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. 2022 May 21;8:48. doi: 10.1038/s41421-022-00395-1

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a–c Transcriptome-wide m⁶A-seq analyses of control or PCIF1-depleted AGS cells. Distribution of m⁶A/m⁶Am peaks across mRNA segments in AGS cells (a). Each segment was normalized according to its average length by RefSeq annotation. Motif analysis of m⁶Am peaks of mRNAs modified by PCIF1 in AGS cells (b). BCA, A = m⁶Am; B = C, G, or U. E-value = 4.5e−54. Boxplot analysis of change of m⁶A/m⁶Am peaks intensity in AGS cells upon PCIF1 knockdown is shown (c). d m⁶A-Seq analysis of top 20 down-regulated genes in m⁶Am abundance in AGS cells. The data are presented by the fold change of peak intensity (shControl/shPCIF1). ASH2L ASH2 (absent, small, or homeotic)-like, BRF1 BRF1 RNA polymerase III transcription initiation factor subunit, C1orf35 chromosome 1 open reading frame 35, CLPTM1L CLPTM1 (cleft lip and palate transmembrane protein 1)-like, COPS8 COP9 signalosome subunit 8, DNTTIP1 deoxynucleotidyltransferase terminal interacting protein 1, DUSP12 dual specificity phosphatase 12, GTPBP3 GTP binding protein 3, mitochondrial; ITPA inosine triphosphatase, MISP3 MISP family member 3, PIDD1 p53-induced death domain protein 1, PRKCE protein kinase C epsilon, SMARCD3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3, SMDT1 single-pass membrane protein with aspartate rich tail 1, SPCS3 signal peptidase complex subunit 3, TGIF1 TGFB induced factor homeobox 1, TM9SF1 transmembrane 9 superfamily member 1, UBE2J2 ubiquitin conjugating enzyme E2 J2, ZNF17 zinc finger protein 17, ZNF276 zinc finger protein 276. e Western analysis of the potential target genes of PCIF1 predicted by m⁶A-Seq and Kaplan–Meier survival curves (Supplementary Fig. S4) in control and PCIF1-depleted AGS cells. And intensities of PCIF1 potential target genes in PCIF1-depleted cells compared to those in control cells are shown. f The analysis of m⁶A/m⁶Am peaks on TM9SF1 gene in control and PCIF1-depleted AGS cells. g, h m⁶A-RIP analysis of TM9SF1 mRNA in AGS cells transfected with the indicated shRNA and plasmids. The enrichment of TM9SF1 mRNA in immunoprecipitation (IP) or input fraction was determined by qRT-PCR. Data are shown as means ± SD. N.S. means not significant; ***P < 0.001, Student’s t-test.