Premium
Discrete LIN28 binding sites in mature messenger RNA sequences reveals regulation of a network of splicing factors and downstream alternative splicing patterns
Author(s) -
Wilbert Melissa L,
Huelga Stephanie C,
Vu Anthony Q,
Stark Thomas J,
Massirer Katlin B,
Chen Stella x,
Liang Tiffany Y,
Yeo Gene W
Publication year - 2012
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.26.1_supplement.951.4
Subject(s) - lin28 , rna splicing , microrna , biology , rna binding protein , reprogramming , translation (biology) , messenger rna , alternative splicing , microbiology and biotechnology , embryonic stem cell , cold shock domain , rna , gene , genetics , induced pluripotent stem cell
LIN28 is a conserved RNA binding protein important for pluripotency, reprogramming and oncogenesis. Studies thus far have focused primarily on the roles of LIN28 through its regulation of the microRNA (miRNA) let‐7. Here, our goal was to identify and characterize the network of mature messenger RNA targets of LIN28 in order to explain its let‐7 independent regulatory mechanisms. Using UV cross‐linking and immunoprecipitation of the LIN28 protein followed by high‐throughput sequencing (CLIP‐seq) we have identified direct LIN28 binding regions on target RNAs in human embryonic stem cells and somatic cells expressing exogenous LIN28. We found that in addition to hundreds of miRNAs, LIN28 directly binds to thousands of human mRNA genes, including LIN28 itself and dozens of splicing regulators. Furthermore, we confirm in a set of targets that this binding results in an increase in translation. Finally, splicing‐sensitive junction arrays demonstrated that LIN28 over‐expression causes widespread downstream alternative splicing differences. These findings show that LIN28 contributes to cellular homeostasis via direct mRNA interactions and downstream AS events, alterations of which may result in cancer and differentiation.