Rachel Patton McCord

University of Massachusetts Amherst, Amherst Center, Massachusetts, United States

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Publications (19)293.66 Total impact

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    ABSTRACT: Background Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. Results Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16–22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16–22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. Conclusions We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0768-0) contains supplementary material, which is available to authorized users.
    Full-text · Article · Sep 2015 · Genome Biology
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    ABSTRACT: The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (∼1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X chromosomes while regulating gene expression chromosome-wide.
    No preview · Article · Jun 2015 · Nature
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    ABSTRACT: Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological domains. This compartmentalization is thought to facilitate the matching of genes and regulatory elements, but its precise function and mechanistic basis remain unknown. Cohesin controls chromosome topology to enable DNA repair and chromosome segregation in cycling cells. In addition, cohesin associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. Although these findings suggest an important role for cohesin in genome organization, this role has not been assessed on a global scale. Unexpectedly, we find that architectural compartments are maintained in non-cycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was however required for specific long-range interactions within compartments where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, while alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within pre-existing chromosomal compartments.
    Full-text · Article · Sep 2013 · Genome Research
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    ABSTRACT: Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that primary HGPS skin fibroblasts experience genome-wide correlated alterations in patterns of H3K27me3 deposition, DNA-lamin A/C associations, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains. We further demonstrate that the H3K27me3 changes associate with gene expression alterations in HGPS cells. Our results support a model that the accumulation of progerin in the nuclear lamina leads to altered H3K27me3 marks in heterochromatin, possibly through the down-regulation of EZH2, and disrupts heterochromatin-lamina interactions. These changes may result in transcriptional misregulation and eventually trigger the global loss of spatial chromatin compartmentalization in late passage HGPS fibroblasts.
    No preview · Article · Feb 2013
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    ABSTRACT: Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that primary HGPS skin fibroblasts experience genome-wide correlated alterations in patterns of H3K27me3 deposition, DNA-lamin A/C associations, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains. We further demonstrate that the H3K27me3 changes associate with gene expression alterations in HGPS cells. Our results support a model that the accumulation of progerin in the nuclear lamina leads to altered H3K27me3 marks in heterochromatin, possibly through the down-regulation of EZH2, and disrupts heterochromatin-lamina interactions. These changes may result in transcriptional misregulation and eventually trigger the global loss of spatial chromatin compartmentalization in late passage HGPS fibroblasts.
    No preview · Article · Nov 2012 · Genome Research
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    ABSTRACT: Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires the elimination of systematic biases. We present a computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate this ICE (iterative correction and eigenvector decomposition) technique on published data obtained by the high-throughput 3C method Hi-C, and we demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes.
    Full-text · Article · Sep 2012 · Nature Methods
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    ABSTRACT: We describe a method, Hi-C, to comprehensively detect chromatin interactions in the mammalian nucleus. This method is based on Chromosome Conformation Capture, in which chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. The ligation products contain the information of not only where they originated from in the genomic sequence but also where they reside, physically, in the 3D organization of the genome. In Hi-C, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. The compatibility of Hi-C with next generation sequencing platforms makes it possible to detect chromatin interactions on an unprecedented scale. This advance gives Hi-C the power to both explore the biophysical properties of chromatin as well as the implications of chromatin structure for the biological functions of the nucleus. A massively parallel survey of chromatin interaction provides the previously missing dimension of spatial context to other genomic studies. This spatial context will provide a new perspective to studies of chromatin and its role in genome regulation in normal conditions and in disease.
    Full-text · Article · May 2012 · Methods
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    ABSTRACT: Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in two Arabidopsis genes, AtMORC1 and AtMORC6, which cause derepression of DNA-methylated genes and TEs but no losses of DNA or histone methylation. AtMORC1 and AtMORC6 are members of the conserved Microrchidia (MORC) adenosine triphosphatase (ATPase) family, which are predicted to catalyze alterations in chromosome superstructure. The atmorc1 and atmorc6 mutants show decondensation of pericentromeric heterochromatin, increased interaction of pericentromeric regions with the rest of the genome, and transcriptional defects that are largely restricted to loci residing in pericentromeric regions. Knockdown of the single MORC homolog in Caenorhabditis elegans also impairs transgene silencing. We propose that the MORC ATPases are conserved regulators of gene silencing in eukaryotes.
    Full-text · Article · May 2012 · Science
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    ABSTRACT: The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and used high-throughput genome-wide translocation sequencing to map translocations from target DNA double-strand breaks (DSBs) within it. RAG endonuclease-cleaved antigen-receptor loci are dominant translocation partners for target DSBs regardless of genomic position, reflecting high-frequency DSBs at these loci and their colocalization in a fraction of cells. To directly assess spatial proximity contributions, we normalized genomic DSBs via ionizing radiation. Under these conditions, translocations were highly enriched in cis along single chromosomes containing target DSBs and within other chromosomes and subchromosomal domains in a manner directly related to pre-existing spatial proximity. By combining two high-throughput genomic methods in a genetically tractable system, we provide a new lens for viewing cancer genomes.
    Full-text · Article · Mar 2012 · Cell
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    ABSTRACT: Table S4. Comparison of high-resolution in vitro DNA binding site motifs for S. cerevisiae TFs.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Detailed methods, additional figures, and additional tables. Figure S1: ClustalW protein sequence alignment of Vhr1 and its homologs in sensu stricto Saccharomyces species. The alignment shows that the second putative basic region of Vhr1 is more conserved than the first basic region. Figure S2: unlike AP-1 bZIPs, Vhr1 and Vhr2 bind only to overlapping half-sites. (a) AP-1 bZIP transcription factors (Gcn4, Yap1, Jundm2, and the Fos-Jun heterodimer) and Vhr1 transcription factors (Vhr1 and Vhr2) bind to overlapping TGAC or TTAC half-sites. For each TF we sorted the 8-mers in decreasing order of their E-score, from 0.5 (highest affinity) to -0.5 (lowest affinity). The black lines show the 8-mers that contain TGACT (or TTACT for Yap1). (b) AP-1 factors (Gcn4, Yap1, Jundm2, and Fos-Jun) also bind to non-overlapping half-sites, while Vhr1 factors (Vhr1 and Vhr2) do not bind to non-overlapping half-sites. The black lines show the 8-mers that contain TGACGT (or TTACGT for Yap1). The PBM data were reported in Zhu et al. [11] (Gcn4, Yap1), Badis et al. [16] (Jundm2), Alibés et al. [76] (Jun-Fos), or this study (Vhr1 and Vhr2). Figure S3: comparison of the DNA binding specificities of Hac1 (both from this study and from Badis et al. [10]) against bHLH and bZIP TFs. (a) PBM-derived motifs for bZIP TF Hac1 match motifs of bHLH TFs better than motifs of bZIP TFs. (b, c) In-depth comparison of the DNA binding specificities of Hac1 and bHLH TF Cbf1. (d) In-depth comparison of the DNA binding specificities of Hac1 (this study) and two bZIP proteins that bind overlapping or adjacent TGAC half-sites: Gcn4 and Sko1, respectively. The scatter plots show the 8-mer E-scores. Figure S4: primary and secondary DNA binding site motifs derived from high-resolution in vitro PBM data. Figure S5: comparison of motif enrichment in ChIP-chip data for the 27 TF motifs reported in this study versus previously reported PBM-derived (Badis et al. [10]), ChIP-derived (MacIsaac et al. [20]), or MITOMI-derived (Fordyce et al. [12]) motifs for these 27 TFs (where available). Figure S6: S. cerevisiae orphan DNA binding site motifs. Figure S7: Schema of PBM experimental pipeline and results. A total of 228 ORFs/DBDs were considered in this study. Those lacking in vitro PBM data refers to initiation of this study in late 2008 after completion of our prior PBM survey (Zhu et al. [11]) and prior to publication of two more recent in vitro surveys (Badis et al. [10]; Fordyce et al. [12]). Table S1: TF DNA binding site motifs from the in vitro PBM data of Badis et al. [10]. Table S2: TF DNA binding site motifs from the in vitro MITOMI data of Fordyce et al. [12]. Table S3: TFs with curated high-resolution DNA binding site motifs derived from in vitro PBM data. The source of the selected motif (PWM) is indicated. Table S5: TFs with DNA binding site motifs reported by MacIsaac et al. [20] according to in vivo ChIP-chip data. TFs for which high-resolution in vitro motifs are also available are marked in boldface font. Table S8: TFs with secondary DNA binding site motifs identified from the curated set of high-resolution PBM data.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles.
    Full-text · Article · Dec 2011 · Genome biology
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    ABSTRACT: Table S13. Categorization of remaining S. cerevisiae potential sequence-specific DNA binding proteins. For each of the 222 yeast proteins below, we list: the systematic name (column A); standard name (column B); structural domain found within protein (column C); designation for sequence specific DNA binding ability, either Likely, Maybe or Unlikely (column D); description of protein from the Saccharomyces Genome Database, including additional literature references to experimental evidence for DNA binding consensus sequences, ChIP motifs or other relevant information (column E). Criteria used for categorizing likelihood of sequence-specific DNA binding for Likely category included having a well characterized sequence-specific DNA binding domain and/or experimental evidence for sequence-specific DNA binding involving direct contact with DNA molecule (as opposed to indirect binding mediated through another protein factor). The Maybe category included proteins that contain structural domains for which instances of sequence-specific DNA binding have been demonstrated in other proteins containing that domain. Additionally, literature evidence for DNA binding ability, though not determined if sequence specific, or directly contacting DNA, was also considered. Finally, the Unlikely category contains proteins with structural domains that have failed to produce sequence-specific DNA binding in vitro, or have ChiP motifs likely to be through indirect interactions with DNA, or completely lack literature evidence for sequence-specific DNA binding by direct contact with DNA.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Table S9. All over-represented functional categories of target genes for each TF examined in this study.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Table S6. Comparison of in vivo motifs (MacIsaac et al. [20]) and in vitro motifs (selected from this study, Zhu et al. [11], or Badis et al. [10]) for 150 S. cerevisiae TFs. TFs for which the in vivo and in vitro motifs are different are marked in red font.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Table S12. DNA binding site motifs available for known or putative S. cerevisiae TFs.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Table S14. List of the 27 S. cerevisiae TFs that successfully yielded PBM data in this study. For each TF the table shows: (A) SGD ID; (B) common gene symbol; (C) Pfam DBD class (if known); (D) clone type (full-length ORF or DBD alone); (E) the Gateway entry clone used; (F) nucleotide sequence of cloned insert; (G) amino acid sequence of cloned insert; (H) the expected molecular weight (kDa) for the GST fusion protein expressed; (I) estimated concentration of protein used on PBM experiment, based on Western blot visual examination. All proteins were expressed by in vitro transcription and translation.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Data file S1. Curated set of high-resolution DNA binding site motifs (PWMs) for 150 S. cerevisiae TFs. The file contains 150 primary motifs and 39 secondary motifs derived from PBM data.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Table S11. Predicted direct and indirect TF-DNA interactions.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Data file S4. Collection of 4,160 previously published PWMs derived from S. cerevisiae TF-DNA binding and gene expression data.
    Preview · Dataset · Dec 2011

Publication Stats

981 Citations
293.66 Total Impact Points

Institutions

  • 2013-2015
    • University of Massachusetts Amherst
      Amherst Center, Massachusetts, United States
  • 2011-2015
    • University of Massachusetts Medical School
      • Department of Biochemistry and Molecular Pharmacology
      Worcester, Massachusetts, United States
  • 2009-2011
    • Harvard University
      Cambridge, Massachusetts, United States
  • 2008
    • Harvard Medical School
      • Department of Medicine
      Boston, Massachusetts, United States
  • 2005
    • Davidson College
      • Biology
      Davidson, North Carolina, United States