Welcome

Welcome to the official website of the laboratory of Maria Ninova, Assistant Professor at the Department of Biochemistry, University of California, Riverside. The lab opened on July 1st 2021 and is actively recruiting curiosity-driven and motivated team members interested in epigenetic regulation, small non-coding RNAs, and transposon control in germ cells and animal development at different career levels, including technicians, undergraduate, graduate, and postdoctoral researchers - click here for more details!

Research

An organism’s genome contains all the information necessary for its development and function, including genes that encode RNA and proteins, regulatory regions that coordinate gene activity to form different cells and respond to stimuli, structural regions responsible for the stability, organization and faithful DNA transmission during cell division, as well as “parasitic” elements and regions of no or unknown role. It is essential that this information is organized and switched on and off in a controlled manner, such that only pieces relevant to a specific cell type and function are active at a given time. One of the most important means of genome regulation in eukaryotes is through the association of DNA with histone proteins into a higher order chromatin structure. Post-translational histone modifications can alter chromatin density and recruit diverse downstream regulatory and structural factors that modulate gene activity. Such epigenetic modifications allow cells to control gene activity without changing the DNA sequence. However, we lack detailed understanding of the regulation of the reader, writer and eraser machineries responsible for different histone modifications. Our lab is interested in fundamental aspects of chromatin regulation such as:

  • What are the mechanisms that identify specific genomic regions for modification?
  • How are different chromatin regions first defined during embryogenesis and then maintained during mitotic divisions?
  • What are the biological functions of different histone marks?

We address these questions by a combiation of molecular biology, imaging, genomics (RNA-seq, ChIP-seq), and proteomics approaches. Most of our projects utilize the Drosophila melanogaster model system, which laid the foundations of modern genetics and has been at the frontier of chromatin, piRNA (see below), and transposon research. Areas of specific interest include:

The mechanism of piRNA-mediated silencing

piRNAs are a class of short non-coding RNAs produced in the germline and some somatic tissues of animals that associate with Argonaute proteins from the Piwi clade, and function to recognize and silence transposons - “jumping genes” that can otherwise damage DNA. Defects in the piRNA pathways lead to transposon activation, defects in gametogenesis, and sterility. Remarkably, specific piRNA-loaded Piwi-s have the ability to enter the nucleus and induce transcriptional silencing of transposons by recruiting repressive chromatin-modifying factors - a great example of non-coding RNAs triggering epigenetic modifications in animal systems. Recent studies identified several new factors essential for Piwi function. For example, it recently emerged that the SUMO (Small Ubiquitin-Like Modifier) pathway is required for transposon silencing and repessive chromatin formation at piRNA targets. However, the precise mechanism by which piRNA/Piwi complexes recruit the silencing effectors is not well understood. Our lab aims to use a combination of molecular biology, genomics, and proteomics strategies, to dissect the process of piRNA-mediated silencing.

Regulation of gene expression by H3K9me3

Heterochromatin was historically identified as the dark staining portion of interphase chromatin which remains condensed and is typically (but not always) transcriptionally silenced. Heterochromatin is essnetial for many aspects of cell function and development, such as dosage compensation, lineage-specific gene silencing during differentiation, maintaining the integrity of the repetitive chromosome ends, and repression of transposons. Histone 3 lysine 9 trimethylation (H3K9me3) is a highly conserved hallmark of silencing and heterochromatin that occupies a substantial portion of the eukaryotic genomes and is implicated in the compaction of repeat-rich sequences near centromeres and telomeres, and transposon repreression. In addition, this mark is found on dozens of host genes and regulatory regions outside constitutive heterochromatin, and appears to play a role in gene regulation and cell specification. Our lab is interested in gaining a deeper understanding of the biological role of H3K9me3 in different cellular and genomic contexts.

Developmental regulation of heterochromatin

The vast majority of histone and DNA modifications are erased during gametogenesis and fertilization, and need to be re-established de novo in a cell-specific manner during the development of the new organism. We are interested in the factors and molecular mechanisms that orchestrate the initiation and maintainance of heterochromatin from the zygote throughout embryogenesis using the fruit fly embryo system as a paradigm.

Lab members

Principal Investigator

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Maria Ninova (she/her)

Assistant Professor

Team

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Hannah Holmes

Undergraduate Student, Cellular, Molecular, and Developmental Biology

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Kun Wu

PhD Student BCMB

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Matea Ibrahim

Undergraduate Student, Biology

Open positions

I am looking for motivated individuals at different career levels interested in the lab’s scientific areas to join my research team. Available projects employ a variety of classic and state-of-the-art approaches, and provide the opportunity to obtain training in either or both experimental biology and bioinformatics. PhD and postdoc positions are open to both US and international (subject to U.S. visa rules) applicants. Women and underrepresented minorities are encouraged to apply!

Contact me directly with any further questions and to apply. Please include a short paragraph describing your scientific interests and motivations, resume/CV, contacts of three referees, and if available - an example publication (preprint is fine) reflecting prior work.

Postdocs

Applicants should be near completion or have completed a PhD program in the following or related disciplines: molecular biology, biochemistry, biophysics, genetics, bioinformatics, and have either substantial hands-on experience with standard biochemistry and molecular biology techniques (such as PCR, Western blotting, protein purification, cloning, etc.), and cell culture, or experience in computational analysis of sequencing data and comparative genomics. Experience with Drosophila is a plus, but is not required. We are particularly interested in individuals with strong background in biochemistry and proteomics for a NIH-funded postdoctoral position.

Graduate (PhD) students

Applicants must be admitted to one a graduate program at UC Riverside, preferably:

Information regarding eligibility criteria, application deadlines (usually in the fall), and application process is available on each program’s website. All programs require students to complete 5-10 weeks laboratory rotations in the first year, before further selection for doctoral thesis advisor/lab is made. Prospective students interested in rotating in the lab are encouraged to get in touch with Maria in advance to discuss research opportunities. Many of the projects will involve next generation sequencing (e.g. RNA-seq, ChIP-seq), and are particularly suitable for individuals who wish to obtain a “mixed” training in biology and bioinformatics. It is not necessary to have prior programming experience, however, background in a biology-related discipline is helpful. Co-mentoring arrangements jointly with other PIs are also a possibility.

Laboratory Assistants/Specialists

We welcome applications for junior staff positions (laboratory assistant or junior specialist) from individuals interested in taking part in our research. Candidates should have at least a bachelor’s degree or equivalent in life sciences and have some prior lab experience. These positions are ideal for recent graduates seeking to gain extra research experience. For inquiries, contact Maria and include [TECHNICIAN] (with the brackets and upper case letters) in the subject line.

Undergraduates

Opportunities are available for undergraduate students with strong commitment to research. Students interested in the lab areas of study should contact Maria to discuss potential projects and timelines. Please include [UNDERGRAD] (with brackets and upper case) in the subject line, briefly describe your research interests and goals (see tips for contacting faculty), relevant courses, and attach a copy of your transcript.

Contact

To get in touch with Maria, please send an email to:

mninova@ucr.edu


About UCR

The University of California, Riverside (UCR) is one of the campuses of the University of California system. Hosting over 20,000 undergraduate and 3,000 graduate students, UC Riverside prides itself on being one of America’s fastest rising and most diverse Universities.

The UCR campus is located in the City of Riverside, part of the Greater Los Angeles metropolitan area. One of the sunniest USA cities, Riverside location provides a rare combination of small-town feel and proximity to great natural and urban areas: within about 1 hour drive (~50 miles) from the Pacific Ocean and popular beaches such as Huntington Beach, mountains (e.g. the Big Bear Lake and Ski Resort in the San Bernardino Mountains), downtown LA and Hollywood. It is also about 1.5-2 hours away from Joshua Tree National park, the Santa Monica and Malibu Recreation Areas, the San Diego metropolitan area, and numerous attractions including Disneyland, SeaWorld, Universal Studios, SixFlags, the Getty Museum.

Please check out the UCR website for more information about our campus, community, and student life.