Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.

Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows of enriched binding. From raw CLIP data, we detail how users can map reproducible RNA-binding sites to call enriched windows and perform downstream analysis. This protocol supports optional customizations for different use cases. For complete details on the use and execution of this protocol, please refer to Boyle et al.1.

The Upper Eye Bias: Rotated Faces Draw Fixations to the Upper Eye.

There is a consistent left-gaze bias when observers fixate upright faces, but it is unknown how this bias manifests in rotated faces, where the two eyes appear at different heights on the face. In two eye-tracking experiments, we measured participants' first and second fixations, while they judged the expressions of upright and rotated faces. We hypothesized that rotated faces might elicit a bias to fixate the upper eye. Our results strongly confirmed this hypothesis, with the upper eye bias completely dominating the left-gaze bias in ±45° faces in Experiment 1, and across a range of face orientations (±11.25°, ±22.5°, ±33.75°, ±45°, and ±90°) in Experiment 2. In addition, rotated faces elicited more overall eye-directed fixations than upright faces. We consider potential mechanisms of the upper eye bias in rotated faces and discuss some implications for research in social cognition.

Cancer/Testis Antigen PASD1 Silences the Circadian Clock.

The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.