Additional file 16 of A Trem2R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques
Creators: name: Tran, Kristine M.
name: Kawauchi, Shimako
name: Kramár, Enikö A.
name: Rezaie, Narges
name: Liang, Heidi Yahan
name: Sakr, Jasmine S.
name: Gomez-Arboledas, Angela
name: Arreola, Miguel A.
name: Cunha, Celia da
name: Phan, Jimmy
name: Wang, Shuling
name: Collins, Sherilyn
name: Walker, Amber
name: Shi, Kai-Xuan
name: Neumann, Jonathan
name: Filimban, Ghassan
name: Shi, Zechuan
name: Milinkeviciute, Giedre
name: Javonillo, Dominic I.
name: Tran, Katelynn
name: Gantuz, Magdalena
name: Forner, Stefania
name: Swarup, Vivek
name: Tenner, Andrea J.
name: LaFerla, Frank M.
name: Wood, Marcelo A.
name: Mortazavi, Ali
name: MacGregor, Grant R.
name: Green, Kim N.
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 16: Supplemental Figure 15. CRISPR-generated Trem2R47H alleles and their impact on induction of cryptic splicing events. DNA sequence alignment of part of exon 2 of mouse (Mm) Trem2 from wild-type and four CRISPR-generated R47H encoding alleles (from top to bottom, Cheng-Hathaway et. al [34], Trem2R47H CSS(JAX 027918), Xiang et. al [35] and Trem2R47H NSS (JAX 034036, this study). The R47 coding triplet and amino acid in mouse is shown in green, with the G to A transition that changes the R to H in each CRISPR allele shown in red. Blue nucleotides in each CRISPR-generated allele denote synonymous DNA bases co-introduced with the G to A transition. The equivalent region of human (Hs) TREM2 is shown at the top with nucleotide differences between mouse and human in brown. A summary of the presence of cryptic splicing and quantity of transcripts relative to the wild type allele is shown at the right of each CRISPR-generated allele (data from this study and [34, 35]. Evidence for cryptic splicing from the R47H Trem2 allele described in Cheng-Hathaway et. al [34] is from transfection of cells with recombinant DNA expression constructs as reported [35]. The underlined AG dinucleotide denotes the end of the “intronic” sequence removed in events using the cryptic splice site (identified in Xiang et. al [35] and this study) with the corresponding underlined TGA stop codon produced by the cryptic splice event. The bottom of the figure shows a consensus sequence for a splice branch point (YUVAY; Y = T or C; V = A, C or G [73]) and a polypyrimidine tract, with bases matching the wildtype mouse Trem2 sequence in green, which may stimulate cryptic splicing. Splice branch sequences in mammals are highly degenerate [74, 75]. Comparison of the sequence of each CRISPR-generated mouse R47H allele combined with results from studies using a cell culture-based assay, including analysis of the related human DNA sequence [35], does not provide clear insight into why transcripts from some mouse CRISPR-generated R47H alleles undergo cryptic splicing while those from the Trem2 R47H NSS allele apparently do not.