Efficient compressive and Bayesian characterization of biphoton frequency spectra

Frequency-bin qudits constitute a promising tool for quantum information processing, but their high dimensionality can make for tedious characterization measurements. Here we introduce and compare compressive sensing and Bayesian mean estimation for recovering the spectral correlations of entangled photon pairs. Using a conventional compressive sensing algorithm, we reconstruct joint spectra with up to a 26-fold reduction in measurement time compared to the equivalent raster scan. Applying a custom Bayesian model to the same data, we then additionally realize reliable and consistent quantification of uncertainty. These efficient methods of biphoton characterization should advance our ability to use the high degree of parallelism and complexity afforded by frequency-bin encoding.

Broadly tunable, low timing jitter, high repetition rate optoelectronic comb generator

We investigate the low timing jitter properties of a tunable single-pass optoelectronic frequency comb generator. The scheme is flexible in that both the repetition rate and center frequency can be continuously tuned. When operated with 10 GHz comb spacing, the integrated residual pulse-to-pulse timing jitter is 11.35 fs (1 Hz to 10 MHz) with no feedback stabilization. The corresponding phase noise at 1 Hz offset from the photodetected 10 GHz carrier is -100 dBc/Hz.

Femtosecond pulse sequences used for optical manipulation of molecular motion

Optical control over elementary molecular motion is enhanced with timed sequences of femtosecond (10(-15) second) pulses produced by pulse-shaping techniques. Appropriately timed pulse sequences are used to repetitively drive selected vibrations of a crystal lattice, in a manner analogous to repetitively pushing a child on a swing with appropriate timing to build up a large oscillation amplitude. This process corresponds to repetitively "pushing" molecules along selected paths in the lattice. Amplification of selected vibrational modes and discrimination against other modes are demonstrated. Prospects for more extensive manipulation of molecular and collective behavior and structure are clearly indicated.

Dual-comb electric-field cross-correlation technique for optical arbitrary waveform characterization

We present an electric-field cross-correlation technique that uses a pair of frequency combs to sweep phase and group delays independently without a mechanical stage. We demonstrate this technique for characterization of optical arbitrary waveforms composed of ~30 spectral lines from a 10 GHz frequency comb. Rapid data acquisition (tens of microseconds) enables interferometric spectral phase measurement of pulses subject to propagation over 20 km of optical fiber.

Generation of 20 GHz, sub-40 fs pulses at 960 nm via repetition-rate multiplication

Optical filtering of a stabilized 1 GHz optical frequency comb produces a 20 GHz comb with approximately 40 nm bandwidth (FWHM) at 960 nm. Use of a low-finesse Fabry-Pérot cavity in a double-pass configuration provides a broad cavity coupling bandwidth (Deltalambda/lambda approximately 10%) and large suppression (50 dB) of unwanted modes. Pulse durations shorter than 40 fs with less than 2% residual amplitude modulation are achieved.

Improved signal-to-noise ratio of 10 GHz microwave signals generated with a mode-filtered femtosecond laser frequency comb

We use a Fabry-Perot cavity to optically filter the output of a Ti:sapphire frequency comb to integer multiples of the original 1 GHz mode spacing. This effectively increases the pulse repetition rate, which is useful for several applications. In the case of low-noise microwave signal generation, such filtering leads to improved linearity of the high-speed photodiodes that detect the mode-locked laser pulse train. The result is significantly improved signal-to-noise ratio at the 10 GHz harmonic with the potential for a shot-noise limited single sideband phase noise floor near -168 dBc/Hz.

Interferometry from a scattering medium

A two-beam random interferometer is demonstrated where coupling is facilitated by a scattering medium. A modulation observed in the normalized second-order intensity frequency correlation of the transmitted light is attributed to the relative temporal delay of the two beams and is insensitive to beam alignment and spacing.

Programmable polarization-independent spectral phase compensation and pulse shaping by use of a single-layer liquid-crystal modulator

What we believe to be the first use of a single-layer liquid-crystal modulator array for spectral phase pulse shaping that operates independently of input polarization is reported. Polarization insensitivity is essential to optical-fiber-based applications such as dispersion compensation.

Line-by-line pulse shaping control for optical arbitrary waveform generation

We demonstrate a fundamental operation for generating complex waveforms in the optical domain - line-by-line pulse shaping control for optical arbitrary waveform generation (O-AWG). Independent manipulation of the spectral amplitude and phase of individual lines from a mode-locked frequency comb, or spectral line-by-line pulse shaping, leads to synthesis of user-specified ultrafast optical waveforms with unprecedented control. Coupled with recent advances in frequency stabilized mode-locked lasers, line-by-line pulse shaping control should have significant impact to fields drawing upon developments in the field of ultrafast science.

Wideband all-order polarization mode dispersion compensation via pulse shaping

We demonstrate the application of ultrafast pulse-shaping techniques for experimental wideband all-order polarization mode dispersion (PMD) compensation, for the first time to our knowledge. PMD is treated as arbitrary variations of state of polarization and phase versus wavelength, in an all-order sense. Consequently, two pulse shapers are implemented in a serial manner to compensate for the polarization and the phase spectra independently. We report compensation of subpicosecond pulses (14 nm bandwidth around 1550 nm) that are anomalously spread to more than 2 ps as a result of PMD. This PMD compensation scheme can potentially be a powerful and cost-effective solution for fiber optic telecommunication networks.

Spectral line-by-line pulse shaping

We experimentally demonstrate pulse-shaping experiments in which the individual spectral lines that are present in the output of a mode-locked laser (8.5 GHz mode spacing, centered at 1542 nm) are resolved. The shaped pulses overlap in time, and this leads to a new way to observe fluctuations of the comb-offset frequency in the time domain.

Fully dispersion-compensated approximately 500 fs pulse transmission over 50 km single-mode fiber

We demonstrate essentially distortionless 50 km fiber transmission for approximately 500 fs pulses, using dispersion-compensating fiber and a programmable pulse shaper as a spectral phase equalizer. This distance is approximately five times longer than previously achieved at similar pulse widths.

Pulse shaper in a loop: demonstration of cascadable ultrafast all-optical code translation

We experimentally demonstrate repetitive M-ary spectral phase pulse shaping by placing a programmable pulse shaper driven by a 10-GHz source in a closed loop. This permits generation of encoded and decoded signals in the same apparatus by forming a closed loop to circulate a part of the output back into the pulse shaper. As a result, a series of M - 1 distinct encoded waveforms is sequentially generated, followed by generation of a properly decoded pulse.

Femtosecond direct space-to-time pulse shaping in an integrated-optic configuration

We demonstrate femtosecond operation of an integrated-optic direct space-to-time pulse shaper for which there is a direct mapping (no Fourier transform) between the spatial position of the masking function and the temporal position in the output waveform. The apparatus is used to generate trains of more than 30 pulses as an ultrafast optical data packet over approximately an 80-ps temporal window.

Spectral and temporal speckle field measurements of a random medium

The zero-mean circular complex Gaussian field statistics of a random medium are experimentally demonstrated in the optical domain, thus verifying this key assumption of statistical optics. Using a frequency-tunable laser source in a fixed-path-length interferometer, we obtain optical field fluctuations in the time and frequency domains that clearly show that the ensemble-averaged temporal intensity converges to the photon transit time distribution, which for the samples used is in excellent agreement with a diffusion model.

Broadband polarization correction with programmable liquid-crystal modulator arrays

We demonstrate a novel method of parallel, multiwavelength state-of-polarization (SOP) correction. Using a new liquid-crystal modulator array design, we are able to rotate the distorted input SOP spectrum to a fixed linear state on a wavelength-by-wavelength basis. We report experimental correction of up to 25.5-dB polarization-dependent loss over a 13-nm bandwidth around 1550 nm.

Fast wavelength-parallel polarimeter for broadband optical networks

We describe a novel wavelength-parallel polarimeter operating in the light-wave band that measures the complete state of polarization of 256 wavelengths in parallel within 20 ms (software-limited), with the potential for submillisecond operation. By use of fast switching ferroelectric liquid crystals in conjunction with an InGaAs arrayed detector, selection and wavelength-parallel detection of individual polarization components can be achieved within approximately 150 microseconds. This instrument offers unprecedented sensing capability that is relevant to the compensation of polarization-related impairments in high-speed light-wave communications.

Direct field-resolved detection of terahertz transients with amplitudes of megavolts per centimeter

Phase-matched difference-frequency mixing in a thin GaSe crystal within the broad spectrum of 25-fs pulses from a Ti:sapphire oscillator multipass amplifier system permits the generation of few-cycle electric field transients, frequencies up to 30 THz, and amplitudes of more than 1 MV/cm. The field transients generated at a 1-kHz repetition rate are directly measured by electro-optic sampling by 12-f probe pulses from the 75-MHz repetition-rate Ti:sapphire oscillator in combination with a novel electronic gating technique.

Millimeter-wave arbitrary waveform generation with a direct space-to-time pulse shaper

By using tailored pulse sequences from a novel, 1.5-microm direct space-to-time pulse shaper driving a high-speed photodetector, we have achieved, for the first time to our knowledge, millimeter-wave arbitrary waveform generation at center frequencies approaching 50 GHz. By appropriately designing the driving optical pulse sequences, we demonstrate the ability to synthesize strongly phase- and frequency-modulated millimeter-wave electrical signals on a cycle-by-cycle basis.

Temporal response of a random medium from third-order laser speckle frequency correlations

We demonstrate for the first time that the temporal response of a random medium can be obtained from optical intensity fluctuations. Our method uses third-order intensity correlations of measured speckle patterns from a multiple scattering random medium as a function of optical frequency. In particular, our experimental results for the temporal response extracted from third-order intensity correlations are in good agreement with the predictions of a diffusion model. Our results are valid for waves in random media where the scattered field is described by circular complex Gaussian statistics.

Collaboration between CC- and A-adding enzymes to build and repair the 3'-terminal CCA of tRNA in Aquifex aeolicus

The universal 3'-terminal CCA sequence of all transfer RNAs (tRNAs) is repaired, and sometimes constructed de novo, by the CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase]. This RNA polymerase has no nucleic acid template, yet faithfully builds the CCA sequence one nucleotide at a time using cytidine triphosphate (CTP) and adenosine triphosphate (ATP) as substrates. All previously characterized CCA-adding enzymes from all three kingdoms are single polypeptides with CCA-adding activity. Here, we demonstrate through biochemical and genetic approaches that CCA addition in Aquifex aeolicus requires collaboration between two related polypeptides, one that adds CC and another that adds A.

Sequences upstream of the branch site are required to form helix II between U2 and U6 snRNA in a trans-splicing reaction

Three different base paired stems form between U2 and U6 snRNA over the course of the mRNA splicing reaction (helices I, II and III). One possible function of U2/U6 helix II is to facilitate subsequent U2/U6 helix I and III interactions, which participate directly in catalysis. Using an in vitro trans-splicing assay, we investigated the function of sequences located just upstream from the branch site (BS). We find that these upstream sequences are essential for stable binding of U2 to the branch region, and for U2/U6 helix II formation, but not for initial U2/BS pairing. We also show that non-functional upstream sequences cause U2 snRNA stem-loop IIa to be exposed to dimethylsulfate modification, perhaps reflecting a U2 snRNA conformational change and/or loss of SF3b proteins. Our data suggest that initial binding of U2 snRNP to the BS region must be stabilized by an interaction with upstream sequences before U2/U6 helix II can form or U2 stem-loop IIa can participate in spliceosome assembly.

Controlled shaping of ultrafast electric field transients in the mid-infrared spectral range

We experimentally demonstrate amplitude and phase shaping of femtosecond mid-infrared pulses in a range centered about 14 mum . Single pulses with a tailored optical phase and phase-locked double pulses are generated by phase-matched difference-frequency mixing in a GaSe crystal of near-infrared pulses shaped with a liquid-crystal modulator. The electric field transients are directly measured by free-space electro-optic sampling, yielding pulse durations of 200-300 fs. Our data are in good agreement with a model that describes phase-matched optical rectification.

Comment on "Time reversal of ultrafast waveforms by wave mixing of spectrally decomposed waves"

In a recent Letter [Opt. Lett. 25, 132 (2000)] the properties of two different techniques for time reversal of ultrafast optical waveforms were compared. Although both techniques, spectral phase conjugation and spectral inversion, perform the same function for real pulses, for pulses with complex envelope functions it was asserted that only spectral inversion gives true time reversal. I argue here for a different interpretation.

Spectral phase correlation of coded femtosecond pulses by second-harmonic generation in thick nonlinear crystals

We demonstrate a novel all-optical scheme for measuring the correlation of spectrally phase-coded ultrashort optical waveforms that uses second-harmonic generation (SHG) in long, periodically poled lithium niobate crystals. The SHG yield can be controlled over a range of ~30 dB, depending on the correlation of the applied phase codes. Such a spectral phase correlator has applications for ultrashort-pulse optical code-division multiple-access networking and could serve as a nonlinear optical but classical analog for certain schemes for coherent quantum control of multiphoton processes.

Chirp control in the direct space-to-time pulse shaper

The dispersion properties of the direct space-to-time pulse shaper are investigated for the first time to our knowledge. We demonstrate that phase-front curvature of the input spatial profile leads to a chirp in the output temporal waveform, which one can compensate for by varying the separation between the pulse-shaping lens and slit. Furthermore, the output intensity profile remains invariant as the chirp is manipulated. These properties are fundamentally different than in the well-known Fourier-transform pulse shaper.

Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human U1, U2, and 5S genes

Infection by adenovirus 12, transfection with the Ad12 E1B 55 kDa gene, or activation of p53 cause metaphase fragility of four loci (RNU1, PSU1, RNU2, and RN5S) each containing tandemly repeated genes for an abundant small RNA (U1, U2, and 5S RNA). We now show that loss of the Cockayne syndrome group B protein (CSB) or overexpression of the p53 carboxy-terminal domain induces fragility of the same loci; moreover, p53 interacts with CSB in vivo and in vitro. We propose that CSB functions as an elongation factor for transcription of structured RNAs, including some mRNAs. Activation of p53 would inhibit CSB, stalling transcription complexes and locally blocking chromatin condensation. Impaired transcription elongation may also explain the diverse clinical features of Cockayne syndrome.

Characterization and imaging in optically scattering media by use of laser speckle and a variable-coherence source

We demonstrate the application of laser-speckle statistics formed by a variable-coherence source illuminating a scattering medium, for determining the scattering parameter mu;(s)>(?) of a diffusion model for the medium. Furthermore, we apply this technique to visualize laterally localized inhomogeneities embedded within a highly scattering sample.

Molecular evolution: aminoacyl-tRNA synthetases on the loose

Modified versions - paralogs - of the catalytic domain of at least three different aminoacyl-tRNA synthetases have been found to serve catalytic or regulatory roles in other reactions. These findings suggest that the first modern tRNA-synthetases could have been derived from amino-acid biosynthetic enzymes.

Concerted evolution of the tandem array encoding primate U2 snRNA (the RNU2 locus) is accompanied by dramatic remodeling of the junctions with flanking chromosomal sequences

The genes encoding primate U2 snRNA are organized as a nearly perfect tandem array (the RNU2 locus) that has been evolving concertedly for >35 Myr since the divergence of baboons and humans. Thus the repeat units of the tandem array are essentially identical within each species, but differ between species. Homogeneity is maintained because any change in one repeat unit is purged from the array or fixed in all other repeats. Intriguingly, the cytological location of RNU2 has remained unchanged despite concerted evolution of the tandem array. We had found previously that junction sequences between the U2 tandem array and flanking DNA were subject to remodeling over a region of 200-300 bp during the past 5 Myr in the hominid lineage. Here we show that the junctions between the U2 tandem array and flanking DNA have undergone dramatic rearrangements over a region of 1 to >10 kbp in the 35 Myr since divergence of the Old World Monkey and hominid lineages. We argue that these rearrangements reflect the high level of genetic activity required to sustain concerted evolution, and propose a model to explain why maintenance of homogeneity within a tandemly repeated multigene family would lead to junctional diversity.

Femtosecond optical packet generation by a direct space-to-time pulse shaper

We demonstrate femtosecond operation of a direct space-to-time pulse shaper in which there is direct mapping (no Fourier transform) between the spatial position of the masking function and the temporal position in the output waveform. We use this apparatus to generate trains of 20 pulses as an ultrafast optical data packet over an approximately 40-ps temporal window.

Generation and characterization of terahertz pulse trains from biased, large-aperture photoconductors

The saturation properties of terahertz emission from biased, large-aperture photoconductors excited by trains of amplified femtosecond optical pulses are presented. A direct comparison is made of the multiple-pulse saturation properties of terahertz emission from semi-insulating GaAs and low-temperature-grown GaAs emitters with different carrier lifetimes. When the carrier lifetime is less than or comparable with the interpulse spacing, a significant enhancement of the narrow-band terahertz output is observed. The enhancement is not observed for emitters with long carrier lifetimes, consistent with the results of a previously derived saturation theory [Opt. Lett. 18, 1340 (1993)].

Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts

BACKGROUND

Coiled bodies are nuclear organelles that are highly enriched in small nuclear ribonucleoproteins (snRNPs) and certain basal transcription factors. Surprisingly, coiled bodies not only contain mature U snRNPs but also associate with specific chromosomal loci, including gene clusters that encode U snRNAs and histone messenger RNAs. The mechanism(s) by which coiled bodies associate with these genes is completely unknown.

RESULTS

Using stable cell lines, we show that artificial tandem arrays of human U1 and U2 snRNA genes colocalize with coiled bodies and that the frequency of the colocalization depends directly on the transcriptional activity of the array. Association of the genes with coiled bodies was abolished when the artificial U2 arrays contained promoter mutations that prevent transcription or when RNA polymerase II transcription was globally inhibited by alpha-amanitin. Remarkably, the association was also abolished when the U2 snRNA coding regions were replaced by heterologous sequences.

CONCLUSIONS

The requirement for the U2 snRNA coding region indicates that association of snRNA genes with coiled bodies is mediated by the nascent U2 RNA itself, not by DNA or DNA-bound proteins. Our data provide the first evidence that association of genes with a nuclear organelle can be directed by an RNA and suggest an autogenous feedback regulation model.

Coexpression of the adenovirus 12 E1B 55 kDa oncoprotein and cellular tumor suppressor p53 is sufficient to induce metaphase fragility of the human RNU2 locus

Adenovirus 12 (Ad12), but not adenovirus 2 or 5, induces metaphase chromosome fragility at four specific loci in humans: RNU1, RNU2, PSU1, and RN5S. As each of these sites corresponds to a tandemly repeated multigene family encoding a small, abundant structural RNA, we proposed that Ad12 hinders metaphase chromatin condensation, interfering either directly or indirectly with transcriptional regulation or chromatin packing of these small RNA genes. We and others subsequently found that Ad12-induced fragility of the RNU2 locus requires U2 promoter elements, viral early functions, and p53. We now show that RNU2 fragility can be induced by transfection with an expression vector encoding Ad12 E1B 55 kDa alone but not by an E1 vector encoding all E1 products (3 E1A proteins, as well as the E1B 19 kDa and 55 kDa proteins). Although Ad12 E1B 55 kDa efficiently induced fragility in transfected cells, Ad2 E1B 55 kDa did not. By swapping domains between the Ad12 and Ad2 E1B, we found that the aminoterminus of Ad12 E1B is required for induction of fragility and that the ability of the hybrid E1B proteins to induce fragility appears to correlate with nuclear localization. Furthermore, in Saos-2 cells lacking p53 function, RNU2 fragility could be induced by cotransfection with vectors encoding Ad12 E1B 55 kDa and either wild-type p53 or the R273H mutant with impaired DNA binding activity. We conclude that a functional (and probably physical) interaction between Ad12 E1B 55 kDa and p53 within the nucleus is sufficient to induce metaphase fragility of the RNU2 locus.

The CCA-adding enzyme has a single active site

The CCA-adding enzyme (tRNA nucleotidyltransferase) synthesizes and repairs the 3'-terminal CCA sequence of tRNA. The eubacterial, eukaryotic, and archaeal CCA-adding enzymes all share a single active-site signature motif, which identifies these enzymes as belonging to the nucleotidyltransferase superfamily. Here we show that mutations at Asp-53 or Asp-55 of the Sulfolobus shibatae signature sequence abolish addition of both C and A, demonstrating that a single active site is responsible for addition of both nucleotides. Mutations at Asp-106 (and to a lesser extent, at Glu-173 and Asp-215) selectively impaired addition of A, but not C. We have previously demonstrated that the tRNA acceptor stem remains fixed on the surface of the CCA-adding enzyme during C and A addition (Shi, P.-Y., Maizels, N., and Weiner, A. M. (1998) EMBO J. 17, 3197-3206). Taken together with this new evidence that there is a single active site for catalysis, our data suggest that specificity of nucleotide addition is determined by a process of collaborative templating: as the single active site catalyzes addition of each nucleotide, the growing 3'-end of the tRNA would progressively refold to create a binding pocket for addition of the next nucleotide.

High-efficiency blue generation by frequency doubling of femtosecond pulses in a thick nonlinear crystal

We have demonstrated highly efficient frequency doubling of femtosecond pulses in a thick, noncritically phase-matched KNbO(3) crystal under conditions of large group-velocity mismatch. At low power we observed a slope efficiency of ~300% nJ (-1) for harmonic conversion, and at higher powers we generated 170 mW of second-harmonic blue output for 300 mW of input light. Furthermore, we have shown that the focusing dependence for our conditions of large group-velocity mismatch is considerably different from that obtained for frequency doubling of continuous-wave light. We have also demonstrated that one can tune the spectral width of the generated blue light by varying the focusing conditions.

Efficient High-Energy Pulse-Train Generation Using a 2 n-Pulse Michelson Interferometer

We demonstrate a novel, Michelson-based, ultrafast multiplexer with a throughput approaching 100% for a polarization-multiplexed train and 50% for a linearly polarized train, which is compatible with a high-energy pulse train and shaped-pulse generation. The interpulse spacings in the resultant 2(n)-pulse train can be adjusted continuously from multinanoseconds through zero. Using this interferometer, we also demonstrate generation of a 16-pulse train of terahertz pulses.

CCA addition by tRNA nucleotidyltransferase: polymerization without translocation?

The CCA-adding enzyme repairs the 3'-terminal CCA sequence of all tRNAs. To determine how the enzyme recognizes tRNA, we probed critical contacts between tRNA substrates and the archaeal Sulfolobus shibatae class I and the eubacterial Escherichia coli class II CCA-adding enzymes. Both CTP addition to tRNA-C and ATP addition to tRNA-CC were dramatically inhibited by alkylation of the same tRNA phosphates in the acceptor stem and TPsiC stem-loop. Both enzymes also protected the same tRNA phosphates in tRNA-C and tRNA-CC. Thus the tRNA substrate must remain fixed on the enzyme surface during CA addition. Indeed, tRNA-C cross-linked to the S. shibatae enzyme remains fully active for addition of CTP and ATP. We propose that the growing 3'-terminus of the tRNA progressively refolds to allow the solitary active site to reuse a single CTP binding site. The ATP binding site would then be created collaboratively by the refolded CC terminus and the enzyme, and nucleotide addition would cease when the nucleotide binding pocket is full. The template for CCA addition would be a dynamic ribonucleoprotein structure.

Characterization of a novel class of interspersed LTR elements in primate genomes: structure, genomic distribution, and evolution

Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13 family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus.

A tandem array of minimal U1 small nuclear RNA genes is sufficient to generate a new adenovirus type 12-inducible chromosome fragile site

Infection of human cells with adenovirus serotype 12 (Ad12) induces metaphase fragility of four, and apparently only four, chromosomal loci. Surprisingly, each of these four loci corresponds to a cluster of genes encoding a small abundant structural RNA: the RNU1 and RNU2 loci contain tandemly repeated genes encoding U1 and U2 small nuclear RNAs (snRNAs), respectively; the PSU1 locus is a cluster of degenerate U1 genes; and the RN5S locus contains the tandemly repeated genes encoding 5S rRNA. These observations suggested that high local levels of transcription, in combination with Ad12 early functions, can interfere with metaphase chromatin packing. In support of this hypothesis, we and others found that an artificial tandem array of transcriptionally active, but not inactive, U2 snRNA genes would generate a novel Ad12-inducible fragile site. Although U1 and U2 snRNA are both transcribed by RNA polymerase II and share similar enhancer, promoter, and terminator signals, the human U1 promoter is clearly more complex than that of U2. In addition, the natural U1 tandem repeat unit exceeds 45 kb, whereas the U2 tandem repeat unit is only 6.1 kb. We therefore asked whether an artificial array of minimal U1 genes would also generate a novel Ad12-inducible fragile site. The exogenous U1 genes were marked by an innocuous U72C point mutation within the U1 coding region so that steady-state levels of U1 snRNA derived from the artificial array could be quantified by a simple primer extension assay. We found that the minimal U1 genes were efficiently expressed and were as effective as minimal U2 genes in generating a novel Ad12-inducible fragile site. Thus, despite significant differences in promoter architecture and overall gene organization, the active U1 transcription units suffice to generate a new virally inducible fragile site.

Adenovirus type 12-induced fragility of the human RNU2 locus requires p53 function

Adenovirus type 12 (Ad12) infection of human cells induces four chromosomal fragile sites corresponding to the U1 small nuclear RNA (snRNA) genes (the RNU1 locus), the U2 snRNA genes (RNU2), the U1 snRNA pseudogenes (PSU1), and the 5S rRNA genes (RN5S). Ad12-induced fragility of the RNU2 locus requires U2 snRNA transcriptional regulatory elements and viral early functions but not viral replication or integration, or chromosomal sequences flanking the RNU2 locus. We now show that Ad12 cannot induce the RNU1, RNU2, or PSU1 fragile sites in Saos-2 cells lacking the p53 and retinoblastoma (Rb) proteins but that viral induction of fragility is rescued in these cells when the expression of wild-type p53 or selected hot-spot mutants (i.e., V143A, R175H, R248W, and R273H) is restored by transient expression or stable retroviral transduction. We also observed weak constitutive fragility of the RNU1 and RNU2 loci in cells belonging to xeroderma pigmentosum complementation groups B and D (XPB and XPD) which are partially defective in the ERCC2 (XPD) and ERCC3 (XPB) helicase activities shared between the repairosome and the RNA polymerase H basal transcription factor TFIIH. We propose a model for Ad12-induced chromosome fragility in which interaction of p53 with the Ad12 E1B 55-kDa transforming protein (and possibly E4orf6) induces a p53 gain of function which ultimately perturbs the RNA polymerase II basal transcription apparatus. The p53 gain of function could interfere with chromatin condensation either by blocking mitotic shutdown of U1 and U2 snRNA transcription or by phenocopying global or local DNA damage. Specific fragilization of the RNU1, RNU2, and PSU1 loci could reflect the unusually high local concentration of strong transcription units or the specialized nature of the U1 and U2 snRNA transcription apparatus.

The microsatellite sequence (CT)n x (GA)n promotes stable chromosomal integration of large tandem arrays of functional human U2 small nuclear RNA genes

The multigene family encoding human U2 small nuclear RNA (snRNA) is organized as a single large tandem array containing 5 to 25 copies of a 6.1-kb repeat unit (the RNU2 locus). Remarkably, each of the repeat units within an individual U2 tandem array appears to be identical except for an irregular dinucleotide tract, known as the CT microsatellite, which exhibits minor length and sequence polymorphism. Using a somatic cell genetic assay, we previously noticed that the CT microsatellite appeared to stabilize artificial tandem arrays of U2 snRNA genes. We now demonstrate that the CT microsatellite is required to establish large tandem arrays of transcriptionally active U2 genes, increasing both the average and maximum size of the resulting arrays. In contrast, the CT microsatellite has no effect on the average or maximal size of artificial arrays containing transcriptionally inactive U2 genes that lack key promoter elements. Our data reinforce the connection between recombination and transcription. Active U2 transcription interferes with establishment or maintenance of the U2 tandem array, and the CT microsatellite opposes these effects, perhaps by binding GAGA or GAGA-related factors which alter local chromatin structure. We speculate that the mechanisms responsible for maintenance of tandem arrays containing active promoters may differ from those that maintain tandem arrays of transcriptionally inactive sequences.