Specific positioning of chromatin at nuclear periphery in Arabidopsis thaliana

• Applicant: Professor Dr. Chang Liu
• Subject Area: Plant Genetics and Genomics ; Plant Cell and Developmental Biology
• Term: from 2016 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 310522986

Transcriptional regulation plays critical roles in orchestrating gene activities in all living organisms. The nuclear space is not a homogenous biochemical environment. A large number of cases have been found that the transcriptional activities of a genes are linked to its positioning in the nuclear space. Despite much effort, it has still remained unclear how transcriptional regulation happens on genes tethered at nuclear envelope, as artificially targeting chromatin there could result in either gene upregulation or suppression. Even less is known in plants. However, substantial progress has been made recently in identifying structural components of the plant nuclear envelope, facilitating in-depth investigations on various biological events happened at nuclear boundary including specific chromatin tethering. By using the Arabidopsis thaliana NUP1 (also known as NUP136), which is specifically localized to nucleoplasmic side of nuclear pore complex, we found that pericentromeric regions and certain genomic fractions located on distal chromosome arm were specifically positioned at nuclear periphery. Here we propose to employ our newly developed methods to investigate specific chromatin tethering at nuclear periphery in detail. The proposed project has three parts, in the first part, high-resolution maps of chromatin positioning at nuclear periphery will be generated from various tissues, and will be analyzed to reveal their associations with other genomic and epigenomic landscapes. In the second part, both genetic and proteomic approaches will be used to study the molecular mechanism of chromatin tethering. A serial of crossing will be performed to assess how structural change on nuclear envelope will affect chromatin tethering; and tandem affinity purification coupled with mass spectrometry will be done to identify proteins associated with tethered chromatin. In the third part, we propose to apply a CRISPR-CAS9-derived method to artificially tether chromatin to nuclear periphery to examine its biological impact. Altogether, we aim to address the molecular and functional properties of the phenomenon of nuclear compartmentation in a context of specifically tethering chromatin at nuclear periphery in plants.

• DFG Programme: Research Grants