Integration of H-2Z1, a Somatosensory Cortex-Expressed Transgene, Interferes with the Expression of the<i>Satb1</i>and<i>Tbc1d5</i>Flanking Genes and Affects the Differentiation of a Subset of Cortical Interneurons

Narboux-Nême, Nicolas; Goïame, Rosette; Matteï, Marie‐Geneviève; Cohen-Tannoudji, Michel; Wassef, Marion

doi:10.1523/jneurosci.6068-11.2012

Cited by 11 publications

(10 citation statements)

References 51 publications

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“…The intragenic elements include secondary promoters, enhancer, repressor and insulating elements, and sequence coding for miRNAs affecting stability of transcripts. There are examples of transgenes acting in cis to affect neighboring gene regulation due to the disruption of regulatory elements [e.g., 11 – 12 , 36 ]. Disruption of cis-regulatory elements was more likely to occur in the DEL targeting strategy than in the TRAP strategy and may account for why local gene effects were more frequently found flanking DEL targets.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression

West¹,

Engelhard

Adkisson³

et al. 2016

PLoS Genet

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The unintended consequences of gene targeting in mouse models have not been thoroughly studied and a more systematic analysis is needed to understand the frequency and characteristics of off-target effects. Using RNA-seq, we evaluated targeted and neighboring gene expression in tissues from 44 homozygous mutants compared with C57BL/6N control mice. Two allele types were evaluated: 15 targeted trap mutations (TRAP); and 29 deletion alleles (DEL), usually a deletion between the translational start and the 3’ UTR. Both targeting strategies insert a bacterial beta-galactosidase reporter (LacZ) and a neomycin resistance selection cassette. Evaluating transcription of genes in +/- 500 kb of flanking DNA around the targeted gene, we found up-regulated genes more frequently around DEL compared with TRAP alleles, however the frequency of alleles with local down-regulated genes flanking DEL and TRAP targets was similar. Down-regulated genes around both DEL and TRAP targets were found at a higher frequency than expected from a genome-wide survey. However, only around DEL targets were up-regulated genes found with a significantly higher frequency compared with genome-wide sampling. Transcriptome analysis confirms targeting in 97% of DEL alleles, but in only 47% of TRAP alleles probably due to non-functional splice variants, and some splicing around the gene trap. Local effects on gene expression are likely due to a number of factors including compensatory regulation, loss or disruption of intragenic regulatory elements, the exogenous promoter in the neo selection cassette, removal of insulating DNA in the DEL mutants, and local silencing due to disruption of normal chromatin organization or presence of exogenous DNA. An understanding of local position effects is important for understanding and interpreting any phenotype attributed to targeted gene mutations, or to spontaneous indels.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression

West¹,

Engelhard

Adkisson³

et al. 2016

PLoS Genet

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“…al, 1999;Mukai et al, 2006) , or the endogenous gene influences expression of the transgene (e.g., Kothary et al, 1988, Sharpe et. al, 1999Narboux-Nême et al, 2012).…”

Section: Mapping Mouse Transgene Integration Sites Is Feasible and Usmentioning

confidence: 99%

Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes

Laboulaye

Duan

Qiao

et al. 2018

Preprint

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Transgenic mouse lines are routinely employed to label and manipulate distinct cell types. The transgene generally comprises cell-type specific regulatory elements linked to a cDNA encoding a reporter or other proteins. However, off-target expression seemingly unrelated to the regulatory elements in the transgene is often observed, and sometimes suspected to reflect influences related to the site of transgene integration in the genome. To test this hypothesis, we used a proximity ligation-based method, Targeted Locus Amplification (TLA), to map the insertion sites of three well-characterized transgenes that appeared to exhibit insertion site-dependent expression in retina. The nearest endogenous genes to transgenes HB9-GFP, Mito-P, and TYW3 are Cdh6, Fat4 and Khdrbs2, respectively. For two lines, we demonstrate that expression reflects that of the closest endogenous gene (Fat4 and Cdh6), even though the distance between transgene and endogenous gene is 550 and 680 kb, respectively. In all three lines, the transgenes decrease expression of the neighboring endogenous genes. In each case, the affected endogenous gene was expressed in at least some of the cell types that the transgenic line has been used to mark and study. These results provide insights into the effects of transgenes and endogenous genes on each other's expression, demonstrate that mapping insertion site is valuable for interpreting results obtained with transgenic lines, and indicate that TLA is a reliable method for integration site discovery.

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“…SATB1 has been shown to be essential for the specification of the SST interneuron phenotype (Batista-Brito et al, 2008;Close et al, 2012;Denaxa et al, 2012;Narboux-Nême et al, 2012). SATB1 can affect gene expression at multiple levels.…”

Section: Discussionmentioning

confidence: 99%

ALK4 coordinates extracellular and intrinsic signals to regulate development of cortical somatostatin interneurons

Göngrich

Krapacher

Munguba

et al. 2019

Journal of Cell Biology

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Although the role of transcription factors in fate specification of cortical interneurons is well established, how these interact with extracellular signals to regulate interneuron development is poorly understood. Here we show that the activin receptor ALK4 is a key regulator of the specification of somatostatin interneurons. Mice lacking ALK4 in GABAergic neurons of the medial ganglionic eminence (MGE) showed marked deficits in distinct subpopulations of somatostatin interneurons from early postnatal stages of cortical development. Specific losses were observed among distinct subtypes of somatostatin+/Reelin+ double-positive cells, including Hpse+ layer IV cells targeting parvalbumin+ interneurons, leading to quantitative alterations in the inhibitory circuitry of this layer. Activin-mediated ALK4 signaling in MGE cells induced interaction of Smad2 with SATB1, a transcription factor critical for somatostatin interneuron development, and promoted SATB1 nuclear translocation and repositioning within the somatostatin gene promoter. These results indicate that intrinsic transcriptional programs interact with extracellular signals present in the environment of MGE cells to regulate cortical interneuron specification.

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Integration of H-2Z1, a Somatosensory Cortex-Expressed Transgene, Interferes with the Expression of theSatb1andTbc1d5Flanking Genes and Affects the Differentiation of a Subset of Cortical Interneurons

Cited by 11 publications

References 51 publications

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression

Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes

ALK4 coordinates extracellular and intrinsic signals to regulate development of cortical somatostatin interneurons

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