Susan Berget

Last updated January 18, 2024

Susan "Sue" M. Berget is a biochemist and professor emeritus at the Baylor College of Medicine. Originally involved in the MIT lab of Phillip Sharp for her postdoctoral fellowship, she was instrumental in the research that led to the discovery of RNA splicing and split genes, which awarded Sharp the 1993 Nobel Prize in Physiology or Medicine. Berget was excluded, however, from receiving credit, which inhibited her attempts to apply for a professorship afterwards, particularly due to Sharp's letter of recommendation also not giving her credit for the research in his lab. Eventually, Nancy Hopkins and David Botstein convinced Sharp to rewrite his letter, allowing Berget to receive a professor invitation from Rice University.

She went on to become a professor at the Baylor College of Medicine, where her research focused on further understanding exons, introns, and the overall mechanisms of RNA splicing. Her research has been highly influential in figuring out the exon definition and recognition system of cells, along with the biochemical factors that help determine how splice sites are determined.

Career

Berget obtained her Ph.D. from the University of Minnesota,^[1] before applying for a postdoctoral fellowship in Phillip Sharp's lab at MIT in 1975. She was tasked with comparing the genomes of human cells with adenovirus to determine the amount of viral genes in the human genome.^[2] This work led to Sharp winning the 1993 Nobel Prize in Physiology or Medicine. Due to the Nobel Committee's long-term rule on only allowing three winners for a Nobel Prize and Richard J. Roberts's lab also having to share the prize, Berget and Roberts' collaborator Louise Chow were excluded from the award.^[3]^[4] Berget stated that she had "made peace" with Sharp and is done with talking about "old issues", but admitted that if she could do that part of her life over again, she would have been a "lot more aggressive" in pushing for credit on her postdoctoral work.^[5]

However, in the fall of 1977 after publication and convention presentations of their work, while Berget was applying for job positions as a professor and received interviews for Harvard, Stanford, the University of Columbia, and the University of California - Berkeley, she was ultimately rejected from all applications. A friend who had "made a call" to one of the schools to inquire found that Sharp's letter of recommendation was unimpressive, as he had only discussed her work prior to joining his lab and mentioned nothing about her involvement in the split gene discovery. Berget went to speak with Nancy Hopkins about the issue, who herself went to speak with Sharp alongside David Botstein, explaining that not extending credit on the discovery to Berget would make him "look petty" and harm his own career in the process. In response, he gave a stronger letter of recommendation to Berget and this led to her being given job offers by Rice University and Carnegie Mellon University, of which she chose the former to become a professor of biochemistry.^[6] She remained in this faculty position from 1978 until 1989.^[7]

Berget moved on to become a professor at the Baylor College of Medicine with her research focusing on exons.^[8] In the mid-1990s, Berget was put in charge of a scientific misconduct inquiry into fellow Baylor professor Kimon Angelides and, over the course of 30 months, the inquiry board returned a guilty verdict for falsifying data in published papers and NIH grant applications. After Angelides was fired in 1995, he filed slander lawsuits against Berget and other inquiry members, which was only settled in 1999 after the NIH had an independent investigation confirm the validity of the guilty conclusion.^[9] During the early 2000's, Berget was made acting chair for the department of pharmacology despite being a biochemistry professor. Then, in May of 2004, she was made vice president and vice dean of academic planning for the college of medicine.^[10]

Research

Discovery of RNA splicing

While working in Phillip Sharp's lab in 1976, Berget started investigating RNA in the cellular cytoplasm and how they were connected to the structure of the genome of adenovirus. She used electron microscopy to visually inspect the structural differences. The lab's technician, Claire Moore, began using R-loop analysis to be able to map a string of RNA on a DNA template and hybridize them, allowing for the isolation of what genes the RNA was sequenced from. Using adenovirus to infect human cells, Berget then purified the messenger RNA (mRNA) from the virus replicating in the cells and hybridized them with the cellular human DNA with Moore and the R-loop analysis process. The R-loop micrographs had an unexpected discrepancy however, with the normal R-loops featuring pieces of RNA extending out from them. Other scientists had found that adenovirus RNA in the cell nucleus is generally longer than the RNA produced in the cytoplasm, so Berget, Moore, and Sharp decided they must just be artifacts that were added on during the hybridization process.^[11]

To fix this, they removed the opposite side of the DNA strand so the RNA sequence would have no competition in binding to its DNA strand counterpart, but the extended tails persisted. Multiple months and experiments to try and remove the tails by perfecting other parts of the hybridization process failed. But Berget's compilation of the data they had collected suggested that perhaps the tail sequences were from a different part of the adenovirus sequence, prompting them to use a longer DNA sequence from the human cells. This was successful, causing the tails to bind to a further part of the DNA and forming the R-loops, proving the discovery of RNA splicing and split genes. Berget, Moore, and Sharp had found out that the reason why nuclear mRNA is longer is because the cytoplasmic mRNA has introns spliced out to allow for protein synthesis.^[2]^[12] They published this finding in PNAS in August 1977.^[13]

Exons and splice sites

After establishing her own laboratory, Berget began work investigating the deeper features of RNA splicing and how introns and exons are processed and what biochemical mechanisms are involved. Using uridine triphosphate marked with a radioisotope, her lab was able to produce multiple radioactive RNA substrates for study each week, along with using HeLa cells to obtain nuclear DNA extracts.^[8] This led her to develop an exon definition model that explained how different splice sites allowed for cellular communication between one exon location and the others in a sequence during RNA transcription, making the sites dependent on each other.^[14] In the late 1980's, she found that by destroying specific snurps involved in splicing, she could prevent the process from happening at all.^[15]

Berget's lab proposed in a 1990 paper that for organisms with longer stretches of introns between each exon, such as vertebrates, that there must be some other system capable of identifying the exon sequences themselves. The paper noted that the existence of a downstream splicing location was necessary for an upstream intron to be spliced, giving credence to some sort of recognition complex of proteins.^[16] They expanded, in 1998, on the mechanisms of differential splicing choices, such as between the pre-mRNA for calcitonin versus CGRP, by showing that there is some sort of "splicing factor" that binds to the splicing site in order to cause polyadenylation upstream of that binding location.^[17]

Organizations

Berget is a member of the advisory council for the Center for Scientific Review, which oversees 70% of the National Institute for Health's annual grant applications.^[18]

Awards

Berget was given the 1996 Outstanding Achievement Award from the University of Minnesota for alumni who have made significant accomplishments in their scientific field.^[19]

Related Research Articles

An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome.

An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word intron is derived from the term intragenic region, i.e., a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons.

RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing all the introns and splicing back together exons. For nuclear-encoded genes, splicing occurs in the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually needed to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing occurs in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). There exist self-splicing introns, that is, ribozymes that can catalyze their own excision from their parent RNA molecule. The process of transcription, splicing and translation is called gene expression, the central dogma of molecular biology.

Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. This means the exons are joined in different combinations, leading to different (alternative) mRNA strands. Consequently, the proteins translated from alternatively spliced mRNAs usually contain differences in their amino acid sequence and, often, in their biological functions.

A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specific proteins to form a small nuclear ribonucleoprotein complex, which in turn combines with other snRNPs to form a large ribonucleoprotein complex called a spliceosome. The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript. This process is generally referred to as splicing. An analogy is a film editor, who selectively cuts out irrelevant or incorrect material from the initial film and sends the cleaned-up version to the director for the final cut.

Phillip Allen Sharp is an American geneticist and molecular biologist who co-discovered RNA splicing. He shared the 1993 Nobel Prize in Physiology or Medicine with Richard J. Roberts for "the discovery that genes in eukaryotes are not contiguous strings but contain introns, and that the splicing of messenger RNA to delete those introns can occur in different ways, yielding different proteins from the same DNA sequence". He has been selected to receive the 2015 Othmer Gold Medal.

<span class="mw-page-title-main">Primary transcript</span> RNA produced by transcription

A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.

Sir Richard John Roberts is a British biochemist and molecular biologist. He was awarded the 1993 Nobel Prize in Physiology or Medicine with Phillip Allen Sharp for the discovery of introns in eukaryotic DNA and the mechanism of gene-splicing. He currently works at New England Biolabs.

Marlene Belfort is an American biochemist known for her research on the factors that interrupt genes and proteins. She is a fellow of the American Academy of Arts and Sciences and has been admitted to the United States National Academy of Sciences.

A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of abnormal proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be included. Introns are supposed to be removed, while the exons are expressed.

Joan Elaine Argetsinger Steitz is Sterling Professor of Molecular Biophysics and Biochemistry at Yale University and Investigator at the Howard Hughes Medical Institute. She is known for her discoveries involving RNA, including ground-breaking insights into how ribosomes interact with messenger RNA by complementary base pairing and that introns are spliced by small nuclear ribonucleic proteins (snRNPs), which occur in eukaryotes. In September 2018, Steitz won the Lasker-Koshland Award for Special Achievement in Medical Science. The Lasker award is often referred to as the 'American Nobel' because 87 of the former recipients have gone on to win Nobel prizes.

In molecular biology, an exonic splicing enhancer (ESE) is a DNA sequence motif consisting of 6 bases within an exon that directs, or enhances, accurate splicing of heterogeneous nuclear RNA (hnRNA) or pre-mRNA into messenger RNA (mRNA).

<span class="mw-page-title-main">U2 spliceosomal RNA</span>

U2 spliceosomal snRNAs are a species of small nuclear RNA (snRNA) molecules found in the major spliceosomal (Sm) machinery of virtually all eukaryotic organisms. In vivo, U2 snRNA along with its associated polypeptides assemble to produce the U2 small nuclear ribonucleoprotein (snRNP), an essential component of the major spliceosomal complex. The major spliceosomal-splicing pathway is occasionally referred to as U2 dependent, based on a class of Sm intron—found in mRNA primary transcripts—that are recognized exclusively by the U2 snRNP during early stages of spliceosomal assembly. In addition to U2 dependent intron recognition, U2 snRNA has been theorized to serve a catalytic role in the chemistry of pre-RNA splicing as well. Similar to ribosomal RNAs (rRNAs), Sm snRNAs must mediate both RNA:RNA and RNA:protein contacts and hence have evolved specialized, highly conserved, primary and secondary structural elements to facilitate these types of interactions.

RNA binding motif protein 9 (RBM9), also known as Rbfox2, is a protein which in humans is encoded by the RBM9 gene.

Numerous key discoveries in biology have emerged from studies of RNA, including seminal work in the fields of biochemistry, genetics, microbiology, molecular biology, molecular evolution and structural biology. As of 2010, 30 scientists have been awarded Nobel Prizes for experimental work that includes studies of RNA. Specific discoveries of high biological significance are discussed in this article.

Periannan Senapathy is a molecular biologist, geneticist, author and entrepreneur. He is the founder, president and chief scientific officer at Genome International Corporation, a biotechnology, bioinformatics, and information technology firm based in Madison, Wisconsin, which develops computational genomics applications of next-generation DNA sequencing (NGS) and clinical decision support systems for analyzing patient genome data that aids in diagnosis and treatment of diseases.

<span class="mw-page-title-main">Minigene</span>

A minigene is a minimal gene fragment that includes an exon and the control regions necessary for the gene to express itself in the same way as a wild type gene fragment. This is a minigene in its most basic sense. More complex minigenes can be constructed containing multiple exons and intron(s). Minigenes provide a valuable tool for researchers evaluating splicing patterns both in vivo and in vitro biochemically assessed experiments. Specifically, minigenes are used as splice reporter vectors and act as a probe to determine which factors are important in splicing outcomes. They can be constructed to test the way both cis-regulatory elements and trans-regulatory elements affect gene expression.

An R-loop is a three-stranded nucleic acid structure, composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA. R-loops may be formed in a variety of circumstances and may be tolerated or cleared by cellular components. The term "R-loop" was given to reflect the similarity of these structures to D-loops; the "R" in this case represents the involvement of an RNA moiety.

The split gene theory is a theory of the origin of introns, long non-coding sequences in eukaryotic genes between the exons. The theory holds that the randomness of primordial DNA sequences would only permit small (< 600bp) open reading frames (ORFs), and that important intron structures and regulatory sequences are derived from stop codons. In this introns-first framework, the spliceosomal machinery and the nucleus evolved due to the necessity to join these ORFs into larger proteins, and that intronless bacterial genes are less ancestral than the split eukaryotic genes. The theory originated with Periannan Senapathy.

Robin Elizabeth Reed was an American professor of cell biology at the Harvard Medical School. Her research considered the molecular mechanisms that underpin neurodegenerative disease.

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