Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 62,198 bioRxiv papers from 276,130 authors.

Deep learning at base-resolution reveals motif syntax of the cis-regulatory code

By Ziga Avsec, Melanie Weilert, Avanti Shrikumar, Amr Mohamed Alexandari, Sabrina Krueger, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje, Julia Zeitlinger

Posted 21 Aug 2019
bioRxiv DOI: 10.1101/737981

Genes are regulated through enhancer sequences, in which transcription factor binding motifs and their specific arrangements (syntax) form a cis-regulatory code. To understand the relationship between motif syntax and transcription factor binding, we train a deep learning model that uses DNA sequence to predict base-resolution binding profiles of four pluripotency transcription factors Oct4, Sox2, Nanog, and Klf4. We interpret the model to accurately map hundreds of thousands of motifs in the genome, learn novel motif representations and identify rules by which motifs and syntax influence transcription factor binding. We find that instances of strict motif spacing are largely due to retrotransposons, but that soft motif syntax influences motif interactions at protein and nucleosome range. Most strikingly, Nanog binding is driven by motifs with a strong preference for ~10.5 bp spacings corresponding to helical periodicity. Interpreting deep learning models applied to high-resolution binding data is a powerful and versatile approach to uncover the motifs and syntax of cis-regulatory sequences.

Download data

  • Downloaded 1,185 times
  • Download rankings, all-time:
    • Site-wide: 5,247 out of 62,198
    • In genomics: 901 out of 4,277
  • Year to date:
    • Site-wide: 1,044 out of 62,198
  • Since beginning of last month:
    • Site-wide: 13,427 out of 62,198

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News