Se-Hee Choe's research while affiliated with Korea Research Institute of Bioscience and Biotechnology KRIBB and other places

... Even though genomic data are a useful tool for examining the genetic architecture of a given species or individual, they often do not provide information about which genes are expressed and where (i.e., which tissue/organ); the magnitude of expression; or the development stage(s) at which they are expressed. Ultimately, the generation of organspecific transcriptomes will be possible at various points in a model organism's life history, as well as under specific experimental conditions, including anti-aging interventions As the field has grown, the human aging transcriptome has been shown to be a robust tool for estimating the biological age of an individual [152], as well as measuring agerelated changes in tissue-specific transcriptomes of model organisms such as monkeys [153], mice [154], D. melanogaster [155,156], C. elegans [157,158], and yeast [159]. Not surprisingly, relatively little is known about the aging transcriptome in birds, with the exception of studies of brain [160] and thymus [161] transcriptomes in populations of domestic chicken. ...

... SLF1 depletion can significantly increase abnormalities in anaphase cells 33 . ACTR8 is a key component of the INO80 complex, which has critical functions in DNA replication, repair and recombination, transcription and heterochromatin maintenance 34 . On the other hand, gas2 and pbrm1 were hypo-methylated in haploid females and males. ...

... Alu insertion induces skipping of exon 3 of the CD58 transcript, originating a frameshifted transcript [202] PKLR PK deficiency by activation of a premature stop codon encoded by an exonized Alu Yb9 [203] BLOC1S2 Requires a SINE-MIR for exonization of the Alu element. Exonization activates premature stop codons [204] FVIII Mutation in hnRNPC binding sites exonizes an Alu Y and truncates F8 protein [205] SMN Alu Y element reduces SMN mRNA levels (byNMD) in Spinal Muscular Atrophy [206] ATP7Bgene ...

... SureSelect MethylSeq is a type of methylation capture sequencing (MC-seq) using biotinylated RNA baits to capture the genomic areas of interest for subsequent bisulfite sequencing. This method allows quantitative analysis of DNA methylation with single base resolution [109,110]. The rat SureSelect MethylSeq has been designed to target non-redundant promoters, CpG islands, island shores as well as previously identified GC-rich sequences [111]. ...

... Multiple alignment revealed that these functional domains were conserved between species. However, there is a transmembrane domain elimination in A. davidianus TYR, similar to that of Macaca fascicularis [32], indicating that the quantity and distribution of TYR functional domains vary among species. ...

... The differential AS number of GCR-Alu-1 versus NC-1 is significantly greater than that of GCR-L1-1 versus NC-1 (P = 0.038, Supplementary Table S5). It is reported that both L1 and Alu contribute for AS and it seems that the function of Alu on AS is even stronger that that of L1 (44)(45)(46)(47). AS of RNA plays important roles in the gene expression regulation of eukaryotes (48) and aberrant AS is an important contribution for carcinogenesis (49). ...

... Efforts to establish the cellular mechanism of pathophysiology in animal models have been inconclusive so far. While the TSEN complex is conserved from archaea, TSEN54 has undergone evolutionary changes in the primate lineage (Lee et al., 2016b). Notably, the amino acid sequence around TSEN54 :c.919G>T, p.(A307S) is not conserved between species (Budde et al., 2008). ...

... For example, researchers discovered that SETD7-mediated H3K4me3 enrichment on the lncRNA DRAIC promoter regulated the growth and metastasis of gliomas (39 (15). In humans, alternatively spliced ZKSCAN5 transcripts with different 5′-untranslated regions have been confirmed (40). However, the biological function of ZKSCAN5 is currently largely unknown. ...

... Alu elements are useful tools to study genome evolution, phylogenetics, and population biology in primates [45,46]. Moreover, Alu-exonized transcripts can be useful for analyzing the mechanism underlying the creation of new transcript variants during primate evolution by estimating the transcript generation time [47][48][49]. ...

... However, this picture has recently changed, with several groups finding evidence of tau pathology similar to human AD in some (but not all) of aged (more than 20 years) African green monkeys 240,241 , rhesus 242,243 and cynomolgus macaques 244 . To artificially replicate the pathophysiological features of AD in NHP, several strategies have also been tested such as the induction of insulin deficiency using streptozotocin 245,246 , the intraventricular injection of synthetic amyloid-beta oligomers 247 , or the injection into the EC of a viral vector expressing a double tau mutation 248 . Finally, the advent of genetic engineering tools in NHPs has recently led to the generation of marmoset monkeys carrying mutations in the PSEN1 gene, which is involved in familial forms of AD 249,250 . ...