Umut Çakır

A single-nucleus regulatory atlas links transposable elements to adult hippocampal neurogenesis

This study uses snATAC-seq and snRNA-seq to identify TE-derived regulatory elements involved in adult hippocampal neurogenesis in response to rhEPO stimulation.

HIF1A recruits primate-specific endogenous retroviruses into the human hypoxic and immune responses

This study identifies HIF1A's role in recruiting primate-specific endogenous retroviruses into hypoxic and immune responses, revealing their regulatory impact on gene expression.

Loss-of-function phenomics, ncORFs, and ambiguity of mutant phenotypes in Medicago truncatula

The paper integrates a comprehensive loss-of-function dataset with ncORF information in Medicago truncatula, revealing their potential impact on phenotypes and highlighting ambiguities in mutant studies.

Erythropoietin reshapes the adult hippocampal chromatin landscape to promote neurogenesis

This study shows EPO induces chromatin remodeling in adult mouse hippocampal neurons, revealing a transposon-mediated mechanism for neurogenesis.

Forebrain-specific loss of erythropoietin provokes compensatory upregulation of different EPO receptors

The paper shows that deleting EPO in the forebrain of mice leads to increased expression of EPOR and EphB4, which may explain the lack of cognitive deficits in these mutants.

Erythropoietin alleviates intellectual disability and autism-like behavior of mice caused by Zbtb20 haploinsufficiency, a construct-valid model of Primrose syndrome

This study shows that erythropoietin treatment improves behavioral and phenotypical symptoms in Zbtb20+/- mice, a model of Primrose syndrome.

Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for the experimental proof of the mosaic translation hypothesis

The paper identifies chimeric peptides and potential mosaic proteins in Medicago truncatula proteomic data, providing indirect evidence for the mosaic translation hypothesis.

A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting

The paper introduces MosaicProt, a pipeline for detecting chimeric protein sequences from PRF, applicable across organisms with transcript sequences and MS proteomic data.

ShiftSCAN, a program that predicts potential alternative sources of mass spectrometry-derived peptides, improves the accuracy of studies on novel amino acid sequences