Welcome to 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!


An organism’s genome contains all the information necessary for its development and function, including genes that encode RNA and protein molecules, 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 thereby modulating the accessibility for transcription, and recruit diverse downstream regulatory and structural factors. In principle, targeting specific modifications to appropriate regions can be achieved via different mechanisms involving DNA-binding proteins or non-coding RNAs that recruit enzymatic “writers”. Once installed, modifications can be recognized by “reader” factors with various regulatory outcomes, and also removed by “eraser” enzymes. However, we lack detailed understanding of the regulation of different chromatin states. 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.

Maria Ninova

Maria Ninova

Assistant Professor

Department of Biochemistry

University of California, Riverside

Principal Investigator

My education and research have always been driven by my natural curiosity about the inner workings of living organisms, particularly how genes and genomes are regulated. After completing my undergraduate degree in molecular biology, I joined the bioinformatics lab of Sam Griffiths-Jones at the University of Manchester, UK, where in collaboration with Matt Ronshaugen’s lab I studied the evolution and function of microRNAs and became an “omics” enthusiast. I then joined the lab of Alexei Aravin at Caltech as a postdoc, where I pursued the mechanism of action of another class of small regulatory RNAs, piRNAs. My research background has involved different areas including chromatin, RNA, genomics, evolutionary and developmental biology, and intergrated both experimental and bioinformatic components. As a PI, I aim to translate this breadth and integrative approach to my lab.

CV Google Scholar

Open positions

I am looking for graduate (PhD) students and postdocs interested in the lab’s scientific areas to join my research team in the summer/fall of 2021 or later. 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. All 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.


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 comuptational analysis of sequencing data and comparative genomics. Experience with Drosophila is a plus, but is not required. Minimum compensation is according to the established University of California salary scales.

Graduate (PhD) students

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

Information regarding eligibility criteria, application deadlines, and application process is available on each program’s website. 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. Prospective students interested in rotating in or joining the lab are encouraged to get in touch with Maria in advance to discuss research opportunities. Co-mentoring arrangements jointly with other PIs are also a possibility.

Laboratory Assistant (Technician)

We are seeking a full time laboratory assistant (technician) to help with various aspects of the research projects and day-to-day lab operations. Job duties include maintaining Drosophila lines and cell cultures, preparing media and solutions, performing basic molecular biology work (such as PCR, molecular cloning, Western blots), maintaining the organization of lab workspaces, and manage purchasing, receving, and storage of laboratory consumables and equipment. A highly motivated individual will have the opportunity to develop independent research projects and author publications in addition to providing support for other lab members. Candidates should ideally hold a bachelor’s degree or equivalent in life sciences and have some prior lab experience. This position is 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. To apply, please use the UCR application system HERE. Individuals without prior lab experience are encouraged to send an academic transcript.


Undergraduate students interested in the lab research areas should contact Maria to discuss potential projects and timelines. Please include [UNDERGRAD] (with brackets and upper case) in the subject line.


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


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.