Robbyn Issner - Academia.edu (original) (raw)

Papers by Robbyn Issner

Proceedings of the National Academy of Sciences of the United States of America, Nov 14, 2000

Genes & Development, Apr 1, 1998

The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S)... more The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S) and arginine (R)-rich protein associated with splicing complexes and is named here SRm160 (SR-related matrix protein of 160 kD). SRm160 contains multiple SR repeats, but unlike proteins of the SR family of splicing factors, lacks an RNA recognition motif. SRm160 and a related protein SRm300 (the 300-kD nuclear matrix antigen recognized by mAb B4A11) form a complex that is required for the splicing of specific pre-mRNAs. The SRm160/300 complex associates with splicing complexes and promotes splicing through interactions with SR family proteins. Binding of SRm160/300 to pre-mRNA is normally also dependent on U1 snRNP and is stabilized by U2 snRNP. Thus, SRm160/300 forms multiple interactions with components bound directly to important sites within pre-mRNA. The results suggest that a complex of the nuclear matrix proteins SRm160 and SRm300 functions as a coactivator of pre-mRNA splicing.

Supplementary Figure S5. Additional details regarding candidate MYC enhancers identified in B cel... more Supplementary Figure S5. Additional details regarding candidate MYC enhancers identified in B cell lymphomas.

Journal of Cell Biology, Nov 1, 1994

mAbs raised against the human nuclear matrix (anti-NM) 1 mAbs have been used to investigate the r... more mAbs raised against the human nuclear matrix (anti-NM) 1 mAbs have been used to investigate the role of nuclear matrix antigens in pre-mRNA processing. The three anti-NM mAbs used in this study recognize antigens that are highly localized to nuclear matrix speckles. Surprisingly, all three of these mAbs preferentially immunoprecipitate splicing complexes containing exon sequences. The anti-NM mAbs efficiently immunoprecipitate the exon product complex but not complexes containing the lariat product after the second step of splicing. Two of the anti-NM mAbs completely inhibit pre-mRNA splicing in vitro. However, none of the.anti-NM mAbs appear to recognize factors stably associated with splicing snRNPs. The three anti-NM mAbs predominantly react with distinct high molecular weight antigens, which belong to a class of nuclear proteins that selectively precipitate with Ser-Arg protein-splicing factors in the presence of high Mg 2+ concentrations. Immunological, biochemical, and cell biological data indicate that two of the NM antigens are related to the defined set of Ser-Arg proteins. The results suggest the existence of an extended Ser-Arg family as a component of the nuclear matrix.

Cell, Jul 1, 2017

Highlights d A non-coding variant on chromosome 6 associates with five vascular diseases d Histon... more Highlights d A non-coding variant on chromosome 6 associates with five vascular diseases d Histone acetylation shows a vascular-specific regulatory element at the causal SNP d Genome editing at the SNP demonstrates distal regulatory effect on endothelin-1 d Endothelin-1 signaling in blood vessels may explain pattern of vascular disease risk

Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncog... more Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncogenic significance detected by PEAR-ChIP. Red bars join discordant intra-chromosomal read pairs.

Specimen code Gender Age at time of procedure Positive 75% BCL6+ CD10+ MCL-01 M Yes No-Alive, in ... more Specimen code Gender Age at time of procedure Positive 75% BCL6+ CD10+ MCL-01 M Yes No-Alive, in clinical remission Mantle cell lymphoma Negative CyclinD1+ MCL-02 M No Yes 48 Alive with disease Mantle cell lymphoma Negative CyclinD1+ MCL-03 F No Yes 53 Alive, in clinical remission Mantle cell lymphoma Negative CyclinD1+ MCL-04 M Yes No-Alive with disease Mantle cell lymphoma Negative CyclinD1+ SLL-01 M No Yes 46 Alive with disease Chronic lymphocytic leukemia / small lymphocytic lymphoma SLL-02 F No No 75 Alive, in clinical remission Chronic lymphocytic leukemia / small lymphocytic lymphoma SLL-03 M Yes No-Alive, in clinical remission Chronic lymphocytic leukemia / small lymphocytic lymphoma

Cross-linked cell line pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris... more Cross-linked cell line pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% IGEPAL CA-630 + PI). Nuclei were pelleted at 3000g, resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for

Supplementary Table S4. Sequences of oligonucleotides used for qRT-PCR, RT-PCR, and 3C.

Supplementary Figure S3. Enhancer looping interactions and TF binding at BCL6 enhancers.

Elsevier eBooks, Dec 1, 2011

Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and... more Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that combines chromatin immunoprecipitation with a signature readout of 487 representative loci. We applied ChIP-string to screen 145 antibodies, thereby identifying effective reagents, which we used to map the genome-wide binding of 29 CRs in two cell types. We found that specific combinations of CRs colocalize in characteristic patterns at distinct chromatin environments, at genes of coherent functions, and at distal regulatory elements. When comparing between cell types, CRs redistribute to different loci but maintain their modular and combinatorial associations. Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function.

PLoS eBooks, Apr 1, 2011

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and ... more The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Biochemistry and Cell Biology, Aug 25, 1999

Page 1. ABSTRACTS / RÉSUMÉS The NuA4 transcription activation/histone H4 acetyltransferase comple... more Page 1. ABSTRACTS / RÉSUMÉS The NuA4 transcription activation/histone H4 acetyltransferase complex contains the essential Esa1 protein as the catalytic subunit and the essential ATM-related cofactor Tra1p Stéphane Allard ...

Journal of Investigative Dermatology, May 1, 2021

Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are both derived from epidermal kera... more Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are both derived from epidermal keratinocytes but phenotypically diverge. To improve understanding of keratinocyte carcinogenesis, it is critical to understand epigenetic alterations, particularly those that govern gene expression. We examined changes to the enhancer-associated histone acetylation mark H3K27ac by mapping matched tumor-normal pairs from 11 patients (5 with BCC and 6 with SCC) undergoing Mohs surgery. Our analysis uncovered cancer-specific enhancers based on differential H3K27ac peaks between matched tumor-normal pairs. We also uncovered biologic pathways potentially altered in keratinocyte carcinoma including enriched epidermal development and Wnt signaling pathways enriched in BCCs, and enriched immune response and cell activation pathways in SCCs. We also observed enrichment of transcription factors that implicated SMAD and JDP2 in BCC pathogenesis and FOXP1 in SCC pathogenesis. Based on these findings, we prioritized three loci with putative regulation events: FGFR2 enhancer in BCC, intragenic regulation of FOXP1 in SCC, and WNT5A promoter in both subtypes and validated our findings with published gene expression data. Our findings highlight unique and shared epigenetic alterations in histone modifications and potential regulators for BCCs and SCCs that likely impact divergent oncogenic pathways, paving the way for targeted drug discoveries.

PubMed, Oct 1, 1995

A family of six highly conserved proteins that contain domains rich in alternating serine/arginin... more A family of six highly conserved proteins that contain domains rich in alternating serine/arginine residues (SR proteins) function in the regulation of splice site selection and are required for splicing. Using a selective precipitation method, more than 35 proteins were detected in nuclear extracts of HeLa cells that co-fractionate with the defined SR family. Many of these proteins were recognized by three monoclonal antibodies that bind to distinct phosphoepitopes on SR proteins. Two of these SR-related proteins were identified as the nuclear matrix antigens B1C8 and B4A11, which previously have been implicated in splicing. A subset of SR proteins, in their phosphorylated state, are associated with spliceosome complexes through both steps of the splicing reaction, remaining preferentially bound to complexes containing the exon-product. In contrast, other SR-related proteins appear to remain specifically associated with the intron-Iariat complex. The results indicate the existence of a potentially large group of SR-related proteins, and also suggest possible additional functions of SR proteins at a post-splicing level.

Supplementary Figure S4. Genome-wide correlation and motif analysis of MEF2B and p300 ChIP-Seq in... more Supplementary Figure S4. Genome-wide correlation and motif analysis of MEF2B and p300 ChIP-Seq in HGB cell lines.

Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncog... more Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncogenic significance detected by PEAR-ChIP. Red bars join discordant intra-chromosomal read pairs.

Proceedings of the National Academy of Sciences of the United States of America, Nov 14, 2000

Genes & Development, Apr 1, 1998

The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S)... more The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S) and arginine (R)-rich protein associated with splicing complexes and is named here SRm160 (SR-related matrix protein of 160 kD). SRm160 contains multiple SR repeats, but unlike proteins of the SR family of splicing factors, lacks an RNA recognition motif. SRm160 and a related protein SRm300 (the 300-kD nuclear matrix antigen recognized by mAb B4A11) form a complex that is required for the splicing of specific pre-mRNAs. The SRm160/300 complex associates with splicing complexes and promotes splicing through interactions with SR family proteins. Binding of SRm160/300 to pre-mRNA is normally also dependent on U1 snRNP and is stabilized by U2 snRNP. Thus, SRm160/300 forms multiple interactions with components bound directly to important sites within pre-mRNA. The results suggest that a complex of the nuclear matrix proteins SRm160 and SRm300 functions as a coactivator of pre-mRNA splicing.

Supplementary Figure S5. Additional details regarding candidate MYC enhancers identified in B cel... more Supplementary Figure S5. Additional details regarding candidate MYC enhancers identified in B cell lymphomas.

Journal of Cell Biology, Nov 1, 1994

mAbs raised against the human nuclear matrix (anti-NM) 1 mAbs have been used to investigate the r... more mAbs raised against the human nuclear matrix (anti-NM) 1 mAbs have been used to investigate the role of nuclear matrix antigens in pre-mRNA processing. The three anti-NM mAbs used in this study recognize antigens that are highly localized to nuclear matrix speckles. Surprisingly, all three of these mAbs preferentially immunoprecipitate splicing complexes containing exon sequences. The anti-NM mAbs efficiently immunoprecipitate the exon product complex but not complexes containing the lariat product after the second step of splicing. Two of the anti-NM mAbs completely inhibit pre-mRNA splicing in vitro. However, none of the.anti-NM mAbs appear to recognize factors stably associated with splicing snRNPs. The three anti-NM mAbs predominantly react with distinct high molecular weight antigens, which belong to a class of nuclear proteins that selectively precipitate with Ser-Arg protein-splicing factors in the presence of high Mg 2+ concentrations. Immunological, biochemical, and cell biological data indicate that two of the NM antigens are related to the defined set of Ser-Arg proteins. The results suggest the existence of an extended Ser-Arg family as a component of the nuclear matrix.

Cell, Jul 1, 2017

Highlights d A non-coding variant on chromosome 6 associates with five vascular diseases d Histon... more Highlights d A non-coding variant on chromosome 6 associates with five vascular diseases d Histone acetylation shows a vascular-specific regulatory element at the causal SNP d Genome editing at the SNP demonstrates distal regulatory effect on endothelin-1 d Endothelin-1 signaling in blood vessels may explain pattern of vascular disease risk

Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncog... more Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncogenic significance detected by PEAR-ChIP. Red bars join discordant intra-chromosomal read pairs.

Specimen code Gender Age at time of procedure Positive 75% BCL6+ CD10+ MCL-01 M Yes No-Alive, in ... more Specimen code Gender Age at time of procedure Positive 75% BCL6+ CD10+ MCL-01 M Yes No-Alive, in clinical remission Mantle cell lymphoma Negative CyclinD1+ MCL-02 M No Yes 48 Alive with disease Mantle cell lymphoma Negative CyclinD1+ MCL-03 F No Yes 53 Alive, in clinical remission Mantle cell lymphoma Negative CyclinD1+ MCL-04 M Yes No-Alive with disease Mantle cell lymphoma Negative CyclinD1+ SLL-01 M No Yes 46 Alive with disease Chronic lymphocytic leukemia / small lymphocytic lymphoma SLL-02 F No No 75 Alive, in clinical remission Chronic lymphocytic leukemia / small lymphocytic lymphoma SLL-03 M Yes No-Alive, in clinical remission Chronic lymphocytic leukemia / small lymphocytic lymphoma

Cross-linked cell line pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris... more Cross-linked cell line pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% IGEPAL CA-630 + PI). Nuclei were pelleted at 3000g, resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for

Supplementary Table S4. Sequences of oligonucleotides used for qRT-PCR, RT-PCR, and 3C.

Supplementary Figure S3. Enhancer looping interactions and TF binding at BCL6 enhancers.

Elsevier eBooks, Dec 1, 2011

Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and... more Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that combines chromatin immunoprecipitation with a signature readout of 487 representative loci. We applied ChIP-string to screen 145 antibodies, thereby identifying effective reagents, which we used to map the genome-wide binding of 29 CRs in two cell types. We found that specific combinations of CRs colocalize in characteristic patterns at distinct chromatin environments, at genes of coherent functions, and at distal regulatory elements. When comparing between cell types, CRs redistribute to different loci but maintain their modular and combinatorial associations. Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function.

PLoS eBooks, Apr 1, 2011

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and ... more The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Biochemistry and Cell Biology, Aug 25, 1999

Page 1. ABSTRACTS / RÉSUMÉS The NuA4 transcription activation/histone H4 acetyltransferase comple... more Page 1. ABSTRACTS / RÉSUMÉS The NuA4 transcription activation/histone H4 acetyltransferase complex contains the essential Esa1 protein as the catalytic subunit and the essential ATM-related cofactor Tra1p Stéphane Allard ...

Journal of Investigative Dermatology, May 1, 2021

Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are both derived from epidermal kera... more Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are both derived from epidermal keratinocytes but phenotypically diverge. To improve understanding of keratinocyte carcinogenesis, it is critical to understand epigenetic alterations, particularly those that govern gene expression. We examined changes to the enhancer-associated histone acetylation mark H3K27ac by mapping matched tumor-normal pairs from 11 patients (5 with BCC and 6 with SCC) undergoing Mohs surgery. Our analysis uncovered cancer-specific enhancers based on differential H3K27ac peaks between matched tumor-normal pairs. We also uncovered biologic pathways potentially altered in keratinocyte carcinoma including enriched epidermal development and Wnt signaling pathways enriched in BCCs, and enriched immune response and cell activation pathways in SCCs. We also observed enrichment of transcription factors that implicated SMAD and JDP2 in BCC pathogenesis and FOXP1 in SCC pathogenesis. Based on these findings, we prioritized three loci with putative regulation events: FGFR2 enhancer in BCC, intragenic regulation of FOXP1 in SCC, and WNT5A promoter in both subtypes and validated our findings with published gene expression data. Our findings highlight unique and shared epigenetic alterations in histone modifications and potential regulators for BCCs and SCCs that likely impact divergent oncogenic pathways, paving the way for targeted drug discoveries.

PubMed, Oct 1, 1995

A family of six highly conserved proteins that contain domains rich in alternating serine/arginin... more A family of six highly conserved proteins that contain domains rich in alternating serine/arginine residues (SR proteins) function in the regulation of splice site selection and are required for splicing. Using a selective precipitation method, more than 35 proteins were detected in nuclear extracts of HeLa cells that co-fractionate with the defined SR family. Many of these proteins were recognized by three monoclonal antibodies that bind to distinct phosphoepitopes on SR proteins. Two of these SR-related proteins were identified as the nuclear matrix antigens B1C8 and B4A11, which previously have been implicated in splicing. A subset of SR proteins, in their phosphorylated state, are associated with spliceosome complexes through both steps of the splicing reaction, remaining preferentially bound to complexes containing the exon-product. In contrast, other SR-related proteins appear to remain specifically associated with the intron-Iariat complex. The results indicate the existence of a potentially large group of SR-related proteins, and also suggest possible additional functions of SR proteins at a post-splicing level.

Supplementary Figure S4. Genome-wide correlation and motif analysis of MEF2B and p300 ChIP-Seq in... more Supplementary Figure S4. Genome-wide correlation and motif analysis of MEF2B and p300 ChIP-Seq in HGB cell lines.

Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncog... more Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncogenic significance detected by PEAR-ChIP. Red bars join discordant intra-chromosomal read pairs.