12 results found
Percharde M, Lin CJ, Ramalho-Santos M, 2021, Depletion of nuclear LINE1 RNA in mouse ESCs and embryos, STAR Protocols, Vol: 2
LINE1 is the most active and abundant family of retrotransposons; it is implicated in a number of pathologies, as well as in early embryo development. We present a protocol to specifically knockdown LINE1 in mouse embryonic stem cells and embryos, including details for the nucleofection and zygote microinjection of LINE antisense oligos, followed by RNA FISH validation. This protocol can be used in development, as well as other cell types where LINE1 is believed to be expressed. For complete information on the use and execution of this protocol, please refer to Percharde et al. (2018).
Lu JY, Chang L, Li T, et al., 2021, Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome, CELL RESEARCH, Vol: 31, Pages: 613-630, ISSN: 1001-0602
Kuwahara A, Lewis AE, Coombes C, et al., 2020, Delineating the early transcriptional specification of the mammalian trachea and esophagus, eLife, Vol: 9
<jats:p>The genome-scale transcriptional programs that specify the mammalian trachea and esophagus are unknown. Though NKX2-1 and SOX2 are hypothesized to be co-repressive master regulators of tracheoesophageal fates, this is untested at a whole transcriptomic scale and their downstream networks remain unidentified. By combining single-cell RNA-sequencing with bulk RNA-sequencing of Nkx2-1 mutants and NKX2-1 ChIP-sequencing in mouse embryos, we delineate the NKX2-1 transcriptional program in tracheoesophageal specification, and discover that the majority of the tracheal and esophageal transcriptome is NKX2-1 independent. To decouple the NKX2-1 transcriptional program from regulation by SOX2, we interrogate the expression of newly-identified tracheal and esophageal markers in Sox2/Nkx2-1 compound mutants. Finally, we discover that NKX2-1 binds directly to Shh and Wnt7b and regulates their expression to control mesenchymal specification to cartilage and smooth muscle, coupling epithelial identity with mesenchymal specification. These findings create a new framework for understanding early tracheoesophageal fate specification at the genome-wide level.</jats:p>
Lu JY, Shao W, Chang L, et al., 2020, Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation, CELL REPORTS, Vol: 30, Pages: 3296-+, ISSN: 2211-1247
Percharde M, Lin C-J, Yin Y, et al., 2018, A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity, CELL, Vol: 174, Pages: 391-+, ISSN: 0092-8674
Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, et al., 2018, The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output, CELL STEM CELL, Vol: 22, Pages: 369-+, ISSN: 1934-5909
Percharde M, Wong P, Ramalho-Santos M, 2017, Global Hypertranscription in the Mouse Embryonic Germline, CELL REPORTS, Vol: 19, Pages: 1987-1996, ISSN: 2211-1247
Percharde M, Bulut-Karslioglu A, Ramalho-Santos M, 2017, Hypertranscription in Development, Stem Cells, and Regeneration, DEVELOPMENTAL CELL, Vol: 40, Pages: 9-21, ISSN: 1534-5807
Percharde M, Azuara V, 2013, Essential roles for the nuclear receptor coactivator Ncoa3 in pluripotency, CELL CYCLE, Vol: 12, Pages: 195-196, ISSN: 1538-4101
Percharde M, Lavial F, Ng J-H, et al., 2012, Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming, GENES & DEVELOPMENT, Vol: 26, Pages: 2286-2298, ISSN: 0890-9369
Lopez J, Percharde M, Coley HM, et al., 2009, The context and potential of epigenetics in oncology, BRITISH JOURNAL OF CANCER, Vol: 100, Pages: 571-577, ISSN: 0007-0920
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