Transcription Factor Networks in Embryonic and Neural Stem Cells:

__Abstract__ The genetic material of any organism is also referred to as the genome and is passed on from generation to generation. The genome contains the hereditary information that is needed to construct the organism and to ensure its survival. This information is encoded in the form of deoxyribonucleic acid (DNA). DNA consists of two complementary strands of consecutively arranged nucleotides, composed of the nucleobase adenine (A), thymine (T), guanine (G) or cytosine (C). Due to selective pairing (A pairs to T, and G to C) they form a double helical structure which was first revealed by Watson and Crick in 1953 1. This discovery led to a revolution in genomic research that over 50 years later resulted in the first sequenced draft of the human genome 2. The diploid human genome comprises roughly 2 x 3 billion nucleotides which are divided over 22 paired chromosomes and the two sex chromosomes. In the genome are units, referred to as genes, that code for proteins or non-coding RNA mol

Mammalian TIMELESS Is Involved in Period Determination and DNA Damage-Dependent Phase Advancing of the Circadian Clock

The transcription/translation feedback loop-based molecular oscillator underlying the generation of circadian gene expression is preserved in almost all organisms. Interestingly, the animal circadian clock proteins CRYPTOCHROME (CRY), PERIOD (PER) and TIMELESS (TIM) are strongly conserved at the amino acid level through evolution. Within this evolutionary frame, TIM represents a fascinating puzzle. While Drosophila contains two paralogs, dTIM and dTIM2, acting in clock/photoreception and chromosome integrity/photoreception respectively, mammals contain only one TIM homolog. Whereas TIM has been shown to regulate replication termination and cell cycle progression, its functional link to the circadian clock is under debate. Here we show that RNAi-mediated knockdown of TIM in NIH3T3 and U2OS cells shortens the period by 1 hour and diminishes DNA damage-dependent phase advancing. Furthermore, we reveal that the N-terminus of TIM is sufficient for interaction with CRY1 and CHK1 as well for homodimerization, and the C-terminus is necessary for nuclear localization. Interestingly

Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type