Argonautes and small RNAs associated with nematode programmed DNA elimination

Area of Science:

• Developmental Biology
• Genetics
• Molecular Biology

Background:

• Programmed DNA elimination (PDE) is a process where parts of the genome are removed during development, challenging the principle of genome constancy.
• While small RNAs are implicated in PDE in single-celled organisms, their role in metazoans remains largely unexplored.
• The parasitic nematode Ascaris exhibits extensive PDE, involving chromosome end remodeling and fusion/fission events, leading to significant karyotype alterations.

Purpose of the Study:

• To investigate the potential involvement of small RNAs and Argonautes in Programmed DNA Elimination (PDE) in the parasitic nematode Ascaris.
• To characterize the small RNAs (siRNAs) associated with identified Argonautes (WAGOs) and their genomic targets within different cellular compartments.

Main Methods:

• Identification of two Argonautes, AsWAGO-2 and AsWAGO-3, potentially involved in Ascaris PDE.
• Cellular fractionation combined with nuclease-treated immunoprecipitation to isolate WAGO-associated siRNAs.
• Characterization of siRNA targets in chromatin, nucleoplasm, and cytoplasm to determine their genomic localization.

Main Results:

• AsWAGO-3 is localized to eliminated chromatin, with its associated siRNAs primarily targeting genes, and a subset targeting repeats in eliminated regions.
• AsWAGO-2 is transiently associated with retained chromosomes during elimination mitoses, with its siRNAs enriched in retained chromatin.
• The study establishes a connection between WAGOs and Ascaris PDE, highlighting the adaptability of small RNA pathways in differentiating between retained and eliminated DNA.

Conclusions:

• WAGO proteins and their associated siRNAs play a crucial role in Programmed DNA Elimination in Ascaris.
• Small RNA pathways demonstrate flexibility in distinguishing and targeting DNA for elimination or retention during development.
• siRNA targeting may function as a response to the significant karyotype changes, including chromosome fusion and PDE, occurring in Ascaris.