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Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
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Sequence design for three-dimensional genome folding using Akita Semifreddo.

Paulina N Smaruj1, David R Kelley2, Geoffrey Fudenberg1

  • 1Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.

Biorxiv : the Preprint Server for Biology
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Summary

Scientists developed Akita Semifreddo, a computational framework to design DNA sequences for predictable 3D genome folding. This tool allows engineering specific chromatin structures, like boundaries and dots, by controlling DNA sequence features.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Mammalian genomes possess intricate 3D structures vital for gene regulation.
  • Local genome organization features like boundaries, dots, and flames are driven by loop extrusion.
  • Designing DNA sequences for specific 3D folding patterns remains a challenge.

Purpose of the Study:

  • To present Akita Semifreddo, a framework for the rational *in silico* design of DNA sequences with programmable 3D folding outcomes.
  • To demonstrate the framework's ability to generate diverse local folding features.
  • To explore the relationship between DNA sequence and chromatin architecture.

Main Methods:

  • Combined a computationally efficient "half-frozen" AkitaV2 genome folding model with the Ledidi sequence optimizer.
  • Systematically designed synthetic DNA sequences (∼2 kb) to induce specific local folding features.
  • Investigated the role of CTCF motifs and transcription-associated features in boundary formation and suppression.

Main Results:

  • Akita Semifreddo successfully generated sequences inducing boundaries, dots, and flames with controllable strengths.
  • CTCF motif configurations were consistent with known mechanisms for boundary formation.
  • Weak boundaries were achieved using transcription-associated features, and strong boundaries were suppressed by SINE B2 retroelement-like sequences.
  • Revealed a many-to-one relationship between DNA sequence and 3D folding outcomes.

Conclusions:

  • Akita Semifreddo enables the rational design of DNA sequences for predictable 3D genome organization.
  • The study uncovers the sequence grammar underlying 3D chromatin architecture.
  • Provides a platform for engineering synthetic regulatory landscapes and dissecting chromatin folding mechanisms.