Telomeres are specialized nucleoprotein structures found at the end of eukaryotic chromosomes. The telomere DNA in humans is composed of the sequence "5'-TTAGGG-3'" tandemly repeated in a stretch of 5-30kb of double stranded DNA. TTAGGG Repeat Factor 2 (TRF2) is a telomere DNA binding protein that has a critical role in telomere end protection. The current model for telomere protection by TRF2 is through its ability to remodel telomeres into looped higher-order structures, called the t-loop, which sequesters the end from DNA damage sensors. Since telomeres are known to be comprised of nucleosomal chromatin, it is important to determine how TRF2 binds to and affects the structure of nucleosomal arrays. The ability of TRF2 to bind to unusual DNA structures such as the t-loop and the single stranded/double (ss/ds) stranded telomere DNA junction may facilitate its binding to DNA in the form of nucleosomal arrays and promote higher-order chromatin structures. In this study, we have reconstituted a 2kb DNA fragment containing 550bp of telomere DNA into nucleosomal arrays and tested the binding of full-lengthTRF2 and four truncation mutants to telomeric nucleosomal arrays. Our data indicates that TRF2 and its truncation mutants bind to telomere nucleosomal arrays as well as it binds to telomere DNA. We used a novel electrophoretic technique, Analytical Agarose Gel Electrophoresis (AAGE), to measure changes in surface charge density, hydrodynamic radius, and conformational flexibility of DNA and nucleosomal arrays upon protein binding. Our results indicate that the C-terminal DNA binding Myb/SANT domain of TRF2 might be rearranging nucleosomal structure through either nucleosome sliding, unwrapping, or changing the arrangement of the linker DNA, while the N-terminal basic DNA binding region is causing nucleosomal arrays compaction. Instead of significant compaction, histone-free DNA undergoes DNA condensation and self-association. This activity is observed with the full-length protein and all regions of the protein, with the exception of TRF2-DBD, participate in the process. We speculate that the ability of TRF2-DBD to rearrange nucleosomal structure and N-terminal basic region to cause nucleosomal fiber compaction may allow TRF2 to promote t-loop formation in the context of chromatin. We propose that TRF2, possessing all the features, has a new role at telomeres as a chromatin architectural protein.

CENP-A est le variant d’histone qui remplace spécifiquement l’histone H3 au niveau des centromères et confère ses propriétés uniques à la chromatine centromérique. La cristallographie aux rayon X, ainsi que la digestion à la MNase des nucléosomes contenant CENP-A suggèrent une flexibilité de l’ADN entrant et sortant de ce nucléosome. Néanmoins ces déductions restent aujourd’hui au stade hypothétique, en particulier, rien n’est connu sur le rôle éventuelle de cette particularité dans la fonction du nucléosome CENP-A. L’utilisation de la cryo-électromicroscopie nous a permis de déterminer les caractéristiques de la dynamique de l’ADN sortant du nucléosome CENP-A. Nos analyses biochimiques, de protéomiques et de pseudo-génétiques révèlent que la flexibilité élevée de l’ADN du nucléosome CENP-A ne permet pas l’interaction avec l’histone de liaison H1. In vitro, remplacer les 2 tours de l’hélice aN de CENP-A avec les 3 tours de l’hélice aN de H3 permet de restaurer l’interaction de l’histone H1. In vivo, le replacement des nucléosomes CENP-A par des nucléosomes contenant ce même nucléosome hybride aN-CENP-A permet également le recrutement de H1, mais cela conduit également à la délocalisation d’un certain nombre de protéines du kinétochore. Ce kinétochore ne permet pas une ségrégation correcte des chromosomes et il conduit à des phases de mitose et de cytokinèse défectueuses. L’ensemble de ces données montre que la conservation au cours de l’évolution de la flexibilité de l’ADN dans le nucléosome CENP-A est essentielle pour l’accomplissement de la division cellulaire. / CENP-A is a histone variant, which replaces histone H3 at centromeres and confers unique properties to centromeric chromatin. The crystal structure and MNase digestion of CENP-A nucleosome suggests flexible nucleosomal DNA ends but their dynamics in solution remains elusive and their implication in centromere function is unknown. Using electron cryo-microscopy we determined the dynamic solution properties of the CENP-A nucleosome. Our biochemical, proteomic and genetic data reveal that the high flexibility of the DNA ends impairs histone H1 binding to the CENP-A nucleosome. Substituting the 2-turn aN-helix of CENP-A with the 3-turn N-helix of H3 results in particles able to bind histone H1. In vivo replacement of CENP-A nucleosomes with the same NH3-CENP-A hybrid nucleosomes leads to H1 recruitment, delocalization of kinetochore proteins and significant mitotic and cytokinesis defects. Put together, ourdata reveal that the evolutionarily conserved flexible ends of the CENP-A nucleosomes are essential to ensure the fidelity of the mitotic pathway.

It has been suggested that organismal complexity correlates with the complexity of gene regulation. Transcriptional control of gene expression is mediated by binding of regulatory proteins to cis-acting sequences on the genome. Hence, it is crucial to identify the chromosomal targets of transcription factors (TFs) to delineate transcriptional regulatory networks underlying gene expression programs. The development of ChIP-chip technology has enabled high throughput mapping of TF binding sites across the genome. However, there are many limitations to the technology including the availability of whole genome arrays for complex organisms such human or mouse. To circumvent these limitations, we developed the Sequence Tag Analysis of Genomic Enrichment (STAGE) methodology that is based on extracting short DNA sequences or “tags” from ChIP-enriched DNA. With improvements in sequencing technologies, we applied the recently developed ChIP-Seq technique i.e. ChIP followed by ultra high throughput sequencing, to identify binding sites for the TF E2F4 across the human genome. We identified previously uncharacterized E2F4 binding sites in intergenic regions and found that several microRNAs are potential E2F4 targets. Binding of TFs to their respective chromosomal targets requires access of the TF to its regulatory element, which is strongly influenced by nucleosomal remodeling. In order to understand nucleosome remodeling in response to transcriptional perturbation, we used ultra high throughput sequencing to map nucleosome positions in yeast that were subjected to heat shock or were grown normally. We generated nucleosome remodeling profiles across yeast promoters and found that specific remodeling patterns correlate with specific TFs active during the transcriptional reprogramming. Another important aspect of gene regulation operates at the post-transcriptional level. MicroRNAs (miRNAs) are ~22 nucleotide non-coding RNAs that suppress translation or mark mRNAs for degradation. MiRNAs regulate TFs and in turn can be regulated by TFs. We characterized a TF-miRNA network involving the oncofactor Myc and the miRNA miR-22 that suppresses the interferon pathway as primary fibroblasts enter a stage of rapid proliferation. We found that miR-22 suppresses the interferon pathway by inhibiting nuclear translocation of the TF NF-kappaB. Our results show how the oncogenic TF Myc cross-talks with other TF regulatory pathways via a miRNA intermediary. / text