Chromatin 3D architecture in Archaea

Introduction

This proposal brings together the field of chromatin evolution and state-of-the-art structural biology to advance our understanding of a fundamental question: the origin of chromatin structural and regulatory complexity.

Background

Eukaryotes and most groups of archaea organize their genomes in the form of histone-based chromatin. Conservation of histones across the tree of life goes beyond protein sequence and histone fold. Tertiary arrangement of histones and DNA geometry in archaeal nucleosomes resemble those in eukaryotes; however, archaea can form special hypernucleosomes and “slinky”-like arrangements.

Similarly to eukaryotes, some archaea have multiple histone variants and extended histone tails, although it is unclear whether their structural and regulatory roles are conserved. Eukaryotes inherited histone-based chromatin from archaea; however, the origins of eukaryotic chromatin complexity are enigmatic.

Objectives

Therefore, this proposal will address the 3D organization of chromatin in archaea to advance the understanding of chromatin evolution. We will test the following hypotheses:

1. Archaeal chromatin, along with hypernucleosomes, contains multiple open structures to maintain DNA accessibility and allow polymerase passage.
2. Histone variant exchange and histone tails in archaea play an important role in chromatin compaction similarly to eukaryotes.

Methodology

To test our hypotheses, we will synergistically apply state-of-the-art cryo-electron microscopy (cryo-EM) in situ and in vitro to selected archaeal systems.

• In situ cryo-EM will provide structural information about chromatin in its native context.
• Cryo-EM of in vitro reconstituted chromatin will provide high-resolution structural information.

Structural analysis complemented with biochemical and biophysical characterization, as well as nucleosome positioning data, will provide insights into 3D chromatin architecture in archaea in the context of eukaryotic chromatin evolution.