Periodic Reporting for period 1 - miRhythm (Understanding mechanisms and functions of miRNA oscillations during development)
Reporting period: 2020-01-01 to 2021-12-31
Many biological systems exhibit rhythmic behaviors, ranging from circadian rhythms, heart muscle contraction, neuron firing, hormone production, to cell divisions. Rhythmic gene expression may drive such behaviors, as illustrated by the oscillations that drive repetitive somite (and ultimately vertebrae) formation during vertebrate development, or the ~24-hour rhythms of the circadian clocks that provide a schedule for cellular, tissue, and organismal activities in animals. Perturbations to these time-keeping mechanisms are an invitation to diseased states. Hence, it is important to understand the physiological function and the pathological aberrations of such mechanisms.
Cellular components such as transcription factors and signaling proteins are well known as important components of gene expression oscillators. We focused on miRNAs, a type of non-coding RNA that is important in regulating gene expression post-transcriptionally, but not known to function very dynamically. We had observed that some miRNAs undergo rhythmic accumulation with a short, ~8-hour period during development of the nematode C. elegans. We hypothesized that these “oscillating miRNAs” would function dynamically and help to time development. We proposed to investigate the functions of these miRNAs as well as the mechanisms that generate and shape these oscillations in the first place. We set the following objectives to dissect the role of oscillating miRNAs in C. elegans development and to characterize the mechanism:
(i) to characterize developmental functions of oscillating miRNAs (osc-miRs) and their rhythmic expression
(ii) to identify osc-miR targets
(iii) to elucidate the mechanisms of miRNA oscillation
We discovered cellular mechanisms that can promote oscillatory miRNA expression while ruling out others. We also investigated what happens when miRNA activity is lost or disrupted, and how it affects organism development in physiological and non-physiological settings. Our findings support the notion that miRNAs can function very dynamically to shape developmental processes, expanding our understanding of this biomedically important class of gene regulators and developmental timing processes.
Cellular components such as transcription factors and signaling proteins are well known as important components of gene expression oscillators. We focused on miRNAs, a type of non-coding RNA that is important in regulating gene expression post-transcriptionally, but not known to function very dynamically. We had observed that some miRNAs undergo rhythmic accumulation with a short, ~8-hour period during development of the nematode C. elegans. We hypothesized that these “oscillating miRNAs” would function dynamically and help to time development. We proposed to investigate the functions of these miRNAs as well as the mechanisms that generate and shape these oscillations in the first place. We set the following objectives to dissect the role of oscillating miRNAs in C. elegans development and to characterize the mechanism:
(i) to characterize developmental functions of oscillating miRNAs (osc-miRs) and their rhythmic expression
(ii) to identify osc-miR targets
(iii) to elucidate the mechanisms of miRNA oscillation
We discovered cellular mechanisms that can promote oscillatory miRNA expression while ruling out others. We also investigated what happens when miRNA activity is lost or disrupted, and how it affects organism development in physiological and non-physiological settings. Our findings support the notion that miRNAs can function very dynamically to shape developmental processes, expanding our understanding of this biomedically important class of gene regulators and developmental timing processes.
To understand the role of rhythmically expressed miRNAs, we performed studies to either delete these miRNAs or express them from a promoter that does not oscillate. We studied timing defects in these miRNA mutant animals using the high throughput luciferase assays and single worm imaging. We identified miRNA target candidates based on sequencing experiments linking targets to miRNA and bioinformatics approaches, and characterized them by genome editing.
We also identified factors and mechanism that are critical to generate the oscillations of miRNAs with systematic experiments using state of the art methodology (molecular biology, genetics, bioinformatics, biochemistry). Therefore, our progress is in line with the expected outcome of the funding phase.
We also identified factors and mechanism that are critical to generate the oscillations of miRNAs with systematic experiments using state of the art methodology (molecular biology, genetics, bioinformatics, biochemistry). Therefore, our progress is in line with the expected outcome of the funding phase.
The project has been concluded within the time-frame of the fellowship.
Precise timing mechanisms are critical for the development and internal organization of multicellular organisms. Disruption of these time management mechanisms lead to diseased states. It is therefore important to gain insight into the molecular mechanisms by which oscillatory gene expression mediates temporal control in an organism. Our project sheds light on the role of oscillatory miRNAs on developmental timing.
A manuscript summarizing the findings of the project is being prepared, which will bring fundamental scientific insights into the dynamic activities of small RNAs and also, the C. elegans developmental oscillator.
Precise timing mechanisms are critical for the development and internal organization of multicellular organisms. Disruption of these time management mechanisms lead to diseased states. It is therefore important to gain insight into the molecular mechanisms by which oscillatory gene expression mediates temporal control in an organism. Our project sheds light on the role of oscillatory miRNAs on developmental timing.
A manuscript summarizing the findings of the project is being prepared, which will bring fundamental scientific insights into the dynamic activities of small RNAs and also, the C. elegans developmental oscillator.