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Thesis advisor: Hugh P. Cam / Meiotic homologous recombination (HR) is not uniform across eukaryotic genomes, creating regions of strong recombination activity dubbed recombination hotspots, and regions of low recombination activity dubbed coldspots. Considerable attention has led to discoveries of a host of factors controlling the formation of hotspots. However, the determinants of coldspots are not as clearly defined. I have previously shown that CENP-B homologs of the fission yeast Schizosaccharomyces pombe have a genome surveillance role in regulating the nuclear organization and expression of Tf2 retrotransposons. Here, I reveal an additional role for CENP-Bs in suppressing meiotic recombination of Tf2s. I describe the development of a random sporulation assay to rapidly screen thousands of meiotic progeny for recombination across a locus in a variety of genetic backgrounds. Loss of any CENP-B family members (Abp1, Cbh1, Cbh2), results in increased HR at Tf2s. I show that Abp1, which acts as the primary determinant of HR suppression at Tf2s, is required to maintain proper recombination exchange of homologous alleles flanking a Tf2. In addition, Abp1-mediated suppression of HR at Tf2s requires all three of its domains with distinct functions in transcriptional repression and higher-order genome organization. I show that this suppression is likely mediated by Abp1 binding to specific motifs near the 3’end of flanking LTRs. I demonstrate that HR suppression of Tf2s can be robustly maintained despite disruption to chromatin factors essential for transcriptional repression and nuclear organization of Tf2s. Intriguingly, I uncover a surprising cooperation between the histone methyltransferase Set1 responsible for histone H3 lysine 4 methylation and the non-homologous end joining pathway in ensuring the suppression of HR at Tf2s. Furthermore, I identify a role for the architectural protein condensin involved in 3D chromatin organization and chromosome condensation in restricting HR at Tf2s. My study identifies a molecular pathway involving functional cooperation between a transcription factor with epigenetic regulators, DNA repair pathway, and chromosome organizers to regulate meiotic recombination at interspersed repeats. / Thesis (PhD) — Boston College, 2015. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

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Meiosis is the process by which diploid cells undergo DNA synthesis, homologous recombination and pairing, followed by the reductional division then the equational division. I present work in this PhD thesis which furthers the understanding of the coordination of the initiation of meiotic recombination and the reductional division. Ten genes are required to initiate recombination in Saccharomyces cerevisiae. The presence of a subset of recombination initiation proteins creates a Recombination Initiation Signal (RIS) that delays the start of MI in wild type cells. I present experiments demonstrating the first division kinetics of the two remaining recombination initiation genes that our lab had not yet studied. Rec107 is part of the RIS, while Ski8 is not. The RIS is conserved in a divergent Saccharomyces strain background. rec102 and rec104 SK1 strains both start the first division earlier that wildtype SK1 strains. I present evidence that suggests that the RIS acts independently of the pathway that controls securin (PDS1) degradation. The work in this thesis expands our knowledge of the mechanism by which the RIS delays the reductional division. In this thesis I present experiments showing that the DNA damage, spindle and S phase checkpoints do not transduce the RIS. I establish the meiosis-specific candidate Mek1 as a candidate for relaying the RIS. Lastly, experiments described in these chapters show that the transcriptional activator of Middle Meiosis, NDT80, is the target of the RIS. NDT80 transcription and activity are both necessary and sufficient to affect an earlier reductional division, similar to the early MI seen in RIS mutants.

<p>Dissociative recombination (DR) is a process in which a positive molecular ion recombines with an electron and subsequently dissociates into neutral fragments. Among the different types of molecular ion-electron reactions DR deserves particular attention due to the important role it plays in low-temperature and low-density plasmas. Despite the apparent simplicity of the DR reaction, its investigation has proven to be a difficult task from both experimental and theoretical perspectives. In order to shed more light upon this process the storage ring technique has been introduced and utilised extensively for the last few decades. This thesis is devoted to experimental studies into the DR reaction at the storage ring CRYRING. The DR reaction has been investigated for the following molecular ions; Na⁺(D₂O), PD₂⁺, O₃⁺, N₃⁺, H₂⁺, D₂H⁺, OPCl⁺, OPCl₂⁺ and H₃O⁺, with the aim to ascertain rotational state effects, to find patterns in the branching products of similar molecular ions, to investigate isotope effects and to study in detail the dynamics involved in the three-body break-up channel.</p>

Dissociative recombination (DR) is a process in which a positive molecular ion recombines with an electron and subsequently dissociates into neutral fragments. Among the different types of molecular ion-electron reactions DR deserves particular attention due to the important role it plays in low-temperature and low-density plasmas. Despite the apparent simplicity of the DR reaction, its investigation has proven to be a difficult task from both experimental and theoretical perspectives. In order to shed more light upon this process the storage ring technique has been introduced and utilised extensively for the last few decades. This thesis is devoted to experimental studies into the DR reaction at the storage ring CRYRING. The DR reaction has been investigated for the following molecular ions; Na+(D2O), PD2+, O3+, N3+, H2+, D2H+, OPCl+, OPCl2+ and H3O+, with the aim to ascertain rotational state effects, to find patterns in the branching products of similar molecular ions, to investigate isotope effects and to study in detail the dynamics involved in the three-body break-up channel.

This thesis presents experimental studies on the dissociative recombination (DR) of the organic molecular ions CD3CND+, CH2CHCNH+, CH3CH2CNH+, CD3CDO+, CH3CHO+ and DCOOD2+. The experiments were all performed at the heavy ion storage ring CRYRING at the Manne Siegbahn Laboratory in Stockholm, Sweden. DR is the process in which a singly charged molecular cation captures a free electron, forming a highly excited intermediate molecule which then dissociates into exclusively neutral fragments. The process plays an important role as a plasma neutralizing mechanism in many cold, low density plasmas such as those encountered in planetary ionospheres and interstellar clouds. DR can also act as the final step in the gas-phase synthesis of different neutral molecules in such environments. Our experimental findings indicate that nitriles that are lost by protonation in Titan’s upper atmosphere or in interstellar clouds to a large extent may be recycled by DR. Also, it appears that the DR of nitrile ions does not break the C-N bond, which supports the hypothesis that nitriles which are formed in Titan’s upper atmosphere do not degrade to recover N2. For the studied acetaldehyde cations, CD3CDO+ and CH3CHO+, we observed a considerable isotopic effect in the cross section, with the lighter isotopologue being more reactive. In the DR of DCOOD2+ an upper limit of only 13% for the branching fraction of the DCOOD + D channel was found. This finding has pronounced effects on the predicted abundance of formic acid in dark clouds.