The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page

Effect of promoter architecture on the cell-to-cell variability in gene expression

According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effort that addresses the question of how changes in promoter architecture affect noise in gene expression in a systematic rather than case-by-case fashion. In this article, we make such a systematic investigation, based on a simple microscopic model of gene regulation that incorporates stochastic effects. In particular, we show how operator strength and operator multiplicity affect this variability. We examine different modes of transcription factor binding to complex promoters (cooperative, independent, simultaneous) and how each of these affects the level of variability in transcription product from cell-to-cell. We propose that direct comparison between in vivo single-cell experiments and theoretical predictions for the moments of the probability distribution of mRNA number per cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte

Search for Dark Matter and Supersymmetry with a Compressed Mass Spectrum in the Vector Boson Fusion Topology in Proton-Proton Collisions at root s=8 TeV

Peer reviewe

International Ocean Discovery Program: Expedition 374 Preliminary Report: Ross Sea West Antarctic Ice Sheet History: Ocean-ice sheet interactions and West Antarctic Ice Sheet vulnerability: clues from the Neogene and Quaternary record of the outer Ross Sea continental margin

The marine-based West Antarctic Ice Sheet (WAIS) is currently retreating due to shifting wind-driven oceanic currents that transport warm waters toward the ice margin, resulting in ice shelf thinning and accelerated mass loss of the WAIS. Previous results from geologic drilling on Antarctica’s continental margins show significant variability in marine-based ice sheet extent during the late Neogene and Quaternary. Numerical models indicate a fundamental role for oceanic heat in controlling this variability over at least the past 20 My. Although evidence for past ice sheet variability has been collected in marginal settings, sedimentologic sequences from the outer continental shelf are required to evaluate the extent of past ice sheet variability and the associated oceanic forcings and feedbacks. International Ocean Discovery Program Expedition 374 drilled a latitudinal and depth transect of five drill sites from the outer continental shelf to rise in the eastern Ross Sea to resolve the relationship between climatic and oceanic change and WAIS evolution through the Neogene and Quaternary. This location was selected because numerical ice sheet models indicate that this sector of Antarctica is highly sensitive to changes in ocean heat flux. The expedition was designed for optimal data-model integration and will enable an improved understanding of the sensitivity of Antarctic Ice Sheet (AIS) mass balance during warmer-than-present climates (e.g., the Pleistocene “super interglacials,” the mid-Pliocene, and the late early to middle Miocene). The principal goals of Expedition 374 were to Evaluate the contribution of West Antarctica to far-field ice volume and sea level estimates; Reconstruct ice-proximal atmospheric and oceanic temperatures to identify past polar amplification and assess its forcings and feedbacks; Assess the role of oceanic forcing (e.g., sea level and temperature) on AIS stability/instability; Identify the sensitivity of the AIS to Earth’s orbital configuration under a variety of climate boundary conditions; and Reconstruct eastern Ross Sea paleobathymetry to examine relationships between seafloor geometry, ice sheet stability/instability, and global climate. To achieve these objectives, we will Use data and models to reconcile intervals of maximum Neogene and Quaternary Antarctic ice advance with far-field records of eustatic sea level change; Reconstruct past changes in oceanic and atmospheric temperatures using a multiproxy approach; Reconstruct Neogene and Quaternary sea ice margin fluctuations in datable marine continental slope and rise records and correlate these records to existing inner continental shelf records; Examine relationships among WAIS stability/instability, Earth’s orbital configuration, oceanic temperature and circulation, and atmospheric pCO2; and Constrain the timing of Ross Sea continental shelf overdeepening and assess its impact on Neogene and Quaternary ice dynamics. Expedition 374 was carried out from January to March 2018, departing from Lyttelton, New Zealand. We recovered 1292.70 m of high-quality cores from five sites spanning the early Miocene to late Quaternary. Three sites were cored on the continental shelf (Sites U1521, U1522, and U1523). At Site U1521, we cored a 650 m thick sequence of interbedded diamictite, mudstone, and diatomite, penetrating the Ross Sea seismic Unconformity RSU4. The depositional reconstructions of past glacial and open-marine conditions at this site will provide unprecedented insight into environmental change on the Antarctic continental shelf during the early and middle Miocene. At Site U1522, we cored a discontinuous upper Miocene to Pleistocene sequence of glacial and glaciomarine strata from the outer shelf, with the primary objective to penetrate and date seismic Unconformity RSU3, which is interpreted to represent the first major continental shelf–wide expansion and coalescing of marine-based ice streams from both East and West Antarctica. At Site U1523, we cored a sediment drift located beneath the westerly flowing Antarctic Slope Current (ASC). Cores from this site will provide a record of the changing vigor of the ASC through time. Such a reconstruction will enable testing of the hypothesis that changes in the vigor of the ASC represent a key control on regulating heat flux onto the continental shelf, resulting in the ASC playing a fundamental role in ice sheet mass balance. We also cored two sites on the continental slope and rise. At Site U1524, we cored a Plio–Pleistocene sedimentary sequence on the continental rise on the levee of the Hillary Canyon, which is one of the largest conduits of Antarctic Bottom Water delivery from the Antarctic continental shelf into the abyssal ocean. Drilling at Site U1524 was intended to penetrate into middle Miocene and older strata but was initially interrupted by drifting sea ice that forced us to abandon coring in Hole U1524A at 399.5 m drilling depth below seafloor (DSF). We moved to a nearby alternate site on the continental slope (U1525) to core a single hole with a record complementary to the upper part of the section recovered at Site U1524. We returned to Site U1524 3 days later, after the sea ice cleared. We then cored Hole U1524C with the rotary core barrel with the intention of reaching the target depth of 1000 m DSF. However, we were forced to terminate Hole U1524C at 441.9 m DSF due to a mechanical failure with the vessel that resulted in termination of all drilling operations and a return to Lyttelton 16 days earlier than scheduled. The loss of 39% of our operational days significantly impacted our ability to achieve all Expedition 374 objectives as originally planned. In particular, we were not able to obtain the deeper time record of the middle Miocene on the continental rise or abyssal sequences that would have provided a continuous and contemporaneous archive to the high-quality (but discontinuous) record from Site U1521 on the continental shelf. The mechanical failure also meant we could not recover sediment cores from proposed Site RSCR-19A, which was targeted to obtain a high-fidelity, continuous record of upper Neogene and Quaternary pelagic/hemipelagic sedimentation. Despite our failure to recover a shelf-to-rise transect for the Miocene, a continental shelf-to-rise transect for the Pliocene to Pleistocene interval is possible through comparison of the high-quality records from Site U1522 with those from Site U1525 and legacy cores from the Antarctic Geological Drilling Project (ANDRILL)

International ocean discovery program expedition 374 preliminary report: Ross sea west antarctic ice sheet history ocean-ice sheet interactions and west antarctic ice sheet vulnerability: Clues from the neogene and quaternary record of the outer ross sea continental margin

The marine-based West Antarctic Ice Sheet (WAIS) is currently retreating due to shifting wind-driven oceanic currents that transport warm waters toward the ice margin, resulting in ice shelf thinning and accelerated mass loss of the WAIS. Previous results from geologic drilling on Antarctica's continental margins show significant variability in marine-based ice sheet extent during the late Neogene and Quaternary. Numerical models indicate a fundamental role for oceanic heat in controlling this variability over at least the past 20 My. Although evidence for past ice sheet variability has been collected in marginal settings, sedimentologic sequences from the outer continental shelf are required to evaluate the extent of past ice sheet variability and the associated oceanic forcings and feedbacks. International Ocean Discovery Program Expedition 374 drilled a latitudinal and depth transect of five drill sites from the outer continental shelf to rise in the eastern Ross Sea to resolve the relationship between climatic and oceanic change and WAIS evolution through the Neogene and Quaternary. This location was selected because numerical ice sheet models indicate that this sector of Antarctica is highly sensitive to changes in ocean heat flux. The expedition was designed for optimal data-model integration and will enable an improved understanding of the sensitivity of Antarctic Ice Sheet (AIS) mass balance during warmer-than-present climates (e.g., the Pleistocene "super interglacials," the mid-Pliocene, and the late early to middle Miocene). The principal goals of Expedition 374 were to • Evaluate the contribution of West Antarctica to far-field ice volume and sea level estimates; • Reconstruct ice-proximal atmospheric and oceanic temperatures to identify past polar amplification and assess its forcings and feedbacks; • Assess the role of oceanic forcing (e.g., sea level and temperature) on AIS stability/instability; • Identify the sensitivity of the AIS to Earth's orbital configuration under a variety of climate boundary conditions; and • Reconstruct eastern Ross Sea paleobathymetry to examine relationships between seafloor geometry, ice sheet stability/instability, and global climate. To achieve these objectives, we will • Use data and models to reconcile intervals of maximum Neogene and Quaternary Antarctic ice advance with far-field records of eustatic sea level change; • Reconstruct past changes in oceanic and atmospheric temperatures using a multiproxy approach; • Reconstruct Neogene and Quaternary sea ice margin fluctuations in datable marine continental slope and rise records and correlate these records to existing inner continental shelf records; • Examine relationships among WAIS stability/instability, Earth's orbital configuration, oceanic temperature and circulation, and atmospheric pCO 2 ; and • Constrain the timing of Ross Sea continental shelf overdeepening and assess its impact on Neogene and Quaternary ice dynamics. Expedition 374 was carried out from January to March 2018, departing from Lyttelton, New Zealand. We recovered 1292.70 m of high-quality cores from five sites spanning the early Miocene to late Quaternary. Three sites were cored on the continental shelf (Sites U1521, U1522, and U1523). At Site U1521, we cored a 650 m thick sequence of interbedded diamictite, mudstone, and diatomite, penetrating the Ross Sea seismic Unconformity RSU4. The depositional reconstructions of past glacial and open-marine conditions at this site will provide unprecedented insight into environmental change on the Antarctic continental shelf during the early and middle Miocene. At Site U1522, we cored a discontinuous upper Miocene to Pleistocene sequence of glacial and glaciomarine strata from the outer shelf, with the primary objective to penetrate and date seismic Unconformity RSU3, which is interpreted to represent the first major continental shelf-wide expansion and coalescing of marine-based ice streams from both East and West Antarctica. At Site U1523, we cored a sediment drift located beneath the westerly flowing Antarctic Slope Current (ASC). Cores from this site will provide a record of the changing vigor of the ASC through time. Such a reconstruction will enable testing of the hypothesis that changes in the vigor of the ASC represent a key control on regulating heat flux onto the continental shelf, resulting in the ASC playing a fundamental role in ice sheet mass balance. We also cored two sites on the continental slope and rise. At Sit e U1524, we cored a Plio-Pleistocene sedimentary sequence on the continental rise on the levee of the Hillary Canyon, which is one of the largest conduits of Antarctic Bottom Water delivery from the Antarctic continental shelf into the abyssal ocean. Drilling at Site U1524 was intended to penetrate into middle Miocene and older strata but was initially interrupted by drifting sea ice that forced us to abandon coring in Hole U1524A at 399.5 m drilling depth below seafloor (DSF). We moved to a nearby alternate site on the continental slope (U1525) to core a single hole with a record complementary to the upper part of the section recovered at Site U1524. We returned to Site U1524 3 days later, after the sea ice cleared. W e then cored Hole U1524C with the rotary core barrel with the intention of reaching the target depth of 1000 m DSF. However, we were forced to terminate Hole U1524C at 441.9 m DSF due to a mechanical failure with the vessel that resulted in termination of all drilling operations and a return to Lyttelton 16 days earlier than scheduled. The loss of 39% of our operational days significantly impacted our ability to achieve all Expedition 374 objectives as originally planned. In particular, we were not able to obtain the deeper time record of the middle Miocene on the continental rise or abyssal sequences that would have provided a continuous and contemporaneous archive to the high-quality (but discontinuous) record from Site U1521 on the continental shelf. The mechanical failure also meant we could not recover sediment cores from proposed Site RSCR-19A, which was targeted to obtain a high-fidelity, continuous record of upper Neogene and Quaternary pelagic/hemipelagic sedimentation. Despite our failure to recover a shelf-to-rise transect for the Miocene, a continental shelf-to-rise transect for the Pliocene to Pleistocene interval is possible through comparison of the high-quality records from Site U1522 with those from Site U1525 an d legacy cores from the Antarctic Geological Drilling Project (ANDRILL)

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases–or recombination directionality factors—RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer

Transcriptional interaction-assisted identification of dynamic nucleosome positioning

<p>Abstract</p> <p>Background</p> <p>Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo.</p> <p>Results</p> <p>Motivated by our observation that transcriptional interaction is discriminative information for nucleosome occupancy, we developed a novel computational approach to identify dynamic nucleosome positions at promoters by combining transcriptional interaction and genomic sequence information. Our approach successfully identified experimentally determined nucleosome positioning dynamics available in three cellular conditions, and significantly improved the prediction accuracy which is based on sequence information alone. We then applied our approach to various cellular conditions and established a comprehensive landscape of dynamic nucleosome positioning in yeast.</p> <p>Conclusion</p> <p>Analysis of this landscape revealed that the majority of nucleosome positions are maintained during most conditions. However, nucleosome occupancy at most promoters fluctuates with the corresponding gene expression level and is reduced specifically at the phase of peak expression. Further investigation into properties of nucleosome occupancy identified two gene groups associated with distinct modes of nucleosome modulation. Our results suggest that both the intrinsic sequence and regulatory proteins modulate nucleosomes in an altered manner.</p

Recombinant Mouse PAP Has pH-Dependent Ectonucleotidase Activity and Acts through A1-Adenosine Receptors to Mediate Antinociception

Prostatic acid phosphatase (PAP) is expressed in nociceptive neurons and functions as an ectonucleotidase. When injected intraspinally, the secretory isoforms of human and bovine PAP protein have potent and long-lasting antinociceptive effects that are dependent on A1-adenosine receptor (A1R) activation. In this study, we purified the secretory isoform of mouse (m)PAP using the baculovirus expression system to determine if recombinant mPAP also had antinociceptive properties. We found that mPAP dephosphorylated AMP, and to a much lesser extent, ADP at neutral pH (pH 7.0). In contrast, mPAP dephosphorylated all purine nucleotides (AMP, ADP, ATP) at an acidic pH (pH 5.6). The transmembrane isoform of mPAP had similar pH-dependent ectonucleotidase activity. A single intraspinal injection of mPAP protein had long-lasting (three day) antinociceptive properties, including antihyperalgesic and antiallodynic effects in the Complete Freund's Adjuvant (CFA) inflammatory pain model. These antinociceptive effects were transiently blocked by the A1R antagonist 8-cyclopentyl-1, 3-dipropylxanthine (CPX), suggesting mPAP dephosphorylates nucleotides to adenosine to mediate antinociception just like human and bovine PAP. Our studies indicate that PAP has species-conserved antinociceptive effects and has pH-dependent ectonucleotidase activity. The ability to metabolize nucleotides in a pH-dependent manner could be relevant to conditions like inflammation where tissue acidosis and nucleotide release occur. Lastly, our studies demonstrate that recombinant PAP protein can be used to treat chronic pain in animal models

Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon

The complete nucleotide sequence of plasmid pP62BP1 (34,467 bp), isolated from Arctic Psychrobacter sp. DAB_AL62B, was determined and annotated. The conserved plasmid backbone is composed of several genetic modules, including a replication system (REP) with similarities to the REP region of the iteron-containing plasmid pPS10 of Pseudomonas syringae. The additional genetic load of pP62BP1 includes two highly related type II restriction-modification systems and a set of genes (slfRCHSL) encoding enzymes engaged in the metabolism of organic sulfates, plus a putative transcriptional regulator (SlfR) of the AraC family. The pP62BP1 slflocus has a compact and unique structure. It is predicted that the enzymes SlfC, SlfH, SlfS and SlfL carry out a chain of reactions leading to the transformation of alkyl sulfates into acyl-CoA, with dodecyl sulfate (SDS) as a possible starting substrate. Comparative analysis of the nucleotide sequences of pP62BP1 and other Psychrobacter spp. plasmids revealed their structural diversity. However, the presence of a few highly conserved DNA segments in pP62BP1, plasmid 1 of P. cryohalolentis K5 and pRWF-101 of Psychrobacter sp. PRwf-1 is indicative of recombinational shuffling of genetic information, and is evidence of lateral gene transfer in the Arctic environment

Intronic L1 Retrotransposons and Nested Genes Cause Transcriptional Interference by Inducing Intron Retention, Exonization and Cryptic Polyadenylation

Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown.Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs) and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals.Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression