Genomic analyses of transcription elongation factors and intragenic transcription

Transcription of protein-coding genes in eukaryotic cells is carried out by the protein complex RNA polymerase II. During the elongation phase of transcription, RNA polymerase II associates with transcription elongation factors which modulate the activity of the transcription complex and are needed to carry out co-transcriptional processes. Chapters 2 and 3 of this dissertation describe studies of Spt6 and Spt5, two conserved transcription elongation factors. Spt6 is a transcription elongation factor thought to replace nucleosomes in the wake of transcription. Saccharomyces cerevisiae spt6 mutants express elevated levels of intragenic transcripts, transcripts appearing to initiate from within gene bodies. We applied high resolution genomic assays of transcription initiation to an spt6-1004 mutant, allowing us to catalog the full extent of intragenic transcription in spt6-1004 and show for the first time on a genome-wide scale that the intragenic transcripts observed in spt6-1004 are largely explained by new transcription initiation. We also assayed chromatin structure genome-wide in spt6-1004, finding a global depletion and disordering of nucleosomes. In addition to increased intragenic transcription in spt6-1004, our results also reveal an unexpected decrease in expression from most canonical genic promoters. Comparing intragenic and genic promoters, we find that intragenic promoters share some features with genic promoters. Altogether, we propose that the transcriptional changes in spt6-1004 are explained by a competition for transcription initiation factors between genic and intragenic promoters, which is made possible by a global decrease in nucleosome protection of the genome. Spt5 is another transcription elongation factor, important for the processivity of the transcription complex and many transcription-related processes. To study the requirement for Spt5 in vivo, we applied multiple genomic assays to Schizosaccharomyces pombe cells depleted of Spt5. Our results reveal an accumulation of RNA polymerase II over the 5 ′ ends of genes upon Spt5 depletion, and a progressive decrease in transcript abundance towards the 3 ′ ends of genes. This is consistent with a model in which Spt5 depletion causes transcription elongation defects and increases early termination. We also unexpectedly discover that Spt5 depletion causes hundreds of antisense transcripts to be expressed across the genome, primarily initiating from within the first 500 base pairs of genes. The expression of intragenic transcripts when transcription elongation factors are disrupted suggests that cells have evolved to prevent spurious intragenic transcription. However, some cases of intragenic transcription are consistently detected in wild-type cells, and some of these cases are known to be important for different biological functions. Chapter 4 of this dissertation describes our efforts to better understand the functions of intragenic transcription in wild-type cells by studying uncharacterized instances of intragenic transcription. To discover uncharacterized instances of intragenic transcription, we applied high resolution genomic assays of transcription initiation to wild-type Saccharomyces cerevisiae under three stress conditions. For the condition of oxidative stress, we show that intragenic transcripts are generally expressed at lower levels than genic transcripts, and that many intragenic transcripts are likely to be translated at some level. By comparing intragenic transcription in three yeast species, we find that most examples of oxidative-stress regulated intragenic transcription identified in S. cerevisiae are not conserved. Finally, we show that the expression of an oxidative-stress-induced intragenic transcript at the gene DSK2 is needed for S. cerevisiae to survive in conditions of oxidative stress

Cubist Algebras

We construct algebras from rhombohedral tilings of Euclidean space obtained as projections of certain cubical complexes. We show that these `Cubist algebras' satisfy strong homological properties, such as Koszulity and quasi-heredity, reflecting the combinatorics of the tilings. We construct derived equivalences between Cubist algebras associated to local mutations in tilings. We recover as a special case the Rhombal algebras of Michael Peach and make a precise connection to weight 2 blocks of symmetric groups

Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway.

The Calvin-Benson-Bassham (CBB) cycle is presumably evolved for optimal synthesis of C3 sugars, but not for the production of C2 metabolite acetyl-CoA. The carbon loss in producing acetyl-CoA from decarboxylation of C3 sugar limits the maximum carbon yield of photosynthesis. Here we design a synthetic malyl-CoA-glycerate (MCG) pathway to augment the CBB cycle for efficient acetyl-CoA synthesis. This pathway converts a C3 metabolite to two acetyl-CoA by fixation of one additional CO2 equivalent, or assimilates glyoxylate, a photorespiration intermediate, to produce acetyl-CoA without net carbon loss. We first functionally demonstrate the design of the MCG pathway in vitro and in Escherichia coli. We then implement the pathway in a photosynthetic organism Synechococcus elongates PCC7942, and show that it increases the intracellular acetyl-CoA pool and enhances bicarbonate assimilation by roughly 2-fold. This work provides a strategy to improve carbon fixation efficiency in photosynthetic organisms

Row and column removal in the q-deformed Fock space

Analogues of James's row and column removal theorems are proved for the q-decomposition numbers arising from the canonical basis in the q-deformed Fock space

Canonical bases for Fock spaces and tensor products

We relate the canonical basis of the Fock space representation of the quantum affine algebra Uq(glˆn), as defined by Leclerc and Thibon [15], to the canonical basis of its restriction to Uq(sln), regarded as a based module in the sense of Lusztig. More generally we consider the restriction to any Levi subalgebra. We deduce results on decomposition numbers and branching coefficients of Schur algebras over fields of positive characteristic, generalizing those of Kleshchev [13] and of Tan and Teo [19]

Inspiration from Intersecting D-branes: General Supersymmetry Breaking Soft Terms in No-Scale F{\cal F}-SU(5)SU(5)

Motivated by D-brane model building, we evaluate the $\cal{F}$-$SU(5)$ model with additional vector-like particle multiplets, referred to as flippons, within the framework of No-Scale Supergravity with non-vanishing general supersymmetry breaking soft terms at the string scale. The viable phenomenology is uncovered by applying all current experimental constraints, including but not limited to the correct light Higgs boson mass, WMAP and Planck relic density measurements, and several LHC constraints on supersymmetric particle spectra. Four interesting regions of the parameter space arise, as well as mixed scenarios, given by: (i) light stop coannihilation; (ii) pure Higgsino dark matter; (iii) Higgs funnel; and (iv) light stau coannihilation. All regions can generate the observed value of the relic density commensurate with a 125 GeV light Higgs boson mass, with the exception of the relatively small relic density value for the pure Higgsino lightest supersymmetric particle (LSP). This work is concluded by gauging the model against present LHC search constraints and derivation of the final states observable at the LHC for each of these scenarios.Comment: 13 pages, 4 Figures, 4 Table

Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.Comment: Includes supporting informatio

Fixed-point adiabatic quantum search

Fixed-point quantum search algorithms succeed at finding one of M target items among N total items even when the run time of the algorithm is longer than necessary. While the famous Grover's algorithm can search quadratically faster than a classical computer, it lacks the fixed-point property—the fraction of target items must be known precisely to know when to terminate the algorithm. Recently, Yoder, Low, and Chuang [Phys. Rev. Lett. 113, 210501 (2014)] gave an optimal gate-model search algorithm with the fixed-point property. Previously, it had been discovered by Roland and Cerf [Phys. Rev. A 65, 042308 (2002)] that an adiabatic quantum algorithm, operating by continuously varying a Hamiltonian, can reproduce the quadratic speedup of gate-model Grover search. We ask, can an adiabatic algorithm also reproduce the fixed-point property? We show that the answer depends on what interpolation schedule is used, so as in the gate model, there are both fixed-point and non-fixed-point versions of adiabatic search, only some of which attain the quadratic quantum speedup. Guided by geometric intuition on the Bloch sphere, we rigorously justify our claims with an explicit upper bound on the error in the adiabatic approximation. We also show that the fixed-point adiabatic search algorithm can be simulated in the gate model with neither loss of the quadratic Grover speedup nor of the fixed-point property. Finally, we discuss natural uses of fixed-point algorithms such as preparation of a relatively prime state and oblivious amplitude amplification.American Society for Engineering Education. National Defense Science and Engineering Graduate FellowshipMIT-Harvard Center for Ultracold Atoms MIT International Science and Technology InitiativeNational Science Foundation (U.S.) (RQCC Project 1111337)Massachusetts Institute of Technology. Undergraduate Research Opportunities Program (Paul E. Gray Endowed Fund