Thesis advisor: Michelle M. Meyer / Existing methods of assaying the function of cis-regulatory RNAs come with significant drawbacks when assaying large RNA libraries. Highly sensitive cell-based assays such as the β galactosidase assay are labor intensive, difficult to scale up and may lose sensitivity with increased throughput. GFP and luciferase reporters can be used with FACS to increase assay throughput, but sorting small bacterial cells is challenging and greatly reduces assay sensitivity. Conversely, in vitro methods allow for fast screening of very large RNA libraries, but only select for properties of binding, not regulation. By combining the principles of classic in cell regulatory assays with modern tools, cis-regulatory RNAs can be quickly screened for regulatory activity at a large scale. The assay under development, Fluorescent Activated Droplet Sorting Regulatory Assay (FADSRA), uses microfluidics to encapsulate single cells expressing a fluorescent protein under the control of a cis-regulatory RNA. These cells are then cultured into microcolonies within the droplets, which are subsequently sorted according to fluorescent signal. Deep amplicon sequencing of the regulatory RNAs can then reveal which sequences can regulate and which cannot. Thus, FADSRA can help bridge the gap between in vitro RNA binding and gene regulation assays, providing a way to answer sophisticated questions about cis-regulatory RNAs requiring high-throughput assay methods. While many applications for FADSRA are possible, such as verifying regulatory activity of in vitro binders or screening synthetic regulators, one such application of FASDRA is the creation of fitness landscapes that probe sequence-function relationships of RNA cis-regulators. This dissertation first develops and optimizes the regulatory assay for ribosomal leaders in Chapter 2, following by creating a single mutant fitness landscape of the E. coli S15 leader RNA in Chapter 3. Results of this fitness landscape largely support previously published mutational studies and highlight the necessity of stable hairpin formation for regulation of the E. coli S15 leader. Chapter 4, examining the regulation of S15 protein and leader homologs, and Chapter 5, testing the adaptability of FADSRA to other cis-regulatory RNAs, examine possible further applications of the assay. / Thesis (PhD) — Boston College, 2022. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Thesis advisor: Michelle M. Meyer / Bacteria commonly utilize cis-acting mRNA structures that bind specific molecules to control gene expression in response to changing cellular conditions. Examples of these ligand-sensing RNA cis-regulators are found throughout the bacterial world and include riboswitches, which interact with small metabolites to modulate the expression of fundamental metabolic genes, and the RNA structures that bind select ribosomal proteins to regulate entire ribosomal protein operons. Despite advances in both non-coding RNA discovery and validation, many predicted regulatory RNA motifs remain uncharacterized and little work has examined how RNA cis-regulators behave within their physiological context in the cell. Furthermore, it is not well understood how structured RNA regulators emerge and are maintained within bacterial genomes. In this thesis, I validate the biological function of a conserved RNA cis-regulator of ribosomal protein synthesis previously discovered by my group using bioinformatic approaches. I then investigate how bacteria respond to the loss of two different cis-regulatory RNA structures. Using Bacillus subtilis as a model organism, I introduce point mutations into the native loci of the ribosomal protein L20-interacting RNA cis-regulator and the tandem glycine riboswitch and assay the strains for fitness defects. I find that disrupting these regulatory RNA structures results in severe mutant phenotypes, especially under harsh conditions such as low temperatures or high glycine concentrations. Together, this body of work highlights the advantages of examining RNA behavior within its biological context and emphasizes the important role RNA cis-regulators play in overall organismal viability. My studies shed light on the selective pressures that impact structured RNA evolution in vivo and reinforce the potential of cis-regulatory RNAs as novel antimicrobial targets. / Thesis (PhD) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Nosso laboratório investiga os mecanismos moleculares que promovem o estabelecimento de padrões de expressão gênica regulados no desenvolvimento em eucariotos superiores. Como modelo, utilizamos o gene de pufe de DNA BhC4-1, que é amplificado e expresso de modo regulado na glândula salivar e na glândula protorácica no final do quarto estadio larval de B. hygida. Estudos funcionais em D. melanogaster resultaram na identificação de módulos cis-reguladores (MCRs) na região promotora do gene BhC4-1. O MCR de glândula anelar de 67 bp (-253/-187), promove a expressão de BhC4-1-lacZ na glândula anelar a partir do final do desenvolvimento embrionário. O MCR de glândula salivar de 129 bp (-186/-58), dirige a expressão do transgene nas glândulas salivares de prépupas. A glândula anelar é o principal órgão endócrino larval e em D. melanogaster é o resultado da fusão das glândulas protorácicas (responsáveis pela síntese de hormônios esteroides), corpus allatum (síntese de hormônio juvenil) e corpus cardiacum (glândula neuroendócrina). Neste trabalho foram obtidas 12 linhagens independentes transformadas com uma construção que contém o fragmento (-253/+40) do promotor do gene de pufe de DNA BhC4-1 clonado à montante do gene repórter GFP. O genótipo destas linhagens foi validado utilizando-se Southern blots. Inicialmente as 12 linhagens obtidas foram analisadas quanto ao padrão de expressão de GFP em larvas de terceiro estadio e em prépupas 2 horas. Em conjunto, esta análise revelou que o padrão de expressão de GFP é bastante variável nestas linhagens. A análise do padrão de expressão da proteína repórter foi estendida em duas linhagens representativas da série (- 253/+40)/GFP. Nestas linhagens a expressão de GFP é inicialmente detectada na glândula salivar durante o estágio de prépupa e na glândula anelar a partir do terceiro estadio larval. Diferentemente do anteriormente observado em linhagens (-253/+40)/lacZ, nestas linhagens não detectamos a expressão de GFP em tempos do desenvolvimento anteriores ao terceiro estadio larval. Experimentos de interação gênica revelaram que na ausência do fator de transcrição br, a expressão de GFP é mantida na glândula anelar e abolida na glândula salivar de larvas de terceiro estadio. Os resultados dos experimentos de interação gênica corroboram dados anteriores que indicavam que o conjunto de fatores de transcrição que regulam a expressão de BhC4-1-lacZ na glândula anelar é distinto daquele que promove a expressão do gene na glândula salivar. As linhagens obtidas neste trabalho constituem uma ferramenta a ser utilizada na caracterização de fatores de transcrição tecido-específicos que regulam o gene BhC4-1 na glândula anelar e/ou na glândula salivar a partir do final do desenvolvimento larval. / Our laboratory investigates the molecular mechanisms that promote the establishment of developmentally regulated gene expression patterns in metazoans. As a model, we employ the BhC4-1 DNA puff gene, which is amplified and expressed in a regulated manner in the salivary gland and in the prothoracic gland at the end of the fourth larval instar in B. hygida. Functional studies in D. melanogaster resulted in the identification of cis-regulatory modules (CRMs) in the BhC4-1 promoter region. The 67 bp (-253/-187) ring gland CRM drives BhC4-1-lacZ expression in the ring gland from late embryonic development. The 129 bp (-186/-58) CRM salivary gland drives transgene expression in the prepupal salivary glands. The ring gland is the major endocrine organ, and comprises the prothoracic glands (synthesis of ecdysteroid hormones), corpus allatum (synthesis of juvenile hormone) and corpus cardiacum (neuroendocrine gland). In this work, 12 independent lines transformed with a construct containing the BhC4-1 promoter fragment (- 253/+40) cloned upstream of the reporter gene GFP were obtained. The genotype of each line was validated using Southern blots. Initially, the 12 obtained lines were analyzed to investigate the pattern of GFP expression in the third instar larvae and in the 2 hours prepupae. This initial screening revealed that the pattern of GFP expression is highly variable in these lines. The developmental pattern of GFP expression was extended in two representative (- 253/+40)/GFP lines. In these lines, GFP expression is initially detected in the larval and prepupal salivary glands and in ring gland third instar. Differently from previously observed in (-253/+40)/lacZ lines, in these lines we did not detect GFP expression at developmental times prior to the third larval instar. Gene interaction experiments revealed that in the absence of the br transcription factor, GFP expression is maintained in the ring gland and abolished in the salivary gland of third instar larvae. The results of gene interaction experiments corroborate previous data indicating the set of transcription factors that regulate BhC4-1-lacZ expression in the ring gland is distinct from that which promotes gene expression in salivary glands. The lines obtained in this work constitute a tool to characterize the tissue-specific transcription factors that regulate BhC4-1 gene in the ring gland and/or in the salivary gland from the end of the larval development.

Nosso laboratório investiga os mecanismos moleculares que promovem o estabelecimento de padrões de expressão gênica regulados no desenvolvimento em eucariotos superiores. Como modelo, utilizamos o gene de pufe de DNA BhC4-1, que é amplificado e expresso de modo regulado na glândula salivar e na glândula protorácica no final do quarto estadio larval de B. hygida. Estudos funcionais em D. melanogaster resultaram na identificação de módulos cis-reguladores (MCRs) na região promotora do gene BhC4-1. O MCR de glândula anelar de 67 bp (-253/-187), promove a expressão de BhC4-1-lacZ na glândula anelar a partir do final do desenvolvimento embrionário. O MCR de glândula salivar de 129 bp (-186/-58), dirige a expressão do transgene nas glândulas salivares de prépupas. A glândula anelar é o principal órgão endócrino larval e em D. melanogaster é o resultado da fusão das glândulas protorácicas (responsáveis pela síntese de hormônios esteroides), corpus allatum (síntese de hormônio juvenil) e corpus cardiacum (glândula neuroendócrina). Neste trabalho foram obtidas 12 linhagens independentes transformadas com uma construção que contém o fragmento (-253/+40) do promotor do gene de pufe de DNA BhC4-1 clonado à montante do gene repórter GFP. O genótipo destas linhagens foi validado utilizando-se Southern blots. Inicialmente as 12 linhagens obtidas foram analisadas quanto ao padrão de expressão de GFP em larvas de terceiro estadio e em prépupas 2 horas. Em conjunto, esta análise revelou que o padrão de expressão de GFP é bastante variável nestas linhagens. A análise do padrão de expressão da proteína repórter foi estendida em duas linhagens representativas da série (- 253/+40)/GFP. Nestas linhagens a expressão de GFP é inicialmente detectada na glândula salivar durante o estágio de prépupa e na glândula anelar a partir do terceiro estadio larval. Diferentemente do anteriormente observado em linhagens (-253/+40)/lacZ, nestas linhagens não detectamos a expressão de GFP em tempos do desenvolvimento anteriores ao terceiro estadio larval. Experimentos de interação gênica revelaram que na ausência do fator de transcrição br, a expressão de GFP é mantida na glândula anelar e abolida na glândula salivar de larvas de terceiro estadio. Os resultados dos experimentos de interação gênica corroboram dados anteriores que indicavam que o conjunto de fatores de transcrição que regulam a expressão de BhC4-1-lacZ na glândula anelar é distinto daquele que promove a expressão do gene na glândula salivar. As linhagens obtidas neste trabalho constituem uma ferramenta a ser utilizada na caracterização de fatores de transcrição tecido-específicos que regulam o gene BhC4-1 na glândula anelar e/ou na glândula salivar a partir do final do desenvolvimento larval. / Our laboratory investigates the molecular mechanisms that promote the establishment of developmentally regulated gene expression patterns in metazoans. As a model, we employ the BhC4-1 DNA puff gene, which is amplified and expressed in a regulated manner in the salivary gland and in the prothoracic gland at the end of the fourth larval instar in B. hygida. Functional studies in D. melanogaster resulted in the identification of cis-regulatory modules (CRMs) in the BhC4-1 promoter region. The 67 bp (-253/-187) ring gland CRM drives BhC4-1-lacZ expression in the ring gland from late embryonic development. The 129 bp (-186/-58) CRM salivary gland drives transgene expression in the prepupal salivary glands. The ring gland is the major endocrine organ, and comprises the prothoracic glands (synthesis of ecdysteroid hormones), corpus allatum (synthesis of juvenile hormone) and corpus cardiacum (neuroendocrine gland). In this work, 12 independent lines transformed with a construct containing the BhC4-1 promoter fragment (- 253/+40) cloned upstream of the reporter gene GFP were obtained. The genotype of each line was validated using Southern blots. Initially, the 12 obtained lines were analyzed to investigate the pattern of GFP expression in the third instar larvae and in the 2 hours prepupae. This initial screening revealed that the pattern of GFP expression is highly variable in these lines. The developmental pattern of GFP expression was extended in two representative (- 253/+40)/GFP lines. In these lines, GFP expression is initially detected in the larval and prepupal salivary glands and in ring gland third instar. Differently from previously observed in (-253/+40)/lacZ lines, in these lines we did not detect GFP expression at developmental times prior to the third larval instar. Gene interaction experiments revealed that in the absence of the br transcription factor, GFP expression is maintained in the ring gland and abolished in the salivary gland of third instar larvae. The results of gene interaction experiments corroborate previous data indicating the set of transcription factors that regulate BhC4-1-lacZ expression in the ring gland is distinct from that which promotes gene expression in salivary glands. The lines obtained in this work constitute a tool to characterize the tissue-specific transcription factors that regulate BhC4-1 gene in the ring gland and/or in the salivary gland from the end of the larval development.