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Physical & Biological Sciences
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RNA Molecular Biology

• Manuel Ares, Jr., (MCD) Intron Removal, Alternative Splicing, and Genomics
• Angela Brooks (BME) Transcriptome Analysis of RNA Splicing and Cancer
• Susan Carpenter (MCD) Long Noncoding RNA and Innate Immunity
• David Haussler (BME) Using Stem Cells and Genomics to Study the Evolution and Function of Human Genes
• Melissa Jurica (MCD) Structure and Functional Analysis of Spliceosomes
• Todd Lowe (BME) Large Scale Approaches to Study Whole-Genome Biology
• Harry Noller (MCD) Structure and Function of the Ribosome
• Jeremy Sanford (MCD) Post Transcriptional Control of Gene Expression
• Bill Scott (Chem) Understanding the Structure-based Mechanisms of Ribozyme-based Theraputic Agents
• Michael Stone (Chem) Structure, Function, and Assembly of the Telomerase Ribonucleoprotein
• Susan Strome (MCD) Regulation of Germ Cell Development in C. elegans
• Alan Zahler (MCD) Regulation of Pre-mRNA Splicing and Post-Transcriptional Regulation by Micro RNAs

Manny AresIntron Removal, Alternative Splicing, and Genomics

Manuel Ares, Jr., MCD Biology

The work of the Ares lab centers on the mechanisms and regulation of splicing. Splicing is required to remove intron sequences from pre-mRNA and create coding sequences for translation. Ares' group tries to understand: (1) the mechanism of action of the core components of the spliceosome, in particular the snRNAs and their rearrangements during assembly of the spliceosome and catalysis of the splicing reactions, (2) the regulation of alternative splicing at a mechanistic level including the coupling of splicing to transcription and RNA decay mechanisms, and (3) the coordinate regulation of splicing events in developing systems. [More]

Ares Publications
Manny Ares' E-Mail

Prof. Angela BrooksTranscriptome Analysis of RNA Splicing and Cancer

Angela Brooks, Dept. of Biomolecular Engineering

The Brooks lab focuses on the study of somatic mutations that cause changes to the transcriptome, particularly through mRNA splicing. We aim to gain a better understanding of how alternative splicing is regulated and the functional consequences of splicing dysregulation through the study of these cancer genome alterations. We are developing computational approaches to analyze genome and transcriptome sequencing data and developing high-throughput experimental approaches to characterize the functional impact of cancer variants. [More]

Brooks' Publications Brooks' E-Mail

Prof Susan CarpenterUse of Random Mutagenesis for Studies of Evolution and for Therapy

Susan Carpenter, Molecular, Cell, & Developmental Biology

One of the most fascinating findings following the sequencing of the human genome is that less than 3% of the genome codes for protein coding exons while over 85% of the genome is actively transcribed. Long noncoding RNA (lncRNA) represent the largest class of RNA transcripts produced from the genome and to date there are 16,000 lncRNAs catalogued in Gencode. In recent years lncRNA have emerged as major regulators of chromatin remodeling, transcription and post-transcriptional regulation of gene expression in diverse biological contexts. Our goal is to understand the functions for lncRNA in inflammatory signaling pathways in macrophages and dendritic cells. [More]

Carpenter's Publications Sue Carpenter's Email

Prof David HausslerUsing Stem Cells and Genomics to Study the Evolution and Function of Human Genes

David Haussler, Dept. of Biomolecular Engineering

Dr. Haussler's investigative team brings together skills of a computational group and "wet lab" researchers to understand the evolution and function of non-protein coding regions of the human genome. A major focus is on identifying DNA elements and non-coding RNAs that play a role in specifying cortical neuron development. They use embryonic or induced pluripotent stem cell neural differentiation assays with human and primate stem cells followed by genomic characterization of this process using RNA-Seq, ChIP-Seq, etc. This approach allows us to identify both primate- and human-specific features of this important developmental pathway. [More]

Haussler's Publications Haussler's E-Mail

Prof Melissa JuricaStructure and Functional Analysis of Spliceosomes

Melissa Jurica, MCD Biology

The Jurica lab investigates the cellular machinery responsible for editing the information contained in the RNA transcripts of nearly all of human genes. This machinery, called the spliceosome, uses a molecular “splicing” reaction to cut out intron sequences that interrupt gene transcripts and joins exon sequences to make messenger RNAs that correctly encode for proteins. Splicing is a key step of gene expression and its misregulation is linked to many genetic diseases, including cancers and neurodegenerative disease. Juric'a goal is to determine how the spliceosome is assembled and how it catalyzes the splicing reaction. The lab's reasearch will provide a basic foundation for understanding what goes wrong with splicing in disease situations. [More]

Melissa Jurica's Publications Melissa Jurica's E-Mail

Prof Todd LoweLarge Scale Approaches to Study Whole-Genome Biology

Todd Lowe, Dept. of Biomolecular Engineering

Todd Lowe's research group uses a mixture of computational and experimental genomics to identify and characterize non-coding RNA (ncRNA) genes and to study the unique biology of Archaeal “extremophiles” – microbes that live at the edge of the limits of life.  His team has created several classes of non-coding RNAs gene-finders, and has created full-genome DNA microarrays for two different hyperthermophile species to study ancient forms of respiration and strategies for thermo-tolerance.  The group has also created a genome browser and functional genomics resource for all archaeal and extremophile species (archaea.ucsc.edu), now funded by the NSF. [More]

Lowe Publications Todd Lowe's Email

Prof Harry NOller

Structure and Function of the Ribosome

Harry Noller, MCD Biology

The Noller laboratory studies ribosome structure and function using a wide range of approaches, including X-ray crystallography, chemical probing methods, molecular genetics, comparative sequence analysis, fluorescence resonance energy transfer (FRET), including the use of single-molecule methods. The ultimate goal of these studies is to understand how the ribosome works at the molecular level: what are the moving parts of the machine, and how do they move in three dimensions to enable translation? [More]
Noller Publications Harry Noller's E-Mail

Prof. Jeremy SanfordPost Transcriptional Control of Gene Expression

Jeremy Sanford , Dept. of MCD Biology

Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA processing reactions such as pre-mRNA splicing, mRNA export, translation and mRNA decay are influenced by the interplay of trans-acting proteins with their cognate cis-acting RNA elements. We think that by elucidating the cis-acting RNA elements recognized by specific RNA binding proteins it will be possible to gain a better understanding of both the physiological relevance and mechanisms of action for these critical regulators of gene expression. [More]

Jeremy Sanford's Publications Jeremy Sanford's Email

Prof Scott
RNA Catalysis

William Scott, Dept. of Chemistry and Biochemistry

Ribozmes are RNA-based enzymes whose comparatively recent discovery came as major surprize to the scientific community, as it has always been assumed that only proteins could be enzymes. Researchers in the Scott laboratory are trying to understand how ribozymes work, using X-ray crystallography and other biochemical and biophysical techniques. The potential use of ribozymes as therapeutic agents that target RNA viruses (such as HIV) and pathological mRNAs (such as oncogene transcripts) is well-documented. Although the primary motive for our research is to answer questions of a fundamental scientific nature, it is hoped that the results of these studies will provide practical information to the scientific and medical communities to enable more potent and effective ribozyme-based pharmaceuticals to be developed by others. [More]

Scott Publications Bill Scott's E-Mail

Prof Michael StoneAssembly, Structure, and Regulation of the Telomerase Ribonucleoprotein

Michael Stone, Dept. of Chemistry and Biochemistry

The Stone Research Group combines the use of biochemical and structural methods with newly emerging single-molecule techniques to probe the dynamics of protein-nucleic acid interactions and the molecular mechanisms of biological motors.  Our current area of focus is the structure and function of the telomerase ribonucleoprotein, an RNA-dependent DNA polymerase that maintains genomic stability by synthesizing repetitive DNA sequences at chromosome termini.  These short DNA repeats provide the foundation for specialized chromatin structures, called telomeres, which prevent deleterious chromosome fusion events by differentiating chromosome ends from sites of DNA damage.  It has been shown that telomere length typically decreases with every round of cell division, leading to the so-called ‘molecular clock’ hypothesis, wherein telomere length serves as a signal to control cellular lifespan. This notion is consistent with the finding that active telomere DNA synthesis is normally restricted to rapidly dividing cell types such as stem cells and the majority of human cancers. Our research seeks to elucidate physical mechanisms governing telomere length regulation, and in turn establish a conceptual framework within which to develop novel diagnostic and therapeutic strategies for human disease. [More]

Stone Publications Michael Stone's Email

Prof Susan StromeRegulation of Germ Cell Development in C. elegans

Professor Susan Strome, MCD Biology

Germ cells (the cells that give rise to eggs and sperm) have special properties. Their immortality allows them to be perpetuated from generation to generation, and their totipotency allows them to generate all of the diverse cell types of the body in each generation. Our lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. We study germ cells in the model organism C. elegans using a wide variety of approaches, including genetics, imaging, molecular biology, biochemistry, and whole-genome microarray and sequencing technologies. Our current focus areas are transmission of chromatin states and control of gene expression in germ cells, and regulation of RNA metabolism by germline-specific cytoplasmic "P granules". [More]

Strome Publications Susan Strome's E-Mail

Prof Al ZahlerRegulation of Pre-mRNA Splicing and Post-Transcriptional Regulation by Micro RNAs

Alan Zahler, MCD Biology

The human genome carries the blueprint for the creation of proteins, the molecular machines that carry out most of the work in the body. However, the diversity of the pool of available proteins is greatly enhanced by alterative splicing of our genes. The Zahler laboratory examines the nematode Caenorhabditis elegans in order to understand the regulatory mechanisms of this alternative splicing. Small RNAs such as miRNAs, piRNAs, and siRNAs play important roles in gene regulation at many different levels. Zahler's group is studying small RNA biogenesis and the role of small RNAs in the regulation of genomic rearrangements in ciliated protozoans. [More]

Zahler Publications Alan Zahler's E-Mail


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