title: Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.
abstract: N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing "basal" degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Schraga
authors: S
authors: Schwartz
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Maxwell R
authors: MR
authors: Mumbach
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Marko
authors: M
authors: Jovanovic
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors: Tim
authors: T
authors: Wang
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Graduate Program in Immunology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA.
authors: Karolina
authors: K
authors: Maciag
authors: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors: G Guy
authors: GG
authors: Bushkin
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Philipp
authors: P
authors: Mertins
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Dmitry
authors: D
authors: Ter-Ovanesyan
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Naomi
authors: N
authors: Habib
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors: Davide
authors: D
authors: Cacchiarelli
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Neville E
authors: NE
authors: Sanjana
authors: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors: Elizaveta
authors: E
authors: Freinkman
authors: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
authors: Michael E
authors: ME
authors: Pacold
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Rahul
authors: R
authors: Satija
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
authors: Tarjei S
authors: TS
authors: Mikkelsen
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA.
authors: Nir
authors: N
authors: Hacohen
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors: Feng
authors: F
authors: Zhang
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors: Steven A
authors: SA
authors: Carr
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA. Electronic address: lander@broadinstitute.org.
authors: Eric S
authors: ES
authors: Lander
authors: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA. Electronic address: aregev@broad.mit.edu.
authors: Aviv
authors: A
authors: Regev
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D057809:HEK293 Cells; D006801:Humans; D008745:Methylation; D008780:Methyltransferases / Q000378:metabolism*; D051379:Mice; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism*
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger; C065638:6-methyladenine mRNA methyltransferase; D008780:Methyltransferases