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Author Notes:

Correspondence should be addressed to Hongjun Song, Ph.D. (Email:shonqjui@jhmi.edu) or Peng Jin, Ph.D. (Email: peng.jin@emory.edu).

Y.Z., B.Y., J.S., P.J. and H.S. conceived the project, L.L. conducted 5hmC-capture and MeDIP experiments, and constructed sequencing libraries.

B.Y. performed bioinformatic analyses.

Y.Z. made FLAG-Lin28A-expressing and Lin28A KD mESC lines, and performed EMSA experiments.

B.Y and Y.Z. performed ChIP experiments.

N.S.K provided HA-Tet1 mESCs. Y.Z. and N.S.K performed IP-Westernblot experiments.

Q.S. provided Lin28A recombinant protein.

S.L. and Q.S. performed KD measurement.

X.C. conducted Lin28-DNA structure modeling and provided recombinant Tet1-CD protein.

H.W. performed statistic analyses.

S.H., H.Z. J.Q. and J.W. assisted with EMSA and protein microarray experiments.

Y.Z., B.Y., G-l.M., P.J. and H.S. wrote the manuscript.

All authors discussed results and commented on the manuscript.

We thank Mingjie Zhang, Kimberly Christian and members of Song, Ming and Jin laboratories for discussion, Shaohui Hu for suggestions on EMSA experiments, and L. Liu and Y. Cai for technical support.

Subjects:

Research Funding:

This work was supported by grants from NIH (NS047344 and MH087874) and MSCRF to H.S.; from NIH (NS079625 and HD073162) to P.J; from MSCRF and NIH (NS048271 and MH105128) and MSCRF to G.-l.M.; by postdoctoral fellowships from MSCRF to Y.Z., N.S.K.; by a postdoctoral fellowship from the National Ataxia Foundation to B.Y.

Keywords:

  • Science & Technology
  • Life Sciences & Biomedicine
  • Biochemistry & Molecular Biology
  • Cell Biology
  • EMBRYONIC STEM-CELLS
  • DNA METHYLATION
  • ADULT BRAIN
  • TRANSCRIPTIONAL REGULATION
  • GENOME
  • RNAS
  • 5-METHYLCYTOSINE
  • DEMETHYLATION
  • INTERACTOME
  • MODULATION

Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression

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Journal Title:

Molecular Cell

Volume:

Volume 61, Number 1

Publisher:

, Pages 153-160

Type of Work:

Article | Post-print: After Peer Review

Abstract:

Lin28, a well-known RNA-binding protein, regulates diverse cellular properties. All physiological functions of Lin28A characterized so far have been attributed to its repression of let-7 miRNA biogenesis or modulation of mRNA translational efficiency. Here we show that Lin28A directly binds to a consensus DNA sequence in vitro and in mouse embryonic stem cells in vivo. ChIP-seq and RNA-seq reveal enrichment of Lin28A binding around transcription start sites and a positive correlation between its genomic occupancy and expression of many associated genes. Mechanistically, Lin28A recruits 5-methylcytosine-dioxygenase Tet1 to genomic binding sites to orchestrate 5-methylcytosine and 5-hydroxymethylcytosine dynamics. Either Lin28A or Tet1 knockdown leads to dysregulated DNA methylation and expression of common target genes. These results reveal a surprising role for Lin28A in transcriptional regulation via epigenetic DNA modifications and have implications for understanding mechanisms underlying versatile functions of Lin28A in mammalian systems. RNA-binding protein Lin28A shapes the post-transcriptional gene expression by influencing RNA metabolism. Zeng et al. define a DNA binding characteristic of Lin28A, providing evidence for its ability to directly regulate transcription. Lin28A preferentially recognizes transcription initiation loci and recruits DNA demethylase Tet1 to modulate target cytosine modification dynamics and, ultimately, transcription.

Copyright information:

© 2016 Elsevier Inc.

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