Explore the vast range of titles available.

Chromatin acts as a key regulator of DNA‐related processes such as DNA damage repair. Although ChIP‐chip is a powerful technique to provide high‐resolution maps of protein–genome interactions, its use to study DNA double strand break (DSB) repair has been hindered by the limitations of the available damage induction methods. We have developed a human cell line that permits induction of multiple DSBs randomly distributed and unambiguously positioned within the genome. Using this system, we have generated the first genome‐wide mapping of γH2AX around DSBs. We found that all DSBs trigger large γH2AX domains, which spread out from the DSB in a bidirectional, discontinuous and not necessarily symmetrical manner. The distribution of γH2AX within domains is influenced by gene transcription, as parallel mappings of RNA Polymerase II and strand‐specific expression showed that γH2AX does not propagate on active genes. In addition, we showed that transcription is accurately maintained within γH2AX domains, indicating that mechanisms may exist to protect gene transcription from γH2AX spreading and from the chromatin rearrangements induced by DSBs.

Chip Kidd: Book Two: Work: 2007-2017 picks up where Book One left off showcasing his impressive body of work from the past decade as well as new works yet to be seen this year. We see not just hundreds of his recent projects, but the working processes behind them--thoughts, sketches, revisions, scrapped drafts, and triumphant final versions.

Several physiological functions have been attributed to class III peroxidases (PRXs) in plants, but the in planta role of most members of this family still remains undetermined. Here, we report the first functional characterization of PRX17 (At2g22420), one of the 73 members of this family in Arabidopsis thaliana. Localization of PRX17 was examined by transient expression in Nicotiana benthamiana. Loss- and gain-of-function mutants in A. thaliana were studied. Regulation at the gene and protein levels was analyzed using β-glucuronidase (GUS) activity, quantitative reverse transcriptase (qRT)-PCR, zymography, and chromatin immunoprecipitation. Phenotypes were characterized including lignin and xylan contents. PRX17 was expressed in various tissues, including vascular tissues, and PRX17 was localized to the cell wall. In prx17, the lignin content was reduced in the stem and siliques and bolting was delayed, while the opposite phenotype was observed in 35S:PRX17 plants, together with a significant increase of lignin and xylan immunofluorescence signal. Finally, we demonstrated that the transcription factor AGAMOUS-LIKE15 (AGL15) binds to the PRX17 promoter and regulates PRX17 expression level. This converging set of structural, transcriptomic and physiological data suggests that PRX17, under the control of AGL15, contributes to developmental programs by playing an essential role in regulating age-dependent lignified tissue formation, including changes in cell wall properties.

\"A biography of Ruth Wakefield's life, and her invention of the chocolate chip cookie\"--Provided by publisher.

Chromatin immunoprecipitation (ChIP) is the gold-standard technique for localizing nuclear proteins in the genome. We used ChIP, in combination with deep sequencing (Seq), to study the genome-wide distribution of the Silent information regulator (Sir) complex in Saccharomyces cerevisiae . We analyzed ChIP-Seq peaks of the Sir2, Sir3, and Sir4 silencing proteins and discovered 238 unexpected euchromatic loci that exhibited enrichment of all three. Surprisingly, published ChIP-Seq datasets for the Ste12 transcription factor and the centromeric Cse4 protein indicated that these proteins were also enriched in the same euchromatic regions with the high Sir protein levels. The 238 loci, termed ”hyper-ChIPable“, were in highly expressed regions with strong polymerase II and polymerase III enrichment signals, and the correlation between transcription level and ChIP enrichment was not limited to these 238 loci but extended genome-wide. The apparent enrichment of various proteins at hyper-ChIPable loci was not a consequence of artifacts associated with deep sequencing methods, as confirmed by ChIP-quantitative PCR. The localization of unrelated proteins, including the entire silencing complex, to the most highly transcribed genes was highly suggestive of a technical issue with the immunoprecipitations. ChIP-Seq on chromatin immunoprecipitated with a nuclear-localized GFP reproduced the above enrichment in an expression-dependent manner: induction of the GAL genes resulted in an increased ChIP signal of the GFP protein at these loci, with presumably no biological relevance. Whereas ChIP is a broadly valuable technique, some published conclusions based upon ChIP procedures may merit reevaluation in light of these findings.

Everyone loves chocolate chip cookies! But not everyone knows where they came from. Meet Ruth Wakefield, the talented chef and entrepreneur who started a restaurant, wrote a cookbook, and invented this delicious dessert st how did she do it, you ask? That's where things get messy!

Explosive growth in demand for data traffic has prompted exploration of the spatial dimension of light waves, which provides a degree of freedom to expand data transmission capacity. Various techniques based on bulky optical devices have been proposed to tailor light waves in the spatial dimension. However, their inherent large size, extra loss, and precise alignment requirements make these techniques relatively difficult to implement in a compact and flexible way. In contrast, three-dimensional (3D) photonic chips with compact size and low loss provide a promising miniaturized candidate for tailoring light in the spatial dimension. Significantly, they are attractive for chip-assisted short-distance spatial mode optical interconnects that are challenging to bulky optics. Here, we propose and fabricate femtosecond laser-inscribed 3D photonic chips to tailor orbital angular momentum (OAM) modes in the spatial dimension. Various functions on the platform of 3D photonic chips are experimentally demonstrated, including the generation, (de)multiplexing, and exchange of OAM modes. Moreover, chip-chip and chip–fiber–chip short-distance optical interconnects using OAM modes are demonstrated in the experiment with favorable performance. This work paves the way to flexibly tailor light waves on 3D photonic chips and offers a compact solution for versatile optical interconnects and other emerging applications with spatial modes.

Most neurological diseases are associated with chronic inflammation initiated by the activation of microglia, which produce cytotoxic and inflammatory factors. Signal transducers and activators of transcription (STATs) are potent regulators of gene expression but contribution of particular STAT to inflammatory gene expression and STAT-dependent transcriptional networks underlying brain inflammation need to be identified. In the present study, we investigated the genomic distribution of Stat binding sites and the role of Stats in the gene expression in lipopolysaccharide (LPS)-activated primary microglial cultures. Integration of chromatin immunoprecipitation-promoter microarray data and transcriptome data revealed novel Stat-target genes including Jmjd3 , Ccl5 , Ezr , Ifih1 , Irf7 , Uba7 , and Pim1 . While knockdown of individual Stat had little effect on the expression of tested genes, knockdown of both Stat1 and Stat3 inhibited the expression of Jmjd3 and inflammatory genes. Transcriptional regulation of Jmjd3 by Stat1 and Stat3 is a novel mechanism crucial for launching inflammatory responses in microglia. The effects of Jmjd3 on inflammatory gene expression were independent of its H3K27me3 demethylase activity. Forced expression of constitutively activated Stat1 and Stat3 induced the expression of Jmjd3 , inflammation-related genes, and the production of pro-inflammatory cytokines as potently as lipopolysacharide. Gene set enrichment and gene function analysis revealed categories linked to the inflammatory response in LPS and Stat1C + Stat3C groups. We defined upstream pathways that activate STATs in response to LPS and demonstrated contribution of Tlr4 and Il-6 and interferon-γ signaling. Our findings define novel direct transcriptional targets of Stat1 and Stat3 and highlight their contribution to inflammatory gene expression. Key Message Combined analysis of genomic Stat occupancy and transcriptome revealed novel Stat target genes in LPS-induced microglia. Jmjd3 transcription factor is a novel transcriptional target of Stat1 and Stat3. Stat1 and Stat3 cooperate with Jmjd3 to induce the expression of pro-inflammatory genes. Constitutively active Stat1 and Stat3 fully mimic the LPS-induced upregulation of inflammatory genes and secretion of cytokines.

Previous studies have led to a picture wherein the replication of DNA progresses at variable rates over different parts of the budding yeast genome. These prior experiments, focused on production of nascent DNA, have been interpreted to imply that the dynamics of replication fork progression are strongly affected by local chromatin structure/architecture, and by interaction with machineries controlling transcription, repair and epigenetic maintenance. Here, we adopted a complementary approach for assaying replication dynamics using whole genome time‐resolved chromatin immunoprecipitation combined with microarray analysis of the GINS complex, an integral member of the replication fork. Surprisingly, our data show that this complex progresses at highly uniform rates regardless of genomic location, revealing that replication fork dynamics in yeast is simpler and more uniform than previously envisaged. In addition, we show how the synergistic use of experiment and modeling leads to novel biological insights. In particular, a parsimonious model allowed us to accurately simulate fork movement throughout the genome and also revealed a subtle phenomenon, which we interpret as arising from low‐frequency fork arrest. Synopsis In mitotic division, cells duplicate their DNA in S phase to ensure that the proper genetic material is passed on to their progeny. This process of DNA replication is initiated from several hundred specific sites, termed origins of replication, spaced across the genome. It is essential for replication to begin only after G 1 and finish before the initiation of anaphase (Blow and Dutta, 2005 ; Machida et al , 2005 ). To ensure proper timing, the beginning stages of DNA replication are tightly coupled to the cell cycle through the activity of cyclin‐dependent kinases (Nguyen et al , 2001 ; Masumoto et al , 2002 ; Sclafani and Holzen, 2007 ), which promote the accumulation of the pre‐RC at the origins and initiate replication. Replication fork movement occurs subsequent to the firing of origins on recruitment of the replicative helicase and the other fork‐associated proteins as the cell enters S phase (Diffley, 2004 ). The replication machinery itself (polymerases, PCNA, etc.) trails behind the helicase, copying the newly unwound DNA in the wake of the replication fork. One component of the pre‐RC, the GINS complex, consists of a highly conserved set of paralogous proteins (Psf1, Psf2, Psf3 and Sld5 (Kanemaki et al , 2003 ; Kubota et al , 2003 ; Takayama et al , 2003 )). Previous work suggests that the GINS complex is an integral component of the replication fork and that its interaction with the genome correlates directly to the movement of the fork (reviewed in Labib and Gambus, 2007 ). Here, we used the GINS complex as a surrogate to measure features of the dynamics of replication—that is, to determine which origins in the genome are active, the timing of their firing and the rates of replication fork progression. The timing of origin firing and the rates of fork progression have also been investigated by monitoring nascent DNA synthesis (Raghuraman et al , 2001 ; Yabuki et al , 2002 ). Origin firing was observed to occur as early as 14 min into the cell cycle and as late as 44 min (Raghuraman et al , 2001 ). A wide range of nucleotide incorporation rates (0.5–11 kb/min) were observed, with a mean of 2.9 kb/min (Raghuraman et al , 2001 ), whereas a second study reported a comparable mean rate of DNA duplication of 2.8±1.0 kb/min (Yabuki et al , 2002 ). In addition to these observations, replication has been inferred to progress asymmetrically from certain origins (Raghuraman et al , 2001 ). These data have been interpreted to mean that the dynamics of replication fork progression are strongly affected by local chromatin structure or architecture, and perhaps by interaction with the machineries controlling transcription, repair and epigenetic maintenance (Deshpande and Newlon, 1996 ; Rothstein et al , 2000 ; Raghuraman et al , 2001 ; Ivessa et al , 2003 ). In this study, we adopted a complementary ChIP‐chip approach for assaying replication dynamics, in which we followed GINS complexes as they traverse the genome during the cell cycle (Figure 1 ). These data reveal that GINS binds to active replication origins and spreads bi‐directionally and symmetrically as S phase progresses (Figure 3 ). The majority of origins appear to fire in the first ∼15 min of S phase. A small fraction (∼10%) of the origins to which GINS binds show no evidence of spreading (category 3 origins), although it remains possible that these peaks represent passively fired origins (Shirahige et al , 1998 ). Once an active origin fires, the GINS complex moves at an almost constant rate of 1.6±0.3 kb/min. Its movement through the inter‐origin regions is consistent with that of a protein complex associated with a smoothly moving replication fork. This progression rate is considerably lower and more tightly distributed than those inferred from previous genome‐wide measurements assayed through nascent DNA production (Raghuraman et al , 2001 ; Yabuki et al , 2002 ). Our study leads us to a different view of replication fork dynamics wherein fork progression is highly uniform in rate and little affected by genomic location. In this work, we also observe a large number of low‐intensity persistent features at sites of high transcriptional activity (e.g. tRNA genes). We were able to accurately simulate these features by assuming they are the result of low probability arrest of replication forks at these sites, rather than fork pausing (Deshpande and Newlon, 1996 ). The extremely low frequency of these events in wild‐type cells suggests they are due to low probability stochastic occurrences during the replication process. It is hoped that future studies will resolve whether these persistent features indeed represent rare instances of fork arrest, or are the result of some alternative process. These may include, for example, the deposition of GINS complexes (or perhaps more specifically Psf2) once a pause has been resolved. In this work, we have made extensive use of modeling to test a number of different hypotheses and assumptions. In particular, iterative modeling allowed us to infer that GINS progression is uniform and smooth throughout the genome. We have also demonstrated the potential of simulations for estimating firing efficiencies. In the future, extending such firing efficiency simulations to the whole genome should allow us to make correlations with chromosomal features such as nucleosome occupancy. Such correlations may help in determining factors that govern the probability of replication initiation throughout the genome. Time‐resolved ChIP‐chip can be utilized to monitor the genome‐wide dynamics of the GINS complex, yielding quantitative information on replication fork movement. Replication forks progress at remarkably uniform rates across the genome, regardless of location. GINS progression appears to be arrested, albeit with very low frequency, at sites of highly transcribed genes. Comparison of simulation with data leads to novel biological insights regarding the dynamics of replication fork progression