A map of the cis-regulatory sequences in the mouse genome
Open accessAbstract
The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 × 10(9) bases of the mouse genome possess a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. So far, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but on its own it cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including humans, Drosophila melanogaster and Caenorhabditis elegans. Here we apply the same experimental approach to a diverse set of 19 tissues and cell types in the mouse to produce a map of nearly 300,000 murine cis-regulatory sequences. The annotated sequences add up to 11% of the mouse genome, and include more than 70% of conserved non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we show that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and for the study of mechanisms regulating tissue-specific gene expression.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
More than 60% of embryonic sites remain accessible in adult liver based on public DNase I hypersensitivity data.
“Furthermore, an analysis of publically available DNase I hypersensitivity data (Shen et al., 2012) confirmed that >60% of embryonic sites remain accessible in the adult liver (data not shown).”
From Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation (2014) · cites this paper as Shen et al., 2012
The paper’s study description (section labeled Abstract; page unavailable) describes ChIP-Seq and RNA-Seq mapping in embryonic and adult tissues, but does not report the cited DNase I hypersensitivity data. Searches for DNase, hypersensitivity, and embryonic-to-adult liver accessibility found no passage establishing that more than 60% of embryonic sites remain accessible in adult liver. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works
Self-citationThe ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302 · see citing works
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · see citing works
Self-citationPruitt, K., Tatusova, T., & Maglott, D. (2004) · Nucleic Acids Res. · doi:10.1093/nar/gki025 · Cited by 3,248 · see citing works
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · see citing works
Self-citationChen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,474 · see citing works
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works
Mediator and cohesin connect gene expression and chromatin architecture
Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939 · see citing works
ChIP-seq accurately predicts tissue-specific activity of enhancers
Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works
Self-citationLi, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.014 · Cited by 1,232 · see citing works
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080 · see citing works
Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · see citing works
Self-citationA high-resolution map of active promoters in the human genome
Kim, T. H., Barrera, L., Zheng, M., Qu, C.-X., Singer, M. A., Richmond, T., Wu, Y. N., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 1,019 · see citing works
Self-citationIntegrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein, M., Lu, Z. J., Nostrand, E. L. V., Cheng, C., Arshinoff, B. I., Liu, T., Yip, K. Y.-L., Robilotto, R., Rechtsteiner, A., Ikegami, K., et al. (2010) · Science · doi:10.1126/science.1196914 · Cited by 959 · see citing works
Transcriptome analysis by strand-specific sequencing of complementary DNA
Parkhomchuk, D., Borodina, T. A., Amstislavskiy, V. S., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H. R., & Солдатов, А. В. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp596 · Cited by 934 · see citing works
Enhancer function: new insights into the regulation of tissue-specific gene expression
Ong, C.-T., & Corces, V. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2957 · Cited by 929 · see citing works
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.018 · Cited by 806 · see citing works
Self-citationCTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus.
Splinter, E., Heath, H., Kooren, J., Palstra, R.-J., Klous, P., Grosveld, F., Galjart, N., & de Laat, W. (2007) · Genes & Development · doi:10.1016/j.bcmd.2006.10.131 · Cited by 742 · see citing works
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
Schmidt, D., Wilson, M. D., Ballester, B., Schwalie, P. C., Brown, G. D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C. P., Mackay, S., et al. (2010) · Science · doi:10.1126/science.1186176 · Cited by 700 · see citing works
Genomic views of distant-acting enhancers
Visel, A., Rubin, E. M., & Pennacchio, L. A. (2009) · Nature · doi:10.1038/nature08451 · Cited by 610 · see citing works
Jordan, I. K., & Huda, A. (2011) · doi:10.3410/f.13354965.14726096 · Cited by 429
Chepelev, I., Wei, G., Wangsa, D., Tang, Q., & Zhao, K. (2012) · Cell Research · doi:10.1038/cr.2012.15 · Cited by 253 · see citing works
Flagged first, then by citations
1 of the 29 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- [3]The ENCODE Project Consortium A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol 9 e1001046 2011 PMC3079585 21526222
- [5]Roy S Identification of functional elements and regulatory circuits by Drosophila modENCODE Science 330 1787 1797 2010 21177974 PMC3192495
Cited by
Sorted by citations
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works
“H3K4me3, H3K4me1, H3K27ac, p300, CTCF, ChIPseq, mESC and cortex RNA-seq Figures 1-4, Supplemental Figures 5,10,2023 Shen, Y. et al. A Map of cis-Regulatory Sequences in the Mouse Genome. in submission (2012).(32) Lung Fibroblast 5C Supplemental Figure 4 Wang, K.C. et al. A long noncoding RNA maintains active chromatin…”
BackgroundInfluentialSelf-citationMaster Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works
“The set of enhancers that are bound by transcription factors and control transcription in any one cell type can promote expression of both cell-type-specific genes and genes that are active in multiple cell types (Dunham et al., 2012; Shen et al., 2012; Yip et al., 2012).”
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662 · see citing works
“The set of enhancers that control any one cell’s gene expression program is probably best defined in murine embryonic stem cells (ESCs).”
InfluentialAn atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works
Long non-coding RNAs: definitions, functions, challenges and recommendations
Mattick, J. S., Amaral, P., Carninci, P., Carpenter, S. B., Chang, H. Y., Chen, L., Chen, R., Dean, C., Dinger, M. E., Fitzgerald, K. A., et al. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00566-8 · Cited by 2,416 · see citing works
Global epigenomic reconfiguration during mammalian brain development
Lister, R., Mukamel, E. A., Nery, J. R., Urich, M., Puddifoot, C. A., Johnson, N. D., Lucero, J., Huang, Y., Dwork, A. J., Schultz, M. D., et al. (2013) · Science · doi:10.1126/science.1237905 · Cited by 1,830 · see citing works
“Genome-wide comparison of mCH/CH with chromatin accessibility, as inferred from ChIP input read density (36, 37), for all 10-kb windows of the mouse genome revealed two discrete groups of genomic regions (Fig.”
BackgroundPlasma proteomic associations with genetics and health in the UK Biobank
Sun, B. B., Chiou, J., Traylor, M., Benner, C., Hsu, Y.-H., Richardson, T. G., Surendran, P., Mahajan, A., Robins, C., Vasquez-Grinnell, S. G., et al. (2023) · Nature · doi:10.1038/s41586-023-06592-6 · Cited by 1,740 · see citing works
Nora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L. A., & Bruneau, B. G. (2017) · Cell · doi:10.1016/j.cell.2017.05.004 · Cited by 1,709 · see citing works
“(10%) connect to an active regulatory region before treatment, based on H3K27Ac enrichment (Shen et al., 2012).”
Transcriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356 · see citing works
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works
Self-citationTwo independent modes of chromatin organization revealed by cohesin removal
Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196 · see citing works
Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174 · see citing works
Long-range enhancer–promoter contacts in gene expression control
Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102 · see citing works
CTCF: an architectural protein bridging genome topology and function
Ong, C., & Corces, V. G. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3663 · Cited by 1,044 · see citing works
Th17 cell induction by adhesion of microbes to intestinal epithelial cells
Atarashi, K., Tanoue, T., Ando, M., Kamada, N., Nagano, Y., Narushima, S., Suda, W., Imaoka, A., Setoyama, H., Nagamori, T., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.058 · Cited by 1,071 · see citing works
Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works
“Computational predictions based on correlations between gene activity and activity of distal elements across panels of cell lines also led to the prediction that genes are regulated by multiple distal elements 54–56 .”
BackgroundReversing DNA Methylation: Mechanisms, Genomics, and Biological Functions
Wu, H., & Zhang, Y. (2014) · Cell · doi:10.1016/j.cell.2013.12.019 · Cited by 1,065 · see citing works
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, D. U., Jung, I., Wu, H., Zhai, Y., Tang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.038 · Cited by 958 · see citing works
“See also Figure S4 and Tables S1, S2, S3, S4, S5, and S6. orientation exist in >60% neighboring TAD boundaries (Figure S4D), suggesting that the boundary reverse-forward CBS pairs play an important role in the formation of most of TADs.”
InfluentialSelf-citationControl of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
Dowen, J. M., Fan, Z. P., Hnisz, D., Ren, G., Abraham, B. J., Zhang, L. N., Weintraub, A. S., Schuijers, J., Lee, T. I., Zhao, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.030 · Cited by 884 · see citing works
“Prior studies have suggested there can be more frequent interactions between enhancers and genes (Kieffer-Kwon et al., 2013; Sanyal et al., 2012; Shen et al., 2012); our high-confidence data is not saturating and does not address the upper limits of these interactions (Figure S1H, Extended Experimental Procedures).”
Shen, L., Shao, N., Liu, X., & Nestler, E. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-284 · Cited by 852 · see citing works
“They often regulate subsets of genes in a cell type specific way and are marked in part by the enrichment of H3K4me1 and H3K27ac [33,34].”
BackgroundMethodInfluentialA compendium of chromatin contact maps reveals spatially active regions in the human genome
Schmitt, A. D., Hu, M., Jung, I., Xu, Z., Qiu, Y., Tan, C. L., Li, Y., Lin, S., Lin, Y., Barr, C. L., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.10.061 · Cited by 866 · see citing works
Self-citationChromatin Domains: The Unit of Chromosome Organization
Dixon, J. R., Gorkin, D. U., & Ren, B. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.018 · Cited by 811 · see citing works
Self-citationDistinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos
Liu, X., Wang, C., Liu, W., Li, J., Li, C., Kou, X., Chen, J., Zhao, Y., Gao, H., Wang, H., et al. (2016) · Nature · doi:10.1038/nature19362 · Cited by 746 · see citing works
The Hierarchy of the 3D Genome
Gibcus, J. H., & Dekker, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.011 · Cited by 695 · see citing works
Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells
Xie, W., Schultz, M. D., Lister, R., Hou, Z., Rajagopal, N., Ray, P. R., Whitaker, J. W., Tian, S., Hawkins, R. D., Leung, D., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.022 · Cited by 721 · see citing works
Self-citationMultiple knockout mouse models reveal lincRNAs are required for life and brain development
Sauvageau, M., Goff, L. A., Lodato, S., Bonev, B., Groff, A. F., Gerhardinger, C., Sanchez-Gomez, D. B., Hacisuleyman, E., Li, E. V., Spence, M. C., et al. (2013) · eLife · doi:10.7554/elife.01749 · Cited by 674 · see citing works
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
Vietri Rudan, M., Barrington, C., Henderson, S., Ernst, C., Odom, D. T., Tanay, A., & Hadjur, S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.004 · Cited by 680 · see citing works
The landscape of accessible chromatin in mammalian preimplantation embryos
Wu, J.-Y., Huang, B., Chen, H., Yin, Q.-Z., Liu, Y., Xiang, Y.-L., Zhang, B., Liu, B.-F., Wang, Q.-J., Xia, W., et al. (2016) · Nature · doi:10.1038/nature18606 · Cited by 669 · see citing works
Xiang, J., Yin, Q.-F., Chen, T., Zhang, Y., Zhang, X.-O., Wu, Z., Zhang, S., Wang, H., Ge, J., Lu, X., et al. (2014) · Cell Research · doi:10.1038/cr.2014.35 · Cited by 729 · see citing works
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
Zhang, B., Zheng, H., Huang, B., Li, W., Xiang, Y.-L., Peng, X., Jia, M., Wu, X., Zhang, Y., Xu, Q.-H., et al. (2016) · Nature · doi:10.1038/nature19361 · Cited by 627 · see citing works
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613 · see citing works
“We compared our ChIP-seq to previous ChIP-Seq studies of Rad21 and CTCF: (Handoko et al., 2011; Nitzsche et al., 2011; Shen et al., 2012) and GSE29218.”
ResultThe role of 3D genome organization in development and cell differentiation
Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works
Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition
Dahl, J. A., Jung, I., Aanes, H., Greggains, G. D., Manaf, A., Lerdrup, M., Li, G., Kuan, S., Li, B., Lee, A. Y., et al. (2016) · Nature · doi:10.1038/nature19360 · Cited by 628 · see citing works
Self-citationEnhancers: five essential questions
Pennacchio, L. A., Bickmore, W. A., Dean, A., Nóbrega, M. A., & Bejerano, G. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3458 · Cited by 584 · see citing works
Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550 · see citing works
Self-citationGenome-wide chromatin state transitions associated with developmental and environmental cues
Zhu, J., Adli, M., Zou, J., Verstappen, G., Coyne, M. J., Zhang, X.-L., Durham, T. J., Miri, M., Deshpande, V., Jager, P. D., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.033 · Cited by 553 · see citing works
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants
Pasquali, L., Gaulton, K. J., Rodríguez‐Seguí, S. A., Mularoni, L., Miguel-Escalada, I., Akerman, İ., Tena, J. J., Morán, I., Gómez-Marín, C., van de Bunt, M., et al. (2014) · Nature Genetics · doi:10.1038/ng.2870 · Cited by 502 · see citing works
CellNet: Network Biology Applied to Stem Cell Engineering
Cahan, P., Li, H., Morris, S. A., da Rocha, E. L., Daley, G. Q., & Collins, J. J. (2014) · Cell · doi:10.1016/j.cell.2014.07.020 · Cited by 522 · see citing works
Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming
Song, C., Szulwach, K. E., Dai, Q., Fu, Y., Mao, S.-Q., Lin, L., Street, C., Li, Y., Poidevin, M., Wu, H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.001 · Cited by 545 · see citing works
“The association between fhMRs and poised enhancers is further strengthened with those predicted as functionally linked to promoters, approaching that observed for Tet1 (Figure S2E, o/e = 10.95, fhMR:hMR = 2.14) (Shen et al., 2012).”
InfluentialEpigenetic balance of gene expression by Polycomb and COMPASS families
Piunti, A., & Shilatifard, A. (2016) · Science · doi:10.1126/science.aad9780 · Cited by 524 · see citing works
Programming and Inheritance of Parental DNA Methylomes in Mammals
Wang, L., Zhang, J., Duan, J., Gao, X., Zhu, W. Z., Lu, X., Yang, L., Zhang, J., Li, G., Ci, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.04.017 · Cited by 532 · see citing works
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contactsPreprint
Ay, F., Bailey, T. L., & Noble, W. S. (2014) · Genome Research · doi:10.1101/gr.160374.113 · Cited by 479 · see citing works
“Both of the genes transcribed from these promoters ( Gucy1a3 , Gucy1b3 ), as well as a third gene that is 212 kb downstream from the Gucy1a3 promoter ( Map9 ), exhibit cortex-specific expression (Shen et al. 2012).”
BackgroundMethodResultInfluentialA single-cell atlas of chromatin accessibility in the human genome
Zhang, K., Hocker, J. D., Miller, M., Hou, X., Chiou, J., Poirion, O. B., Qiu, Y., Li, Y. E., Gaulton, K. J., Wang, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.10.024 · Cited by 502 · see citing works
“However, conventional assays have, in large part, used heterogeneous tissues as input materials to produce population average measurements, and consequently, the current catalogs of candidate regulatory sequences in the human genome (Andersson et al., 2014; Meuleman et al., 2020; Moore et al., 2020; Kundaje et al., 20…”
Self-citationGenome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics
Shen, L., Wu, H., Diep, D., Yamaguchi, S., D’Alessio, A. C., Fung, H.-L., Zhang, K., & Zhang, Y. (2013) · Cell · doi:10.1016/j.cell.2013.04.002 · Cited by 497 · see citing works
“…5mC oxidation Cell 153, 692–706, April 25, 2013 ª2013 Elsevier Inc. 697 (legend continued on next page) 698 Cell 153, 692–706, April 25, 2013 ª2013 Elsevier Inc. derivatives in wild-type and Tdg-deficient mouse ESCs at tissuespecific enhancers identified by mouse ENCODE project (Shen et al., 2012).”
InfluentialAllelic reprogramming of 3D chromatin architecture during early mammalian development
Du, Z., Zheng, H., Huang, B., Ma, R., Wu, J., Zhang, X., He, J., Xiang, Y., Wang, Q., Li, Y., et al. (2017) · Nature · doi:10.1038/nature23263 · Cited by 517 · see citing works
Self-citationKe, Y., Xu, Y., Chen, X., Feng, S., Liu, Z., Sun, Y., Yao, X., Li, F., Zhu, W. Z., Gao, L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.029 · Cited by 514 · see citing works
Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461 · see citing works
H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation
Lauberth, S. M., Nakayama, T., Wu, X., Ferris, A. L., Tang, Z., Hughes, S. H., & Roeder, R. G. (2013) · Cell · doi:10.1016/j.cell.2013.01.052 · Cited by 473 · see citing works
“Also, ubiquitylated H2B, which directly stimulates hSET1dependent H3K4 di- and trimethylation (Shilatifard, 2006), accumulates at the p21 promoter in response to DNA damage (Kim et al., 2009).”
Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations
Zhang, Y., Wong, C., Birnbaum, R. Y., Li, G., Favaro, R., Ngan, C. Y., Lim, J., Tai, E., Poh, H. M., Wong, E., et al. (2013) · Nature · doi:10.1038/nature12716 · Cited by 470 · see citing works
Enhancer transcripts mark active estrogen receptor binding sitesPreprint
Hah, N., Murakami, S., Nagari, A., Danko, C. G., & Kraus, W. L. (2013) · Genome Research · doi:10.1101/gr.152306.112 · Cited by 475 · see citing works
“Differential association of these features with enhancers in a given cell may define distinct classes of enhancers that specify distinct gene regulatory mechanisms and biological outcomes (Creyghton et al. 2010; Ghisletti et al. 2010; Rada-Iglesias et al. 2011; Wang et al. 2011; Zentner et al. 2011; Pham et al. 2012;…”
BackgroundRNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity
Pefanis, E., Wang, J., Rothschild, G., Lim, J., Kazadi, D., Sun, J., Federation, A., Chao, J., Elliott, O., Liu, Z.-P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.034 · Cited by 464 · see citing works
Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated <i>Myc</i> regulation
Shi, J., Whyte, W. A., Zepeda-Mendoza, C. J., Milazzo, J. P., Shen, C., Roe, J.-S., Minder, J. L., Mercan, F., Wang, E., Eckersley-Maslin, M. A., et al. (2013) · Genes & Development · doi:10.1101/gad.232710.113 · Cited by 463 · see citing works
“10A; Shen et al. 2012).”
Giorgetti, L., Galupa, R., Nora, E. P., Piolot, T., Lam, F., Dekker, J., Tiana, G., & Heard, E. (2014) · Cell · doi:10.1016/j.cell.2014.03.025 · Cited by 460 · see citing works
“Indeed, most identified enhancer/promoter pairs are found to belong to the same TADs (Shen et al., 2012; Smallwood and Ren, 2013).”
BackgroundThe pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460 · see citing works
Functional and topological characteristics of mammalian regulatory domains
Symmons, O., Uslu, V. V., Tsujimura, T., Ruf, S., Nassari, S., Schwarzer, W., Ettwiller, L., & Spitz, F. (2014) · Genome Research · doi:10.1101/gr.163519.113 · Cited by 455 · see citing works
“This depletion was largely maintained, even when we considered po- tentially confounding factors, such as the clustering of CTCF sites and TSS (Kim et al. 2007; Shen et al. 2012) or the overlap of CTCF sites and SINE B2 elements (Schmidt et al. 2012) (Supplemental Fig.”
BackgroundComprehensive analysis of single cell ATAC-seq data with SnapATAC
Fang, R., Preissl, S., Li, Y., Hou, X., Lucero, J., Wang, X., Motamedi, A., Shiau, A. K., Zhou, X., Xie, F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21583-9 · Cited by 455 · see citing works
Self-citationTranscription factors and 3D genome conformation in cell-fate decisions
Stadhouders, R., Filion, G. J. P., & Graf, T. (2019) · Nature · doi:10.1038/s41586-019-1182-7 · Cited by 519 · see citing works
Born to run: control of transcription elongation by RNA polymerase II
Chen, F. X., Smith, E. R., & Shilatifard, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0010-5 · Cited by 447 · see citing works
Breaking TADs: How Alterations of Chromatin Domains Result in Disease
Lupiáñez, D. G., Spielmann, M., & Mundlos, S. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.01.003 · Cited by 439 · see citing works
Genome-scale functional characterization of Drosophila developmental enhancers in vivo
Kvon, E. Z., Kazmar, T., Stampfel, G., Yáñez-Cuna, J. O., Pagani, M., Schernhuber, K., Dickson, B. J., & Stark, A. (2014) · Nature · doi:10.1038/nature13395 · Cited by 436 · see citing works
A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs
Andrey, G., Montavon, T., Mascrez, B., Gonzãlez, F., Noordermeer, D., Leleu, M., Trono, D., Spitz, F., & Duboule, D. (2013) · Science · doi:10.1126/science.1234167 · Cited by 409 · see citing works
Endogenous retroviruses function as species-specific enhancer elements in the placenta
Chuong, E. B., Rumi, M. A. K., Soares, M. J., & Baker, J. C. (2013) · Nature Genetics · doi:10.1038/ng.2553 · Cited by 429 · see citing works
RNA Binding to CBP Stimulates Histone Acetylation and Transcription
Bose, D. A., Donahue, G., Reinberg, D., Shiekhattar, R., Bonasio, R., & Berger, S. L. (2017) · Cell · doi:10.1016/j.cell.2016.12.020 · Cited by 426 · see citing works
Methods for mapping 3D chromosome architecture
Kempfer, R., & Pombo, A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0195-2 · Cited by 502 · see citing works
The Role of Chromosome Domains in Shaping the Functional Genome
Sexton, T., & Cavalli, G. (2015) · Cell · doi:10.1016/j.cell.2015.02.040 · Cited by 400 · see citing works
“This model is supported by the finding that TADs determine the scope of most enhancers’ activities (Ghavi-Helm et al., 2014; Shen et al., 2012; Symmons et al., 2014).”
Robust 4C-seq data analysis to screen for regulatory DNA interactions
van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes‐Quezada, C., Öz, Y., Bouwman, B. A. M., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2173 · Cited by 376 · see citing works
BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure
Anand, P., Brown, J. D., Lin, C. Y., Qi, J., Zhang, R., Artero, P. C., Alaiti, M. A., Bullard, J., Alazem, K., Margulies, K. B., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.013 · Cited by 406 · see citing works
“Experimental data obtained for BRD4 and Pol II were integrated with publicly available data fromBing Ren and colleagues, which provided epigenomic landscapes for murine cardiac euchromatin (Shen et al., 2012).”
Integrated genomics and proteomics define huntingtin CAG length-dependent networks in mice
Langfelder, P., Cantle, J. P., Chatzopoulou, D., Wang, N., Gao, F., Al-Ramahi, I., Lu, X.-H., Ramos, E. M., El-Zein, K., Zhao, Y., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4256 · Cited by 385 · see citing works
“A list of Ctcf target genes was created by scanning the canonical promoter region (1,000bp upstream of transcription start site) of Mus musculus RefSeq genes (assembly mm9) for the presence of Ctcf peaks in the “Cortex Adult 8 weeks CTCF TFBS Chip-Seq Peaks from ENCODE/LICR” UCSC track 66 .”
Weischenfeldt, J., Dubash, T., Drainas, A. P., Mardin, B. R., Chen, Y., Stütz, A. M., Waszak, S. M., Bosco, G., Halvorsen, A. R., Raeder, B., et al. (2017) · Nature Genetics · doi:10.1038/ng.3722 · Cited by 404 · see citing works
Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome
Schoenfelder, S., Sugar, R., Dimond, A., Javierre, B.-M., Armstrong, H., Mifsud, B., Dimitrova, E., Matheson, L., Tavares-Cadete, F., Furlan-Magaril, M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3393 · Cited by 398 · see citing works
Iwafuchi-Doi, M., Donahue, G., Kakumanu, A., Watts, J. A., Mahony, S., Pugh, B. F., Lee, D., Kaestner, K. H., & Zaret, K. S. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.001 · Cited by 390 · see citing works
The cis-Regulatory Atlas of the Mouse Immune System
Yoshida, H., Lareau, C. A., Ramírez, R. N., Rose, S. A., Maier, B. B., Wroblewska, A., Desland, F. A., Chudnovskiy, A., Mortha, A., Dominguez, C. X., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.036 · Cited by 375 · see citing works
“, 2017), and enhancer catalogs have generally shown them to be tissue-specific (Shen et al., 2012).”
Cohesin-mediated interactions organize chromosomal domain architecture
Sofueva, S., Yaffe, E., Chan, W., Georgopoulou, D., Vietri Rudan, M., Mira‐Bontenbal, H., Pollard, S. M., Schroth, G. P., Tanay, A., & Hadjur, S. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.237 · Cited by 394 · see citing works
“We mapped Rad21 binding sites using ChIP-seq in ASTs and NSCs and compared them to published data sets of mouse CTCF binding sites (Shen et al , 2012).”
The 3D genome in transcriptional regulation and pluripotency
Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391 · see citing works
“Within this framework, other factors may contribute more directly to lineage-specific transcriptional regulation (Shen et al., 2012; Neph et al., 2012).”
BackgroundSelf-citationBenayoun, B. A., Pollina, E. A., Singh, P. P., Mahmoudi, S., Harel, I., Casey, K. M., Dulken, B. W., Kundaje, A., & Brunet, A. (2019) · Genome Research · doi:10.1101/gr.240093.118 · Cited by 360 · see citing works
Data integration in the era of omics: current and future challenges
Gómez-Cabrero, D., Abugessaisa, I., Maier, D., Teschendorff, A. E., Merkenschlager, M., Gisel, A., Ballestar, E., Bongcam‐Rudloff, E., Conesa, A., & Tegner, J. N. (2014) · BMC Systems Biology · doi:10.1186/1752-0509-8-s2-i1 · Cited by 411 · see citing works
“…models organisms were nearly completed, ENCODE ( Homo Sapiens ), modENCODE ( C . elegans and D . melanogaster [44]), and mouseENCODE ( Mus musculus [55,56]) projects were launched with the common goal of identifying all functional elements within the genome, including “ protein-coding genes,…”
BackgroundGenetic dissection of the α-globin super-enhancer in vivo
Hay, D., Hughes, J. R., Babbs, C., Davies, J. O. J., Graham, B. J., Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Sharpe, J. A., Suciu, M. C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3605 · Cited by 385 · see citing works
Genome Organization Drives Chromosome Fragility
Canela, A., Maman, Y., Jung, S., Wong, N., Callen, E., Day, A., Kieffer-Kwon, K.-R., Pekowska, A., Zhang, H., Rao, S. S. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.034 · Cited by 383 · see citing works
Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
Nord, A. S., Blow, M. J., Attanasio, C., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.033 · Cited by 375 · see citing works
Integrated spatial genomics reveals global architecture of single nuclei
Takei, Y., Yun, J., Zheng, S., Ollikainen, N., Pierson, N. G., White, J. A., Shah, S., Thomassie, J., Suo, S., Eng, C.-H. L., et al. (2021) · Nature · doi:10.1038/s41586-020-03126-2 · Cited by 399 · see citing works
Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes
Rheaume, B. A., Jereen, A., Bolisetty, M. T., Sajid, M. S., Yang, Y. J., Renna, K., Sun, L., Robson, P., & Trakhtenberg, E. F. (2018) · Nature Communications · doi:10.1038/s41467-018-05134-3 · Cited by 401 · see citing works
Grundberg, E., Meduri, E., Sandling, J. K., Hedman, Å. K., Keildson, S., Buil, A., Busche, S., Yuan, W., Nisbet, J., Sekowska, M., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.004 · Cited by 370 · see citing works
Corradin, O., Saiakhova, A., Akhtar-Zaidi, B., Myeroff, L., Willis, J., Cowper-Sal·lari, R., Lupien, M., Markowitz, S., & Scacheri, P. C. (2014) · Genome Research · doi:10.1101/gr.164079.113 · Cited by 366 · see citing works
“…given cell type contains ;75,000 H3K4me1 sites, and these putative enhancers can be located considerably far upstream of or downstream from the gene whose expression they influence, and can even influence the expression of multiple target genes (Spilianakis and Flavell 2004; Vernimmen et al. 2009).”
BackgroundThe Hitchhiker’s guide to Hi-C analysis: Practical guidelines
Lajoie, B. R., Dekker, J., & Kaplan, N. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.031 · Cited by 377 · see citing works
Cabezas-Wallscheid, N., Klimmeck, D., Hansson, J., Lipka, D., Reyes, A., Wang, Q., Weichenhan, D., Lier, A., von Paleske, L., Renders, S., et al. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.07.005 · Cited by 352 · see citing works
Widespread transcriptional pausing and elongation control at enhancers
Henriques, T., Scruggs, B. S., Inouye, M. O., Muse, G. W., Williams, L. H., Burkholder, A. B., Lavender, C. A., Fargo, D. C., & Adelman, K. (2018) · Genes & Development · doi:10.1101/gad.309351.117 · Cited by 350 · see citing works
“Spt5was of particular interest in this regard, since recentwork in Saccharomyces cerevisiae (Shetty et al. 2017) demonstrated that Spt5 loss impacted mRNA synthesis and noncoding RNA production differently: mRNA levels were significantly reduced in the absence of Spt5, but noncoding antisense…”
BackgroundResultInfluentialTranscriptomics in the RNA-seq era
McGettigan, P. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.12.008 · Cited by 360 · see citing works
CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets
Merkenschlager, M., & Odom, D. T. (2013) · Cell · doi:10.1016/j.cell.2013.02.029 · Cited by 345 · see citing works
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A. D., & Ren, B. (2016) · Cell Research · doi:10.1038/cr.2016.137 · Cited by 344 · see citing works
Self-citationChemical Genetic Discovery of PARP Targets Reveals a Role for PARP-1 in Transcription Elongation
Gibson, B. A., Zhang, Y.-J., Jiang, H., Hussey, K. M., Shrimp, J. H., Lin, H.-N., Schwede, F., Yu, Y.-H., & Kraus, W. (2016) · Science · doi:10.1126/science.aaf7865 · Cited by 342 · see citing works
Hon, G. C., Song, C., Du, T., Jin, F., Selvaraj, S., Lee, A. Y., Yen, C., Ye, Z., Mao, S.-Q., Wang, B.-A., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.026 · Cited by 332 · see citing works
“…H3K27ac (Heintzman et al., 2009) (Figure S1F); and significant overlap with coactivator p300 binding sites (o/e = 5.9, p < 1 3 10 200), DNase I hypersensitive sites (Consortium, 2011) (o/e = 4.5, p < 1 3 10 200), and predicted enhancers (Shen et al., 2012) (o/e = 7.1, p < 1 3 10 200) (Figure 2C).”
InfluentialSelf-citationBenayoun, B., Pollina, E., Singh, P., Mahmoudi, S., Harel, I., Casey, K. M., Dulken, B. W., Kundaje, A., & Brunet, A. (2018) · bioRxiv · doi:10.1101/336172 · Cited by 336 · see citing works
A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies
Bahr, C., von Paleske, L., Uslu, V. V., Remeseiro, S., Takayama, N., Ng, S. W., Murison, A., Langenfeld, K., Petretich, M., Scognamiglio, R., et al. (2018) · Nature · doi:10.1038/nature25193 · Cited by 328 · see citing works
Architectural and Functional Commonalities between Enhancers and Promoters
Kim, T.-K., & Shiekhattar, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.008 · Cited by 331 · see citing works
An atlas of dynamic chromatin landscapes in mouse fetal development
Gorkin, D. U., Barozzi, I., Zhao, Y., Zhang, Y., Huang, H., Lee, A. Y., Li, B., Chiou, J., Wildberg, A., Ding, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2093-3 · Cited by 364 · see citing works
Self-citationEpigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D., & Ren, B. (2013) · Nature Genetics · doi:10.1038/ng.2746 · Cited by 457 · see citing works
Self-citationThe second decade of 3C technologies: detailed insights into nuclear organizationPreprint
Denker, A., & de Laat, W. L. (2016) · Genes & Development · doi:10.1101/gad.281964.116 · Cited by 346 · see citing works
“A TAD forms a framework within which promoters can find their respective enhancers and vice versa (Shen et al. 2012).”
TopDom: an efficient and deterministic method for identifying topological domains in genomes
Shin, H., Shi, Y. Y., Dai, C., Tjong, H., Gong, K. Q., Alber, F., & Zhou, X. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1505 · Cited by 319 · see citing works
“For mouse cortex and mESC cells, we collected ChipSeq data from Shen et al. 2012 (17) for the architectural protein CTCF, promoter-related marks (RNA Polymerase II and H3K4me3) and enhancer-related histone modifications (H3K4me1 and H3K27ac).”
MethodSeitan, V. C., Faure, A. J., Zhan, Y., McCord, R. P., Lajoie, B. R., Ing-Simmons, E., Lenhard, B., Giorgetti, L., Heard, E., Fisher, A. G., et al. (2013) · Genome Research · doi:10.1101/gr.161620.113 · Cited by 318 · see citing works
Zhang, Y., Li, T., Preißl, S., Amaral, M. L., Grinstein, J. D., Farah, E. N., Destici, E., Qiu, Y., Hu, R., Lee, A. Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0479-7 · Cited by 367 · see citing works
Self-citation
- Authors
- Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., & Ren, B.
- Affiliations
- Ludwig Cancer Research (US)
- University of California San Diego (US)
- National Institutes of Health (US)
- Corresponding author
- Ren, Bing
- ORCID
- Venue
- Nature
- Published
- 2012-07-01
- Volume
- 488
- Issue
- 7409
- Pages
- 116-120
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4041622
- OpenAlex
- W2042930277
- Cited by
- 1,361
- References
- 29
- Citations by year
- 2026: 12 · 2025: 24 · 2024: 51 · 2023: 75 · 2022: 88 · 2021: 119 · 2020: 90 · 2019: 107 · 2018: 97 · 2017: 110 · 2016: 125 · 2015: 137 · 2014: 167 · 2013: 132 · 2012: 26
- FWCI
- 59.44
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG003991)
- National Institute of General Medical Sciences (T32GM007198)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- cis-regulatory sequences, mouse genome, enhancers, promoter, CTCF binding sites, tissue-specific gene expression, transcription factor binding, conserved non-coding elements, genome annotation, ChIP-seq
- MeSH terms
- Acetylation, Animals, Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Male, Methylation, Mice, Inbred C57BL, Organ Specificity, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Transcription Factors, Genome, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular, Physical Chromosome Mapping, Chromatin Immunoprecipitation, Mice, Molecular Sequence Annotation, Nucleotide Motifs
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
