i>M. spretus</i> males with C57BL/6J females with or without an <i>Xist</i> mutation (<i>Xist^Δ</i> and <i>Xist^Δ−</i>). SNPs to distinguish <i>Rhox6</i> and <i>9</i> alleles on the active X (Xa) and on inactive X (Xi) are indicated below. In ovary from both <i>Xist^Δ</i> and <i>Xist^Δ−</i> mice the gDNA shows heterozygosity at the SNPs while the cDNA shows only the maternal allele, consistent with paternal imprinting. (E) By qRT-PCR <i>Rhox6</i> and <i>9</i> are more highly expressed in ovary from <i>Xist^Δ</i> mice in which the maternal X chromosome is expressed in all cells, compared to <i>Xist^Δ−</i> mice in which there is random X inactivation (1.7-fold and 3-fold, respectively), suggesting that <i>Rhox6</i> and <i>9</i> are silenced by X inactivation. Values represent the expression ratio between <i>Xist^Δ</i> and <i>Xist^Δ−</i> ovaries.</p

Validation of <i>Rlim</i>, <i>Shroom4</i>, <i>Car5b</i>, <i>Hdac6</i>, <i>5530601H04Rik</i> expression profiles and <i>Firre</i> mRNA profiles.

<p>(A) Sanger sequencing tracings of <i>Rlim</i> cDNA confirm bi-allelic expression in Patski cells but not brain, while gDNA sequence tracings show SNP heterozygosity (C in BL6 and T in <i>spretus</i>). Arrows indicate SNP positions. (B, C) Sanger sequencing tracings of <i>Shroom4</i> (B) and <i>Carb5</i> (C) cDNA confirm that these genes are subject to XCI in F1 kidney while they were shown to escape XCI in Patski cells [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005079#pgen.1005079.ref018" target="_blank">18</a>]. gDNA sequence tracings show SNP heterozygosity (<i>Shroom4</i>—G in BL6 and A in <i>spretus</i>; <i>Car5b</i>—G and C in BL6; A and T in <i>spretus</i>). Arrows indicate SNP positions. (D, E) Validation of escape from XCI for <i>Hdac6</i>. (D) Gel electrophoresis of RT-PCR products using non-species-specific primers, <i>spretus</i>-specific primers, and BL6-specific primers (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005079#pgen.1005079.s014" target="_blank">S10 Table</a>) in BL6, <i>spretus</i>, Patski cells and F1 kidney. <i>ActinB</i> was used as a control. Control reactions include "No RT" (no reverse transcriptase) and H₂O (instead of primers). Sanger sequencing tracing confirms heterozygosity (A in BL6 and G in <i>spretus</i>) in the left primer (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005079#pgen.1005079.s014" target="_blank">S10 Table</a>). (E) Xi expression of <i>Hdac6</i> was determined to be 9% of total expression in Patski cells by gel band quantification measured by ImageJ. (F) Sanger sequencing tracings of <i>5530601H04Rik</i> cDNA confirms that the lncRNA escapes XCI in kidney and Patski cells, while gDNA sequence tracings show heterozygosity (T and A in BL6; A and G in <i>spretus</i>). Arrows indicate SNP positions. (G) mRNA SNP read distribution profiles on the Xi and Xa for <i>Firre</i>, a lncRNA that escapes XCI in mouse tissues and Patski cells. Note that <i>Firre</i> is classified as a variable escape gene in brain (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005079#pgen.1005079.s015" target="_blank">S1 Dataset</a>). Xa SNP reads are in blue and Xi SNP reads in green.</p

Xi-associated but not Xa-associated CTCF peak clusters co-localize with escape regions.

<p>(A) Significant CTCF Xi-binding clusters were mapped along the Xi in brain and Patski cells. Xi- and both-preferred peaks were determined by a binomial model and used for density analysis. Red bars represent merger of clusters of CTCF Xi-binding peaks, while purple dots represent escape genes. Significant Xi-binding CTCF binding clusters tend to co-localize with chromatin containing escape genes. Little change was seen after removal of promoter-associated CTCF binding (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005079#pgen.1005079.s003" target="_blank">S3B Fig</a>). Horizontal axis represents the Xi in Mb. The vertical axis is the negative log of the calculated binomial p-value (-log (p-value)). The thin red dashed line represents a 0.01 p-value cutoff. (B) Similar analysis for CTCF Xa- and both-preferred peaks. There was no significant CTCF co-localization with escape genes on the Xa in either brain or Patski cells. (C) Average CTCF Xi-SNP read counts in ten 100bp windows at promoters (0.5kb upstream and downstream of the TSS) is plotted against mRNA-seq Xi-SNP read counts escape genes (purple) and for genes subject to XCI (gray) in brain and Patski cells. In brain, a higher proportion of escape genes (6/14; Fisher’s exact test, p = 5e^-9) had an average ≥10 reads (black line) at their promoter compared to genes subject to XCI (0/403). Similarly, in Patski cells a higher proportion of escape genes (9/65; Fisher’s exact test, p = 0.0004) had an average of ≥1 read (black line) at their promoter compared to genes subject to XCI (3/204).</p

Escape from X Inactivation Varies in Mouse Tissues

<div><p>X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape genes in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a binomial model to assess allelic expression, we demonstrate a continuum between complete silencing and expression from the inactive X (Xi). The validity of the RNA-seq approach was verified using RT-PCR with species-specific primers or Sanger sequencing. Both common escape genes and genes with significant differences in XCI status between tissues were identified. Such genes may be candidates for tissue-specific sex differences. Overall, few genes (3–7%) escape XCI in any of the mouse tissues examined, suggesting stringent silencing and escape controls. In contrast, an in vitro system represented by the embryonic-kidney-derived Patski cell line showed a higher density of escape genes (21%), representing both kidney-specific escape genes and cell-line specific escape genes. Allele-specific RNA polymerase II occupancy and DNase I hypersensitivity at the promoter of genes on the Xi correlated well with levels of escape, consistent with an open chromatin structure at escape genes. Allele-specific CTCF binding on the Xi clustered at escape genes and was denser in brain compared to the Patski cell line, possibly contributing to a more compartmentalized structure of the Xi and fewer escape genes in brain compared to the cell line where larger domains of escape were observed.</p></div