Sean Taverna - Academia.edu (original) (raw)

Papers by Sean Taverna

Research paper thumbnail of Additional file 9: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

List of primers used for qPCR validation. (XLSX 13 kb)

Research paper thumbnail of Additional file 8: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Scatterplots of the log2FPKM of the initially sequenced batch versus the log2FPKM of the resequen... more Scatterplots of the log2FPKM of the initially sequenced batch versus the log2FPKM of the resequenced batch for each sample resequenced. (TIF 506 kb)

Research paper thumbnail of Additional file 7: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Paw withdrawal thresholds to mechanical stimulation. (TIF 218 kb)

Research paper thumbnail of Additional file 6: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

qPCR validation of RNA-seq data. Quantitative PCR was used to confirm the relationship of gene ex... more qPCR validation of RNA-seq data. Quantitative PCR was used to confirm the relationship of gene expression after nerve injury of DRGs from male and female rats: A) Increased relative expression in females only was confirmed in Ahr, Cdkn1a and Tnfaip6, B) Increased relative expression in males only was confirmed in Faim2, Phyhipl, and Trpm6, C) Increased expression in both sexes after injury confirmed in Csf1 and Oprm1, and D) no change in relative expression in Sec62, Stk38l. Values represent the mean standard deviation log2Expression of 2 biological replicates. (TIF 1039 kb)

Research paper thumbnail of Additional file 5: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Co-expression networks of differentially expressed genes. A) Schematic diagram of experiment. Mal... more Co-expression networks of differentially expressed genes. A) Schematic diagram of experiment. Male and female rats were randomly assigned to the naïve group or receive CCI. RNA-seq performed on ipsilateral L4-L6 DRGs from each animal. Differentially expressed genes (DEG) defined as genes expressed after CCI versus naïve with a |log2FC| > 0.5 and an adjusted p-value 0.5 (dashed lines) with an adjusted p-value

Research paper thumbnail of Additional file 4: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Complete list of genes that are significantly differentially regulated between males and females.... more Complete list of genes that are significantly differentially regulated between males and females. (XLSX 164 kb)

Research paper thumbnail of Additional file 3: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Overlap of differentially expressed genes after CCI between males and females in common functiona... more Overlap of differentially expressed genes after CCI between males and females in common functional pathways. (TIF 932 kb)

Research paper thumbnail of Additional file 2: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

List of genes with increased expression in female versus male rats in the naive DRG. (XLSX 43 kb)

Research paper thumbnail of Additional file 1: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

List of genes with increased expression in male versus female rats in the naive DRG. (XLSX 75 kb)

Research paper thumbnail of 2015 - Ciliate Molecular Biology Congress

Research paper thumbnail of Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

Efforts to understand genetic variability involved in an individual’s susceptibility to chronic p... more Efforts to understand genetic variability involved in an individual’s susceptibility to chronic pain support a role for upstream regulation by epigenetic mechanisms. To examine the transcriptomic and epigenetic basis of chronic pain that resides in the peripheral nervous system, we used RNA-seq and ATAC-seq of the rat dorsal root ganglion (DRG) to identify novel molecular pathways associated with pain hypersensitivity in two well-studied persistent pain models induced by Chronic Constriction Injury (CCI) of the sciatic nerve and intra-plantar injection of Complete Freund’s Adjuvant (CFA) in rats. Our RNA-seq studies identify a variety of biological process related to synapse organization, membrane potential, transmembrane transport, and ion binding. Interestingly, genes that encode transcriptional regulators were disproportionately downregulated in both models. Our ATAC-seq data provide a comprehensive map of chromatin accessibility changes in the DRG. A total of 1123 regions showed...

Research paper thumbnail of Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae

PeerJ, 2020

The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editin... more The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potent...

Research paper thumbnail of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Pain is a subjective experience derived from complex interactions among biological, environmental... more Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular causes underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Here we sought to identify shared and distinct gene networks functioning in the peripheral nervous systems that may contribute to sex differences of pain after nerve injury. We performed RNA-seq on dorsal root ganglia following chronic constriction injury of the sciatic nerve in male and female rats. Analysis from paired naive and injured tissues showed that 1456 genes were differentially expressed between sexes. Appreciating sex-related gene expression differences and similarities in neuropathic pain models may help to improve the translational relevance to clinical populations and efficacy of clinical trials of this maj...

Research paper thumbnail of Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin

Nucleic acids research, Dec 3, 2016

The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally... more The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impa...

Research paper thumbnail of The bromodomain of Gcn5 regulates site specificity of lysine acetylation on histone H3

Molecular & cellular proteomics : MCP, 2014

In yeast, the conserved histone acetyltransferase (HAT) Gcn5 associates with Ada2 and Ada3 to for... more In yeast, the conserved histone acetyltransferase (HAT) Gcn5 associates with Ada2 and Ada3 to form the catalytic module of the ADA and SAGA transcriptional coactivator complexes. Gcn5 also contains an acetyl-lysine binding bromodomain that has been implicated in regulating nucleosomal acetylation in vitro, as well as at gene promoters in cells. However, the contribution of the Gcn5 bromodomain in regulating site specificity of HAT activity remains unclear. Here, we used a combined acid-urea gel and quantitative mass spectrometry approach to compare the HAT activity of wild-type and Gcn5 bromodomain-mutant ADA subcomplexes (Gcn5-Ada2-Ada3). Wild-type ADA subcomplex acetylated H3 lysines with the following specificity; H3K14 > H3K23 > H3K9 ≈ H3K18 > H3K27 > H3K36. However, when the Gcn5 bromodomain was defective in acetyl-lysine binding, the ADA subcomplex demonstrated altered site-specific acetylation on free and nucleosomal H3, with H3K18ac being the most severely dimini...

Research paper thumbnail of A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions

Molecular & cellular proteomics : MCP, 2014

Post-translational modifications of histones, such as acetylation and methylation, are differenti... more Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical...

Research paper thumbnail of ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus

Cell reports, Jan 26, 2012

The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that pr... more The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that provide for the localization of a defined protein or posttranslationally modified protein to specific chromosomal sites. While these approaches have helped us conceptualize epigenetic mechanisms, the field has been limited by the inability to define features such as the proteome and histone modifications at a specific genomic locus in an unbiased manner. We developed an unbiased approach whereby a unique native genomic locus was isolated, which was followed by high-resolution proteomic identification of specifically associated proteins and histone posttranslational modifications. This chromatin affinity purification with mass spectrometry (ChAP-MS) technique was used to specifically enrich a ~1,000 base pair section of GAL1 chromatin under transcriptionally active and repressive conditions, as well as to identify the specifically bound proteins and histone posttranslational modifications. ...

Research paper thumbnail of A CRISPR-based approach for proteomic analysis of a single genomic locus

Epigenetics, 2014

Any given chromosomal activity (e.g., transcription) is governed predominantly by the local epipr... more Any given chromosomal activity (e.g., transcription) is governed predominantly by the local epiproteome. However, defining local epiproteomes has been limited by a lack of effective technologies to isolate discrete sections of chromatin and to identify with precision specific proteins and histone posttranslational modifications (ptMs). We report the use of the Cas9 and guide rNA (grNA) components of the CriSpr system for grNA-directed purification of a discrete section of chromatin. Quantitative mass spectrometry provides for unambiguous identification of proteins and histone ptMs specifically associated with the enriched chromatin. this CriSpr-based Chromatin Affinity purification with Mass Spectrometry (CriSpr-ChAp-MS) approach revealed changes in the local epiproteome of a promoter during activation of transcription. CriSpr-ChAp-MS thus has broad applications for discovering molecular components and dynamic regulation of any in vivo activity at a given chromosomal location.

Research paper thumbnail of Post-Translational Modifications

Epigenetics, Environment, and Genes, 2013

Research paper thumbnail of Purification of Specific Chromatin Loci for Proteomic Analysis

Methods in Molecular Biology, 2014

Purification of small, native chromatin sections for proteomic identification of specifically bou... more Purification of small, native chromatin sections for proteomic identification of specifically bound proteins and histone posttranslational modifications is a powerful approach for studying mechanisms of chromosome metabolism. We detail a Chromatin Affinity Purification with Mass Spectrometry (ChAP-MS) approach for affinity purification of ~1 kb sections of chromatin for targeted proteomic analysis. This approach utilizes quantitative, high resolution mass spectrometry to categorize proteins and histone posttranslational modifications co-enriching with the given chromatin section as either "specific" to the targeted chromatin or "non-specific" contamination. In this way, the ChAP-MS approach can help define and redefine mechanisms of chromatintemplated activities.

Research paper thumbnail of Additional file 9: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

List of primers used for qPCR validation. (XLSX 13 kb)

Research paper thumbnail of Additional file 8: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Scatterplots of the log2FPKM of the initially sequenced batch versus the log2FPKM of the resequen... more Scatterplots of the log2FPKM of the initially sequenced batch versus the log2FPKM of the resequenced batch for each sample resequenced. (TIF 506 kb)

Research paper thumbnail of Additional file 7: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Paw withdrawal thresholds to mechanical stimulation. (TIF 218 kb)

Research paper thumbnail of Additional file 6: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

qPCR validation of RNA-seq data. Quantitative PCR was used to confirm the relationship of gene ex... more qPCR validation of RNA-seq data. Quantitative PCR was used to confirm the relationship of gene expression after nerve injury of DRGs from male and female rats: A) Increased relative expression in females only was confirmed in Ahr, Cdkn1a and Tnfaip6, B) Increased relative expression in males only was confirmed in Faim2, Phyhipl, and Trpm6, C) Increased expression in both sexes after injury confirmed in Csf1 and Oprm1, and D) no change in relative expression in Sec62, Stk38l. Values represent the mean standard deviation log2Expression of 2 biological replicates. (TIF 1039 kb)

Research paper thumbnail of Additional file 5: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Co-expression networks of differentially expressed genes. A) Schematic diagram of experiment. Mal... more Co-expression networks of differentially expressed genes. A) Schematic diagram of experiment. Male and female rats were randomly assigned to the naïve group or receive CCI. RNA-seq performed on ipsilateral L4-L6 DRGs from each animal. Differentially expressed genes (DEG) defined as genes expressed after CCI versus naïve with a |log2FC| > 0.5 and an adjusted p-value 0.5 (dashed lines) with an adjusted p-value

Research paper thumbnail of Additional file 4: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Complete list of genes that are significantly differentially regulated between males and females.... more Complete list of genes that are significantly differentially regulated between males and females. (XLSX 164 kb)

Research paper thumbnail of Additional file 3: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Overlap of differentially expressed genes after CCI between males and females in common functiona... more Overlap of differentially expressed genes after CCI between males and females in common functional pathways. (TIF 932 kb)

Research paper thumbnail of Additional file 2: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

List of genes with increased expression in female versus male rats in the naive DRG. (XLSX 43 kb)

Research paper thumbnail of Additional file 1: of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

List of genes with increased expression in male versus female rats in the naive DRG. (XLSX 75 kb)

Research paper thumbnail of 2015 - Ciliate Molecular Biology Congress

Research paper thumbnail of Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

Efforts to understand genetic variability involved in an individual’s susceptibility to chronic p... more Efforts to understand genetic variability involved in an individual’s susceptibility to chronic pain support a role for upstream regulation by epigenetic mechanisms. To examine the transcriptomic and epigenetic basis of chronic pain that resides in the peripheral nervous system, we used RNA-seq and ATAC-seq of the rat dorsal root ganglion (DRG) to identify novel molecular pathways associated with pain hypersensitivity in two well-studied persistent pain models induced by Chronic Constriction Injury (CCI) of the sciatic nerve and intra-plantar injection of Complete Freund’s Adjuvant (CFA) in rats. Our RNA-seq studies identify a variety of biological process related to synapse organization, membrane potential, transmembrane transport, and ion binding. Interestingly, genes that encode transcriptional regulators were disproportionately downregulated in both models. Our ATAC-seq data provide a comprehensive map of chromatin accessibility changes in the DRG. A total of 1123 regions showed...

Research paper thumbnail of Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae

PeerJ, 2020

The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editin... more The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potent...

Research paper thumbnail of Sex differences in gene regulation in the dorsal root ganglion after nerve injury

Pain is a subjective experience derived from complex interactions among biological, environmental... more Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular causes underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Here we sought to identify shared and distinct gene networks functioning in the peripheral nervous systems that may contribute to sex differences of pain after nerve injury. We performed RNA-seq on dorsal root ganglia following chronic constriction injury of the sciatic nerve in male and female rats. Analysis from paired naive and injured tissues showed that 1456 genes were differentially expressed between sexes. Appreciating sex-related gene expression differences and similarities in neuropathic pain models may help to improve the translational relevance to clinical populations and efficacy of clinical trials of this maj...

Research paper thumbnail of Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin

Nucleic acids research, Dec 3, 2016

The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally... more The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impa...

Research paper thumbnail of The bromodomain of Gcn5 regulates site specificity of lysine acetylation on histone H3

Molecular & cellular proteomics : MCP, 2014

In yeast, the conserved histone acetyltransferase (HAT) Gcn5 associates with Ada2 and Ada3 to for... more In yeast, the conserved histone acetyltransferase (HAT) Gcn5 associates with Ada2 and Ada3 to form the catalytic module of the ADA and SAGA transcriptional coactivator complexes. Gcn5 also contains an acetyl-lysine binding bromodomain that has been implicated in regulating nucleosomal acetylation in vitro, as well as at gene promoters in cells. However, the contribution of the Gcn5 bromodomain in regulating site specificity of HAT activity remains unclear. Here, we used a combined acid-urea gel and quantitative mass spectrometry approach to compare the HAT activity of wild-type and Gcn5 bromodomain-mutant ADA subcomplexes (Gcn5-Ada2-Ada3). Wild-type ADA subcomplex acetylated H3 lysines with the following specificity; H3K14 > H3K23 > H3K9 ≈ H3K18 > H3K27 > H3K36. However, when the Gcn5 bromodomain was defective in acetyl-lysine binding, the ADA subcomplex demonstrated altered site-specific acetylation on free and nucleosomal H3, with H3K18ac being the most severely dimini...

Research paper thumbnail of A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions

Molecular & cellular proteomics : MCP, 2014

Post-translational modifications of histones, such as acetylation and methylation, are differenti... more Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical...

Research paper thumbnail of ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus

Cell reports, Jan 26, 2012

The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that pr... more The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that provide for the localization of a defined protein or posttranslationally modified protein to specific chromosomal sites. While these approaches have helped us conceptualize epigenetic mechanisms, the field has been limited by the inability to define features such as the proteome and histone modifications at a specific genomic locus in an unbiased manner. We developed an unbiased approach whereby a unique native genomic locus was isolated, which was followed by high-resolution proteomic identification of specifically associated proteins and histone posttranslational modifications. This chromatin affinity purification with mass spectrometry (ChAP-MS) technique was used to specifically enrich a ~1,000 base pair section of GAL1 chromatin under transcriptionally active and repressive conditions, as well as to identify the specifically bound proteins and histone posttranslational modifications. ...

Research paper thumbnail of A CRISPR-based approach for proteomic analysis of a single genomic locus

Epigenetics, 2014

Any given chromosomal activity (e.g., transcription) is governed predominantly by the local epipr... more Any given chromosomal activity (e.g., transcription) is governed predominantly by the local epiproteome. However, defining local epiproteomes has been limited by a lack of effective technologies to isolate discrete sections of chromatin and to identify with precision specific proteins and histone posttranslational modifications (ptMs). We report the use of the Cas9 and guide rNA (grNA) components of the CriSpr system for grNA-directed purification of a discrete section of chromatin. Quantitative mass spectrometry provides for unambiguous identification of proteins and histone ptMs specifically associated with the enriched chromatin. this CriSpr-based Chromatin Affinity purification with Mass Spectrometry (CriSpr-ChAp-MS) approach revealed changes in the local epiproteome of a promoter during activation of transcription. CriSpr-ChAp-MS thus has broad applications for discovering molecular components and dynamic regulation of any in vivo activity at a given chromosomal location.

Research paper thumbnail of Post-Translational Modifications

Epigenetics, Environment, and Genes, 2013

Research paper thumbnail of Purification of Specific Chromatin Loci for Proteomic Analysis

Methods in Molecular Biology, 2014

Purification of small, native chromatin sections for proteomic identification of specifically bou... more Purification of small, native chromatin sections for proteomic identification of specifically bound proteins and histone posttranslational modifications is a powerful approach for studying mechanisms of chromosome metabolism. We detail a Chromatin Affinity Purification with Mass Spectrometry (ChAP-MS) approach for affinity purification of ~1 kb sections of chromatin for targeted proteomic analysis. This approach utilizes quantitative, high resolution mass spectrometry to categorize proteins and histone posttranslational modifications co-enriching with the given chromatin section as either "specific" to the targeted chromatin or "non-specific" contamination. In this way, the ChAP-MS approach can help define and redefine mechanisms of chromatintemplated activities.