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RNA-seq analysis reveals downregulation of TGFb/BMP pathway genes in Mcm5 mutants.

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posted on 23.06.2022, 20:05 authored by Irene Rubio-Ferrera, Pablo Baladrón-de-Juan, Luis Clarembaux-Badell, Marta Truchado-Garcia, Sheila Jordán-Álvarez, Stefan Thor, Jonathan Benito-Sipos, Ignacio Monedero Cobeta

(A) Bland-Altman graph showing differences in the expression of every gene analyzed through RNA-seq from control and Mcm5 mutants in St16-AFT embryos. The expression of every gene is represented by a dot. Dots are located in the graph according to change in expression between conditions in a logarithmic scale, when compared with the media of the normalized expression. Genes with differences in expression between genotypes are represented in red, otherwise they are grey. Genes represented in positive values show higher expression in Mcm5 mutants than in controls and vice versa (graph made with DESeq2, statistical analysis performed by hypergeometric distribution adjusted by Benjamini-Hochberg; p-value < 0,05). (B) Fold change histogram of the relative expression in Mcm5 mutants compared to the control of representative genes involved in Tv4 specification, ap, eya, nab, sqz, dimm, dac, svp, and genes involved in BMP signaling pathway, gbb, Mad, sax and tkv. (C) Alignment distribution of reads obtained after RNA-seq analysis of tkv gene in control and Mcm5 mutants. The top of the graph shows the enrichment in sequences corresponding to every exonic region and the gene sequence of tkv gene represented in indigo (TopHat2) and blue (Flybase). A striking reduction in read coverage for the exons 1 and 2 (black arrows) of the tkv gene in Mcm5 mutants comparing to the control is shown. On the bottom, the graph shows the different isoforms of tkv RNAm represented in magenta, other genes located in the same chromosome region in green (its RNAm in yellow), and non-coding RNAs in orange (Flybase) (graph made with TopHat2, IGV). Genotypes: (A, B) w1118 and Mcm5exc222/Mcm5exc222.