RT Journal Article
SR Electronic
T1 VEGFA’s distal enhancer regulates its alternative splicing in CML
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.01.09.426072
DO 10.1101/2021.01.09.426072
A1 Sara Dahan
A1 Klil Cohen
A1 Mercedes Bentata
A1 Eden Engal
A1 Ahmad Siam
A1 Gillian Kay
A1 Yotam Drier
A1 Shlomo Elias
A1 Maayan Salton
YR 2021
UL http://biorxiv.org/content/early/2021/01/10/2021.01.09.426072.abstract
AB Enhancer demethylation in leukemia and lymphoma was shown to lead to overexpression of genes which promote cancer characteristics. The vascular endothelial growth factor A (VEGFA) enhancer, located 157 Kb downstream of its promoter, is demethylated in chronic myeloid leukemia (CML). VEGFA has several alternative splicing isoforms with different roles in vascularization and cancer progression. Since transcription and splicing are coupled in space and time, we hypothesized that the VEGFA enhancer can also regulate the gene’s alternative splicing to contribute to the pathology of CML. Our results show that mutating the VEGFA +157 enhancer promotes exclusion of exons 6b and 7 and activating the enhancer by tethering a chromatin activator has the opposite effect. In line with these results, CML patients display high enhancer activity and inclusion of VEGFA exons 6b and 7. To search for a key protein connecting transcription with alternative splicing, we analyzed 161 chromatin immunoprecipitation (ChIP)-seq experiments for DNA binding proteins and found that PML and CCNT2 bind VEGFA’s promoter and enhancer. CCNT2 is a positive regulator of RNA polymerase II (RNAPII) transcription elongation and indeed its silencing promotes exclusion of exons 6b and 7. Slowing down RNAPII elongation promotes exclusion of exons 6b and 7. Thus our results suggest that VEGFA’s +157 enhancer regulates its alternative splicing by increasing RNAPII elongation rate via CCNT2. Our work demonstrates the importance of the interplay between transcription and alternative splicing.Competing Interest StatementThe authors have declared no competing interest.