Regulation of DNA Damage Processing by Covalent Modification of Thymine DNA Glycosylase

Thymine DNA glycosylase (TDG) is an essential DNA repair enzyme mediating excision of uracil and thymine mispaired with guanine within CpG contexts. Unrepaired, these lesions result in G:C to A:T transitions which are major contributors to genome instability. Interestingly, TDG interacts functionally with transcriptional regulators and participates in directed cytosine demethylation at promoters. TDG is subject to multiple post-translational modifications (PTM) and we undertook an analysis of how these regulate TDG function. Initially, we examined TDG regulation by small ubiquitin-like modifier (SUMO) and identified a novel SUMO binding motif (SBM1, residues 144-148). We hypothesized that SBM1, along with SBM2 (319-322), would facilitate non-covalent SUMO interactions upon conjugation of SUMO (sumoylation) to lysine 341, altering TDG conformation and function. Biochemical and cell based analyses supported our hypothesis, showing SUMO interactions allosterically regulate TDG protein-protein and substrate interactions, altering TDG subnuclear localization and enzymatic function. Furthermore, sumoylation drastically reduced acetylation of TDG occurring at lysines 70, 94, 95, and 98. Secondly, we examined TDG regulation by phosphorylation and demonstrated that serines 96 and 99 are phosphorylated by protein kinase C α in vivo. Biochemical analysis of covalently modified recombinant TDG showed that acetylation and phosphorylation of TDG are mutually exclusive and both are suppressed by TDG-DNA interactions. Furthermore, acetylated TDG did not interact stably with DNA or efficiently excise thymine from G:T mispairs, while phosphorylated TDG was indistinguishable from unmodified protein. Lastly, we examined TDG regulation in aging cells. Immunostaining showed TDG redistributed from nucleus to cytoplasm in aged cells. Interestingly, treatment with histone deacetylase inhibitors resulted in similar redistribution and immunoblotting indicated that an increase in TDG modification consistent with sumoylation or monoubiquitination had occurred. Similar results were obtained by exposing cells to oxidative stress. Analysis of a sumoylation-minus mutant of TDG identified sumoylation as an important regulator of TDG localization. Interestingly, we found extensive colocalization of TDG with sites of active transcription which was reduced by phorbol ester treatments which surprisingly promoted entry into heterochromatic regions from which TDG is generally excluded. Together, these findings suggest that TDG function may be regulated by PTM, consequently affecting genome stability and expression

Regulation of the BRCA1 gene by an SRC3/53BP1 complex

<p>Abstract</p> <p>Background</p> <p>Steroid Receptor coactivator 3(SRC3) is an oncogene and a member of the SRC family of nuclear receptor coactivator proteins that mediate the transcriptional effects of nuclear hormone receptors as well as other transcription factors.</p> <p>Results</p> <p>We have used protein purification and mass spectrometry to identify the 53BP1 tumour suppressor as a novel SRC3-associated protein. Copurification was demonstrated using multiple antibodies, and was not dependent on DNA damage suggesting that SRC3 is not directly involved in the DNA damage response. However using chromatin immunoprecipitation(ChIP) and siRNA knockdown, we have demonstrated that both SRC3 and 53BP1 co-occupy the same region of the BRCA1 promoter and both are required for BRCA1 expression in HeLa cells.</p> <p>Conclusions</p> <p>Our results suggest that both 53BP1 and SRC3 have a common function that converge at the BRCA1 promoter and possibly other genes important for DNA repair and genomic stability.</p

The Berkeley Sample of Stripped-Envelope Supernovae

We present the complete sample of stripped-envelope supernova (SN) spectra observed by the Lick Observatory Supernova Search (LOSS) collaboration over the last three decades: 888 spectra of 302 SNe, 652 published here for the first time, with 384 spectra (of 92 SNe) having photometrically-determined phases. After correcting for redshift and Milky Way dust reddening and reevaluating the spectroscopic classifications for each SN, we construct mean spectra of the three major spectral subtypes (Types IIb, Ib, and Ic) binned by phase. We compare measures of line strengths and widths made from this sample to the results of previous efforts, confirming that O I {\lambda}7774 absorption is stronger and found at higher velocity in Type Ic SNe than in Types Ib or IIb SNe in the first 30 days after peak brightness, though the widths of nebular emission lines are consistent across subtypes. We also highlight newly available observations for a few rare subpopulations of interest.Comment: 13 pages; 14 figures; 3 tables. Accepted for publication in MNRA

The Massive Progenitor of the Type II-Linear Supernova 2009kr

We present early-time photometric and spectroscopic observations of supernova (SN) 2009kr in NGC 1832. We find that its properties to date support its classification as Type II-linear (SN II-L), a relatively rare subclass of core-collapse supernovae (SNe). We have also identified a candidate for the SN progenitor star through comparison of pre-explosion, archival images taken with WFPC2 on board the Hubble Space Telescope with SN images obtained using adaptive optics plus NIRC2 on the 10 m Keck-II telescope. Although the host galaxy's substantial distance (similar to 26 Mpc) results in large uncertainties in the relative astrometry, we find that if this candidate is indeed the progenitor, it is a highly luminous (M(V)(0) = -7.8 mag) yellow supergiant with initial mass similar to 18-24 M(circle dot). This would be the first time that an SN II-L progenitor has been directly identified. Its mass may be a bridge between the upper initial mass limit for the more common Type II-plateau SNe and the inferred initial mass estimate for one Type II-narrow SN.Hungarian OTKA K76816NSF AST-0707769, AST-0908886Sylvia & Jim Katzman FoundationTABASGO FoundationNASA through STScI AR-11248, GO-10877Harvard UniversityUC BerkeleyUniversity of VirginiaNASA/Swift NNX09AQ66GDOEAstronom

Hubble Space Telescope and Ground-Based Observations of the Type Iax Supernovae SN 2005hk and SN 2008A

We present Hubble Space Telescope (HST) and ground-based optical and near-infrared observations of SN 2005hk and SN 2008A, typical members of the Type Iax class of supernovae (SNe). Here we focus on late-time observations, where these objects deviate most dramatically from all other SN types. Instead of the dominant nebular emission lines that are observed in other SNe at late phases, spectra of SNe 2005hk and 2008A show lines of Fe II, Ca II, and Fe I more than a year past maximum light, along with narrow [Fe II] and [Ca II] emission. We use spectral features to constrain the temperature and density of the ejecta, and find high densities at late times, with n_e >~ 10^9 cm^-3. Such high densities should yield enhanced cooling of the ejecta, making these objects good candidates to observe the expected "infrared catastrophe," a generic feature of SN Ia models. However, our HST photometry of SN 2008A does not match the predictions of an infrared catastrophe. Moreover, our HST observations rule out a "complete deflagration" that fully disrupts the white dwarf for these peculiar SNe, showing no evidence for unburned material at late times. Deflagration explosion models that leave behind a bound remnant can match some of the observed properties of SNe Iax, but no published model is consistent with all of our observations of SNe 2005hk and 2008A.Comment: 20 pages, 15 figure

Berkeley Supernova Ia Program I: Observations, Data Reduction, and Spectroscopic Sample of 582 Low-Redshift Type Ia Supernovae

In this first paper in a series we present 1298 low-redshift (z\leq0.2) optical spectra of 582 Type Ia supernovae (SNe Ia) observed from 1989 through 2008 as part of the Berkeley SN Ia Program (BSNIP). 584 spectra of 199 SNe Ia have well-calibrated light curves with measured distance moduli, and many of the spectra have been corrected for host-galaxy contamination. Most of the data were obtained using the Kast double spectrograph mounted on the Shane 3 m telescope at Lick Observatory and have a typical wavelength range of 3300-10,400 Ang., roughly twice as wide as spectra from most previously published datasets. We present our observing and reduction procedures, and we describe the resulting SN Database (SNDB), which will be an online, public, searchable database containing all of our fully reduced spectra and companion photometry. In addition, we discuss our spectral classification scheme (using the SuperNova IDentification code, SNID; Blondin & Tonry 2007), utilising our newly constructed set of SNID spectral templates. These templates allow us to accurately classify our entire dataset, and by doing so we are able to reclassify a handful of objects as bona fide SNe Ia and a few other objects as members of some of the peculiar SN Ia subtypes. In fact, our dataset includes spectra of nearly 90 spectroscopically peculiar SNe Ia. We also present spectroscopic host-galaxy redshifts of some SNe Ia where these values were previously unknown. [Abridged]Comment: 34 pages, 11 figures, 11 tables, revised version, re-submitted to MNRAS. Spectra will be released in January 2013. The SN Database homepage (http://hercules.berkeley.edu/database/index_public.html) contains the full tables, plots of all spectra, and our new SNID template

A Non-stop identity complex (NIC) supervises enterocyte identity and protects from premature aging

A hallmark of aging is loss of differentiated cell identity. Age

The Peculiar SN 2005hk: Do Some Type Ia Supernovae Explode as Deflagrations?

We present extensive u'g'r'i'BVRIYJHKs photometry and optical spectroscopy of SN 2005hk. These data reveal that SN 2005hk was nearly identical in its observed properties to SN 2002cx, which has been called ``the most peculiar known type Ia supernova.'' Both supernovae exhibited high ionization SN 1991T-like pre-maximum spectra, yet low peak luminosities like SN 1991bg. The spectra reveal that SN 2005hk, like SN 2002cx, exhibited expansion velocities that were roughly half those of typical type Ia supernovae. The R and I light curves of both supernovae were also peculiar in not displaying the secondary maximum observed for normal type Ia supernovae. Our YJH photometry of SN 2005hk reveals the same peculiarity in the near-infrared. By combining our optical and near-infrared photometry of SN 2005hk with published ultraviolet light curves obtained with the Swift satellite, we are able to construct a bolometric light curve from ~10 days before to ~60 days after B maximum. The shape and unusually low peak luminosity of this light curve, plus the low expansion velocities and absence of a secondary maximum at red and near-infrared wavelengths, are all in reasonable agreement with model calculations of a 3D deflagration which produces ~0.25 M_sun of 56Ni.Comment: Accepted by PASP, to appear in April 2007 issue, 63 pages, 16 figures, 11 table

The Massive Progenitor of the Possible Type II-Linear Supernova 2009hd in Messier 66

We present observations of SN2009hd in the nearby galaxy M66. This SN is one of the closest to us in recent years but heavily obscured by dust, rendering it unusually faint in the optical, given its proximity. We find that the observed properties of SN2009hd support its classification as a possible Type II-L SN, a relatively rare subclass of CC-SNe. High-precision relative astrometry has been employed to attempt to identify a SN progenitor candidate, based on a pixel-by-pixel comparison between HST F555W and F814W images of the SN site prior to explosion and at late times. A progenitor candidate is identified in the F814W images only; this object is undetected in F555W. Significant uncertainty exists in the astrometry, such that we cannot definitively identify this object as the SN progenitor. Via insertion of artificial stars into the pre-SN HST images, we are able to constrain the progenitor's properties to those of a possible supergiant, with M(F555W)0>-7.6 mag and (V-I) 0>0.99 mag. The magnitude and color limits are consistent with a luminous RSG; however, they also allow for the possibility that the star could have been more yellow than red. From a comparison with theoretical massive-star evolutionary tracks, which include rotation and pulsationally enhanced mass loss, we can place a conservative upper limit on the initial mass for the progenitor of <20 M_sun. If the actual mass of the progenitor is near the upper range allowed by our derived mass limit, then it would be consistent with that for the identified progenitors of the SNII-L 2009kr and the high-luminosity SNII-P 2008cn. The progenitors of these three SNe may possibly bridge the gap between lower-mass RSG that explode as SNeII-P and LBV, or more extreme RSG, from which the more exotic SNeII-n may arise. Very late-time imaging of the SN2009hd site may provide us with more clues regarding the true nature of its progenitor.Comment: 19 pages, 9 figures, 3 tables, accepted for publication in Ap