Steve Mount

• University of Maryland, College Park

Hutchinson–Gilford Progeria Syndrome (HGPS) is a premature aging disease caused primarily by a C1824T mutation in LMNA. This mutation activates a cryptic splice donor site, producing a lamin variant called progerin. Interestingly, progerin has also been detected in cells and tissues of non-HGPS patients. Here, we investigated progerin expression us...

Strings of nucleotides carrying biological information are typically described as sequence motifs represented by weight matrices or consensus sequences. However, many signals in DNA or RNA are recognized by multiple factors in temporal sequence, consist of distinct alternative motifs, or are best described by base composition. Here we apply the lat...

The spliceosome is a megadalton protein-RNA complex which removes introns from pre-mRNA, yet the dynamic early assembly steps have not been structurally resolved. Specifically, how the spliceosome selects the correct 3’ splice site (3’SS) amongst highly similar non-functional sites is not known. Here, we develop a kinetic model of splice site selec...

Splicing factor 3b subunit 1 (SF3B1) is the largest subunit and core component of the spliceosome. Inhibition of SF3B1 was associated with an increase in broad intron retention (IR) on most transcripts, suggesting that IR can be used as a marker of spliceosome inhibition in chronic lymphocytic leukemia (CLL) cells. Furthermore, we separately analyz...

In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step toward tailoring healthcare interventions. However, the critical aspect of equitably selecting molecular features across multiple patients is often overlooked. To address this challenge, we introduce FALAFL (FAir muLti-sAmple Fea...

In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step towards tailoring healthcare interventions. However, the critical aspect of equitably selecting molecular features across multiple patients is often overlooked. To address this challenge, we introduce FALAFL (FAir muLti-sAmple Fe...

Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from g...

Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3′ end of polyadenylated RNAs, recent studies have shown that “off-target” reads can constitute a substantial portion of the read population....

Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant’s impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here, we present the results of the...

Strings of nucleotides that carry biological information are typically described using sequence motifs that can be represented by weight matrices or consensus sequences. However, many biological signals in DNA or RNA are recognized by multiple factors in temporal sequence, consist of a mixture of sometimes dissimilar alternative motifs, or may be d...

Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understanding and progress toward increasing fruit yield and quality. With the ever-increasing high-throughput sequenci...

Belonging to Rosaceae, red raspberry (Rubus idaeus) and wild strawberry (Fragaria vesca) are closely related species with distinct fruit types. While the numerous ovaries become the juicy drupelet fruits in raspberry, their strawberry counterparts become dry and tasteless achenes. In contrast, while the strawberry receptacle, the stem tip, enlarges...

Background Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant’s impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here we present the resu...

Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression histor...

Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression histor...

Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 167 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-m...

Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 170 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-m...

Background Alternative splicing (AS) is a fundamental process in eukaryotes contributing to the diversity of mRNA isoforms with variable ratios of intron/exon. SF3B1 is a pivotal protein of the spliceosome machinery. Mutations in the SF3B1 gene have prognostic value in Chronic Lymphocytic Leukemia (CLL). Our previous studies have shown that SF3B1 i...

Fruits represent key evolutionary innovations in angiosperms and exhibit diverse types adapted for seed dissemination. However, the mechanisms that underlie fruit type diversity are not understood. The Rosaceae family comprises many different fruit types including “pome” and “drupe” fruits and hence is an excellent family for investigating the gene...

Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 170 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-m...

p>The heritability of methylation patterns in tumor cells, as shown in recent studies, suggests that tumor heterogeneity and progression can be interpreted and predicted in the context of methylation changes. To elucidate methylation-based evolution trajectory in tumors, we introduce a novel computational method for methylation phylogeny reconstruc...

Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due t...

CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expand the targeting scope of Cas12a, we screen nine Cas12a orthologs that have not been demonstrated in plants, and identify six, ErCas12a, Lb5Ca...

Recent studies on the heritability of methylation patterns in tumor cells, suggest that tumor heterogeneity and progression can be studied through methylation changes. To elucidate methylation-based evolution trajectories in tumors, we introduce a novel computational frame-work for methylation phylogeny reconstruction, leveraging single cell bisulf...

The most popular CRISPR-SpCas9 system recognizes canonical NGG PAMs. Previously engineered SpCas9 variants such as Cas9-NG, still favor G-rich PAMs in genome editing. In this manuscript, we describe a new plant genome editing system based on a hybrid iSpyMacCas9 that allows for targeted mutagenesis, C to T base editing and A to G base editing at A-...

Background: Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing o...

Precision medicine and sequence‐based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype–phenotype prediction challenges; participants build models, undergo assessment, and share key finding...

The red raspberry, Rubus idaeus, is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. Genomic resources such as a complete ge...

The uptake and destruction of bacteria by phagocytic cells is an essential defense mechanism in metazoans. To identify novel genes involved in the phagocytosis of Staphylococcus aureus, a major human pathogen, we assessed the phagocytic capacity of adult blood cells (hemocytes) of the fruit fly, Drosophila melanogaster, by testing several lines of...

Fragaria vesca, a diploid strawberry, is a developing model system for the economically important Rosaceae family. Unlike tomato, the traditional model for fleshy fruit development, strawberry fleshy fruit develops from the floral receptacle and its ripening is non-climacteric. Additionally, the external seed configuration of strawberry fruit facil...

Introduction: Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, besides, the annotated transcripts are often a small subset of the possible transcripts of a gene. Here we describe Yanagi, a tool for segmenting transcriptome to create a library of maximal L...

Background Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regulatory proteins and spliceosomal subunits. Although SR45 has orthologs in diverse eukaryotes, including human RNPS1, the sr45–1...

Splicing is a post‐transcriptional processing step in which intervening sequences (introns) are excised and coding sequences (exons) are ligated together to create the mature mRNA (messenger ribonucleic acid) molecule. It is a sequential process that is facilitated by the information in the RNA (ribonucleic acid) sequence (splicing regulatory eleme...

Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism datasets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of inform...

Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism datasets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of inform...

Thirty-five years ago, as young graduate students, we had the pleasure and privilege of being in Joan Steitz's laboratory at a pivotal point in the history of RNA molecular biology. Introns had recently been discovered in the laboratories of Philip Sharp and Richard Roberts, but the machinery for removing them from mRNA precursors was entirely unkn...

Background Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been the centerpiece of several popular applications. Each of these approaches generates an undirected graph that represents sequences as...

To predict in vivo occupancy of a transcription factor (TF), current models consider only the immediate genomic context of a putative binding site (BS) – impact of the site’s spatial chromatin context is not known. Using clusters of spatially proximal enhancers, or archipelagos, and DNase footprints to quantify TF occupancy, we report for the first...

Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been the centerpiece of several popular applications. Each of these approaches generates an undirected graph that represents sequences as nodes conn...

Background / Purpose: GWAS data provide information about significant single nucleotide polymorphisms (SNPs) in thousands of loci which are associated with increased risk of complex trait diseases without any knowledge about underlying mechanisms involved in these loci. Here we compare the role of three mechanisms: presence of missense SNPs, pres...

We introduce Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads, a time-consuming step in all current methods, it provides quantification estimates much faster than do existing approaches (typically 20 times faster) without loss of acc...

Here we present several examples of the evolutionary fates of specific U12-type introns. These examples illustrate the modes of evolutionary changes for U12 introns.

Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns. U12-type in...

The serine-arginine-rich (SR) proteins constitute a conserved family of pre-mRNA splicing factors. In Arabidopsis (Arabidopsis thaliana), they are encoded by 19 genes, most of which are themselves alternatively spliced. In the case of SR45, the use of alternative 3' splice sites 21 nucleotides apart generates two alternatively spliced isoforms. Iso...

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but conta...

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, anan...

FGA-generated features produce a significant overlap with experimentally identified ESE sequences table in [22] (ESE-ESS-overlap-sequences.xls). The first worksheet in the Excel file contains the table of experimentally identified ESE sequences in [22] and the overlap with the FGA identified hexamers from feature sets A-6mer [0,80] and D-6mer [2,82...

FGA-generated features produce significant overlap with computationally identified lists of exonic splicing regulator signals [23,26] (candidate-ese-esr-overlap.txt). A text file with the list of FGA features overlapping with RescueESE and AstESR exonic splicing regulator lists.

FGA identified features that contribute to Table 2. (Table2_features_A3mer3.txt). A text file with the complete list of features associated with the branch-point interval [-40,-20], from the feature set A-3mer3. The features are ranked according to the absolute value or their assigned weight. The top-scoring 20 features of this list are shown in Ta...

Features that contribute to Figure 2 and other features that show similar behaviour (tetramers-of-figure2.txt). A text file with the complete list of selected features from feature set A-3mer1 [-60,-5].

FGA identified hexamers in acceptor splice-site prediction and donor splice-site prediction (FGA-hexamers.txt). A text file with the complete list of hexamers that our method indicates they are likely to be ESEs or ESSs.

SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human splice sites. Feature selection...

Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA) that is capable of achieving high classification accuracy on human 3' spli...

Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. We have developed a new computational technique to identify significantly conserved...

The removal of introns from the primary transcripts of protein-coding genes is accomplished by the spliceosome, a large macromolecular complex of which small nuclear RNAs (snRNAs) are crucial components. Following the recent sequencing of the honeybee (Apis mellifera) genome, we used various computational methods, ranging from sequence similarity s...

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, anan...

Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in bo...

Transcript support data for all alternative splicing classes including those with one transcript.

Coordinates for the alternative donor splicing sites in the two isoforms for rice.

Coordinates for the alternative donor splicing sites in the two isoforms for Arabidopsis.

Distribution of alternative splicing isoforms per cluster.

Coordinates for the alternative acceptor splicing sites in the two isoforms for rice.

Coordinates for the alternative acceptor splicing sites in the two isoforms for Arabidopsis.

The conserved spliceosomal U1-70K protein is thought to play a key role in RNA splicing by linking the U1 snRNP particle to regulatory RNA-binding proteins. Although these protein interactions are mediated by repeating units rich in arginines and serines (RS domains) in vitro, tests of this domain's importance in intact multicellular organisms have...

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all...

Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics prob...

Alternative splicing of the Sex-lethal pre-mRNA has long served as a model example of a regulated splicing event, yet the mechanism by which the female-specific SEX-LETHAL RNA-binding protein prevents inclusion of the translation-terminating male exon is not understood. Thus far, the only general splicing factor for which there is in vivo evidence...

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studie...

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studie...

Splicing signals are elements in the DNA sequence of a gene that specify the accurate splicing of its primary RNA transcript to generate its mature RNA product. Keywords: splice site selection; consensus sequences; splicing enhancers; exon definition; small nuclear ribonucleoprotein particles (snRNPs)

In eukaryotes, messenger RNAs are generated by a process that includes coordinated splicing and 3 end formation. Factors essential for the splicing of mRNA precursors (pre-mRNA) 1 in eukaryotes have been identified primarily through the study of nuclear extracts derived from mammalian cells and Saccharomyces cerevisiae genetics. Here, we identify h...

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of t...

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the ∼120-megabase euchromatic portion of theDrosophila...

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of t...

Life today requires the transmission of genetic information in the form of DNA, and a large number of catalytic and structural functions carried out by proteins. Without DNA to specify useful sequences of amino acids, functional proteins would not exist. Without proteins to carry out high-fidelity DNA replication and gene expression, DNA could not...

SR proteins are essential for the splicing of messenger RNA precursors in vitro, where they also alter splice site selection in a concentration-dependent manner. Although experiments involving overexpression or dominant mutations have confirmed that these proteins can influence RNA processing decisions in vivo, similar results with loss-of-function...

Small nucleolar RNAs direct the location of certain methylations in ribosomal RNA by direct base pairing; although evolutionarily conserved, the physiological significance of these modifications remains unclear.

Messenger RNAs are initially made as long precursor molecules from which final, transcribable mRNAs are assembled. A specialized organelle, the spliceosome, contains small RNAs with pairs of dinucleotides that can pick out complementary pairs of nucleotides at the ends of the introns that are to be spliced together. It has been assumed that these p...

SR proteins are essential for pre-mRNA splicing in vitro, act early in the splicing pathway, and can influence alternative splice site choice. Here we describe the isolation of both dominant and loss-of-function alleles of B52, the gene for a Drosophila SR protein. The allele B52ED was identified as a dominant second-site enhancer of white-apricot...

Many introns in Drosophila and other invertebrates are less than 80 nucleotides in length, too small to be recognized by the vertebrate splicing machinery. Comparison of nuclear splicing extracts from human HeLa and Drosophila Kc cells has revealed species-specificity, consistent with the observed size differences. Here we present additional result...

Although the role of U1 small nuclear RNAs (snRNAs) in 5' splice site recognition is well established, suppressor U1 snRNAs active in intact multicellular animals have been lacking. Here we describe suppression of a 5' splice site mutation in the Drosophila melanogaster white gene (wDR18) by compensatory changes in U1 snRNA. Mutation of positions -...