Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex.

BackgroundThe genetic programs required for development of the cerebral cortex are under intense investigation. However, non-coding DNA elements that control the expression of developmentally important genes remain poorly defined. Here we investigate the regulation of Fezf2, a transcription factor that is necessary for the generation of deep-layer cortical projection neurons.ResultsUsing a combination of chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) we mapped the binding of four deep-layer-enriched transcription factors previously shown to be important for cortical development. Building upon this we characterized the activity of three regulatory regions around the Fezf2 locus at multiple stages throughout corticogenesis. We identified a promoter that was sufficient for expression in the cerebral cortex, and enhancers that drove reporter gene expression in distinct forebrain domains, including progenitor cells and cortical projection neurons.ConclusionsThese results provide insight into the regulatory logic controlling Fezf2 expression and further the understanding of how multiple non-coding regulatory domains can collaborate to control gene expression in vivo

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Motivation: The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets

Disruption of SATB2 or its long-range cis-regulation by SOX9 causes a syndromic form of Pierre Robin Sequence

Heterozygous loss-of-function (LOF) mutations in the gene encoding the DNA-binding protein, SATB2, result in micrognathia and cleft palate in both humans and mice. In three unrelated individuals, we show that translocation breakpoints (BPs) up to 896 kb 3′ of SATB2 polyadenylation site cause a phenotype which is indistinguishable from that caused by SATB2 LOF mutations. This syndrome comprises long nose, small mouth, micrognathia, cleft palate, arachnodactyly and intellectual disability. These BPs map to a gene desert between PLCL1 and SATB2. We identified three putative cis-regulatory elements (CRE1–3) using a comparative genomic approach each of which would be placed in trans relative to SATB2 by all three BPs. CRE1–3 each bind p300 and mono-methylated H3K4 consistent with enhancer function. In silico analysis suggested that CRE1–3 contain one or more conserved SOX9-binding sites, and this binding was confirmed using chromatin immunoprecipitation on cells derived from mouse embryonic pharyngeal arch. Interphase bacterial artificial chromosome fluorescence in situ hybridization measurements in embryonic craniofacial tissues showed that the orthologous region in mice exhibits Satb2 expression-dependent chromatin decondensation consistent with Satb2 being a target gene of CRE1–3. To assess their in vivo function, we made multiple stable reporter transgenic lines for each enhancer in zebrafish. CRE2 was shown to drive SATB2-like expression in the embryonic craniofacial region. This expression could be eliminated by mutating the SOX9-binding site of CRE2. These observations suggest that SATB2 and SOX9 may be acting together via complex cis-regulation to coordinate the growth of the developing jaw

A Half-Colonization: The Problem of the White Colonial Woman Writer

In the 1986 book, A Double Colonization: Colonial and Post-Colonial Women\u27s Writing, the editors (Kirsten Hoist Petersen and Anna Rutherford) claim that all women in colonial and post-colonial countries are doubly-colonized: by patriarchal society as well as by the dominant imperial or metropolitan power. In my view, A Double Colonization makes insufficient distinction between the position of Australian, Canadian, South African, or Creole women of European descent and their Aboriginal, Native Indian, Black African, or West Indian counterparts - that is, between the daughters of the colonizers and the colonized.^ The white-settler woman and her descendants occupy a privileged position in comparison to their darker native or slave-descended sisters. While the native woman is truly doubly-oppressed or doubly-colonized, by male dominance as well as by white economic and social dominance, the white settler woman can best be described as half-colonized. Although she too is oppressed by white men and patriarchal structures, she shares in the power and guilt of the colonists

Review of Louise Yelin, From the Margins of Empire: Christina Stead, Doris Lessing, Nadine Gordimer.

Louise Yelin, From the Margins of Empire: Christina Stead, Doris Lessing, Nadine Gordimer. Ithaca: Cornell University Press, 1998. 240 pp. ISBN 0801485053

White Eve in the "petrified garden" : the colonial African heroine in the writing of Olive Schreiner, Isak Dinesen, Doris Lessing and Nadine Gordimer

Olive Schreiner, writing in the tradition of George Eliot and the Brontës, was an isolated yet original figure who opened up new directions in women's fiction. In her novels, The Story of an African Farm (1883) and From Man to Man (1926) she developed a feminist critique of colonialism that was based on her own coming-of-age as a writer in South Africa. Schreiner's work inspired and influenced Isak Dinesen, Doris Lessing and Nadine Gordimer, who have pursued their visions of the colonial African heroine in changing forms which nevertheless consciously hark back to the "mother novel." Dinesen's Out of Africa (1937), Lessing's Martha Quest (1952) and Gordimer's The Lying Days (1953) are in a sense revisions of Schreiner's Story of an African Farm. These texts, together with later novels by Lessing and Gordimer (such as Shikasta and Burger's Daughter, 1979) and key short stories by the four writers, form a body of writing I call the "African Farm" texts. Written in different colonial countries—South Africa, Kenya and Rhodesia—in response to different historical circumstances, from different ideological and aesthetic stances, the "African Farm" fictions depict the problematic situation of the white African heroine who is alienated both from white colonial society and from black Africa. Through her own rebellion against patriarchal mores as she struggles to define herself as an artistic, intellectual woman in a hostile environment, she uncovers the connections between patriarchy and racism under colonialism. She begins to identify with the black Africans in their oppression and their incipient struggle for independence; however she cannot shed her white inheritance of privilege and guilt. Just as colonial society (the white "African Farm") becomes for her a desert, a cemetery, a false, barren, "petrified garden," so black Africa becomes its idealized counterpart: a fertile realm of harmony and possibility, the true Garden of Eden from which she, as White Eve, is exiled. I trace the "African Farm" theme and imagery through the work of other white Southern African writers, such as J.M. Coetzee, whose stark, poetic, postmodernist novels can be read as a coda to the realistic fiction of the four women writers. Finally, I look at the post-"African Farm" texts of such transitional writers as Bessie Head, whose novels of black Africa preserve a suggestive link with Schreiner.Arts, Faculty ofEnglish, Department ofGraduat

Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex.

BackgroundThe genetic programs required for development of the cerebral cortex are under intense investigation. However, non-coding DNA elements that control the expression of developmentally important genes remain poorly defined. Here we investigate the regulation of Fezf2, a transcription factor that is necessary for the generation of deep-layer cortical projection neurons.ResultsUsing a combination of chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) we mapped the binding of four deep-layer-enriched transcription factors previously shown to be important for cortical development. Building upon this we characterized the activity of three regulatory regions around the Fezf2 locus at multiple stages throughout corticogenesis. We identified a promoter that was sufficient for expression in the cerebral cortex, and enhancers that drove reporter gene expression in distinct forebrain domains, including progenitor cells and cortical projection neurons.ConclusionsThese results provide insight into the regulatory logic controlling Fezf2 expression and further the understanding of how multiple non-coding regulatory domains can collaborate to control gene expression in vivo

Massively parallel functional dissection of mammalian enhancers in vivo

The functional consequences of genetic variation in mammalian regulatory elements are poorly understood. We report the in vivo dissection of three mammalian liver enhancers at single nucleotide resolution via a massively parallelized reporter assay. For each enhancer, we synthesized a library of >100,000 mutant haplotypes with 2–3% divergence from wild-type. Each haplotype was linked to a unique sequence tag embedded within a transcriptional cassette. We introduced each enhancer library into mouse liver and measured the relative activities of individual haplotypes en masse by sequencing of the transcribed tags. Linear regression yielded highly reproducible estimates of the impact of every possible single nucleotide change on enhancer activity. The functional impact of most mutations was modest, with ~22% impacting activity by >1.2-fold, and only ~3% by >2-fold. These results suggest that mammalian enhancers are relatively robust to single nucleotide changes. Several, but not all positions with higher impact showed evidence for purifying selection, or co-localized with known liver-associated transcription factor binding sites, demonstrating the value of empirical high-resolution functional analysis