The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Open accessAbstract
Genome-scale studies have revealed extensive, cell type-specific colocalization of transcription factors, but the mechanisms underlying this phenomenon remain poorly understood. Here, we demonstrate in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions. PU.1 binding initiates nucleosome remodeling, followed by H3K4 monomethylation at large numbers of genomic regions associated with both broadly and specifically expressed genes. These locations serve as beacons for additional factors, exemplified by liver X receptors, which drive both cell-specific gene expression and signal-dependent responses. Together with analyses of transcription factor binding and H3K4me1 patterns in other cell types, these studies suggest that simple combinations of lineage-determining transcription factors can specify the genomic sites ultimately responsible for both cell identity and cell type-specific responses to diverse signaling inputs.
Overview
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
Verification
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“or as a collaboration-dependent partner in binding complexes, either with activation-dependent factors like NF-κB or with lineage-defining partners like C/EBPα (or β) or IRF4/8 (13–15)”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [13]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“PU.1 binding sites and PU.1 binding partners are not the same in early T-cell precursors as in myeloid cells or B lineage cells (13, 80, 84, 85)”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [13]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“MLL4 binding at enhancers has been shown to coincide with the binding of master regulators42–44.”
From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [42]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The intronic Myc peak was also present in two independent published macrophage datasets (Heinz et al., 2010; GEO accession no. GSE21512).”
From PU.1 enforces quiescence and limits hematopoietic stem cell expansion during inflammatory stress (2021) · cites this paper as Heinz et al., 2010
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Microglial enhancers are primed by relatively simple combinations of LDTFs (31, 32) to become sites of activity of broadly expressed signal-dependent transcription factors (SDTFs).”
From An environment-dependent transcriptional network specifies human microglia identity (2017) · cites this paper as [31]
Experimental — accuracy not yet measured
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Within cell-specific enhancers, DNA sequences provide information about the identities of key LDTFs and the activity states of signaling pathways that control the functions of SDTFs (31, 33–35).”
From An environment-dependent transcriptional network specifies human microglia identity (2017) · cites this paper as [31]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Differentially regulated H3K27ac or STAT3 sites were identified from three (H3K27ac) or two (STAT3) biological replicates using DESeq65 in the default parameters through HOMER66 (http://homer.salk.edu/homer/).”
From Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading (2017) · cites this paper as [66]
In the citing paper
“In myeloid and B-lymphoid cells, SPI1 activates lineage-specific genes due to lineage-specific coactivators at enhancers (6,7,68).”
From HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia (2022) · cites this paper as [7]
In the citing paper
“Instead, activation of common housekeeping genes is associated with an enrichment of SPI1 occupancy at promoters without requiring lineage-specific coactivators but with a higher affinity of binding to chromatin compared to enhancers (6,7,68).”
From HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia (2022) · cites this paper as [7]
In the citing paper
“A parallel analysis of Spi-1 genomic occupancy in macrophages and B cells showed that differentially bound sites between the two lineages were mostly located at the enhancers, whereas similar occupancy levels in both cell types were observed at TSS-proximal regions (13,14).”
From Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia (2012) · cites this paper as [14]
In the citing paper
“Moreover, in a recent study, several Spi-1 motifs within 100 bp of the central Spi-1 motif inside a Spi-1 binding site were identified in macrophages-specific or macrophages and B cells commonly bound sites of Spi-1 (14), but the impact of the Spi-1 motif multiplicity was not investigated in regard to the gene transactivation and binding regions in this study.”
From Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia (2012) · cites this paper as [14]
In the citing paper
“Consistent with the observed GO associations, the top de novo motifs identified by HOMER35 were for PU.1 (34%), CEBPβ (15%), HIF1α (68%) and RUNX1 (30% Figure 2d).”
From Vitamin C-induced epigenomic remodelling in IDH1 mutant acute myeloid leukaemia (2018) · cites this paper as [35]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
RAG-1-deficient mice have no mature B and T lymphocytes
Mombaerts, P., Iacomini, J., Johnson, R. S., Herrup, K., Tonegawa, S., & Papaioannou, V. E. (1992) · Cell · doi:10.1016/0092-8674(92)90030-g · Cited by 2,898
Chen, 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 2,547
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536
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
Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,473
Métivier, R., Penot, G., Hübner, M. R., Reid, G., Brand, H., Koš, M., & Gannon, F. (2003) · Cell · doi:10.1016/s0092-8674(03)00934-6 · Cited by 1,431
High-Resolution Mapping and Characterization of Open Chromatin across the Genome
Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415
Flagged first, then by citations
Cited by
Sorted by citations
Items 301–400 of 483
Wang, C., Rabadan Ros, R., Martinez-Redondo, P., Ma, Z., Shi, L., Xue, Y., Guillen-Guillen, I., Huang, L., Hishida, T., Liao, H.-K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23353-z · Cited by 119
Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Giles, H., Bruch, P.-M., Huber, W., Dietrich, S., Helin, K., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.106 · Cited by 119
Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
Yuan, Q., & Duren, Z. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02182-7 · Cited by 118
“We perform the motif enrichment analysis 86 to identify the motifs significantly enriched in the binding sites of the top 5,000 cell type-specific REs.”
Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population
Kim, E. J., Zhang, Z., Huang, L., Ito-Cole, T., Jacobs, M. W., Juavinett, A. L., Senturk, G., Hu, M., Ku, M., Ecker, J. R., et al. (2020) · Neuron · doi:10.1016/j.neuron.2020.04.018 · Cited by 103
Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo
Soccio, R. E., Chen, E. R., Rajapurkar, S. R., Safabakhsh, P., Marinis, J. M., Dispirito, J. R., Emmett, M. J., Briggs, E. R., Fang, B., Everett, L. J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.06.025 · Cited by 117
Evidence for additive and synergistic action of mammalian enhancers during cell fate determination
Choi, J., Lysakovskaia, K., Stik, G., Demel, C., Söding, J., Tian, T. V., Graf, T., & Cramer, P. (2021) · eLife · doi:10.7554/elife.65381 · Cited by 117
“Previous work showed that a subset of TFs is critical for enhancer priming and chromatin remodeling (Heinz et al., 2010; Takaku et al., 2016).”
BackgroundLau, S.-F., Chen, C., Fu, W.-Y., Qu, J. Y., Cheung, T. H., Fu, A. K. Y., & Ip, N. Y. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107530 · Cited by 114
Koester, J., Miroshnikova, Y. A., Ghatak, S., Chacón-Martínez, C. A., Morgner, J., Li, X., Atanassov, I., Altmüller, J., Birk, D. E., Koch, M., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00705-x · Cited by 117
Cross-species analysis of enhancer logic using deep learning
Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., et al. (2020) · Genome Research · doi:10.1101/gr.260844.120 · Cited by 116
Tansey, K. E., Cameron, D., & Hill, M. J. (2018) · Genome Medicine · doi:10.1186/s13073-018-0523-8 · Cited by 115
Human retinoic acid–regulated CD161+ regulatory T cells support wound repair in intestinal mucosa
Povoleri, G. A. M., Nova-Lamperti, E., Scottà, C., Fanelli, G., Chen, Y.-C., Becker, P. D., Boardman, D., Costantini, B., Romano, M., Pavlidis, P., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0230-z · Cited by 114
ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation
van der Weegen, Y., de Lint, K., van den Heuvel, D., Nakazawa, Y., Mevissen, T. E. T., van Schie, J. J. M., San Martin Alonso, M., Boer, D. E. C., González-Prieto, R., Narayanan, I. V., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00688-9 · Cited by 114
PD-L1 checkpoint blockade promotes regulatory T cell activity that underlies therapy resistance
van Gulijk, M., van Krimpen, A., Schetters, S., Eterman, M., van Elsas, M., Mankor, J., Klaase, L., de Bruijn, M., van Nimwegen, M., van Tienhoven, T., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.abn6173 · Cited by 110
Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1
Pham, T.-H., Minderjahn, J., Schmidl, C., Hoffmeister, H., Schmidhofer, S., Chen, W., Längst, G., Benner, C., & Rehli, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt355 · Cited by 102
Self-citationLarge-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging
Liu, Z., Ji, Q., Ren, J., Yan, P., Wu, Z., Wang, S., Sun, L., Wang, Z., Li, J., Sun, G., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.05.004 · Cited by 109
Ginno, P. A., Burger, L., Seebacher, J., Iesmantavicius, V., & Schübeler, D. (2018) · Nature Communications · doi:10.1038/s41467-018-06007-5 · Cited by 91
Lee, K.-W., Yeo, S.-Y., Gong, J.-R., Koo, O.-J., Sohn, I., Lee, W. Y., Kim, H. C., Yun, S. H., Cho, Y. B., Choi, M.-A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30484-4 · Cited by 103
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence
Parry, A. J., Hoare, M., Bihary, D., Hänsel-Hertsch, R., Smith, S., Tomimatsu, K., Mannion, E., Smith, A., D’Santos, P., Russell, I. A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04283-9 · Cited by 102
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
González-Blas, C. B., De Winter, S., Hulselmans, G., Hecker, N., Matetovici, I., Christiaens, V., Poovathingal, S., Wouters, J., Aibar, S., & Aerts, S. (2022) · doi:10.1101/2022.08.19.504505 · Cited by 778
A tissue injury sensing and repair pathway distinct from host pathogen defense
Liu, S., Hur, Y. H., Cai, X., Cong, Q., Yang, Y., Xu, C., Bilate, A. M., Gonzales, K. A. U., Parigi, S. M., Cowley, C. J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.03.031 · Cited by 108
Wang, M., Wei, P.-C., Lim, C. K., Gallina, I. S., Marshall, S., Marchetto, M. C., Alt, F. W., & Gage, F. H. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2019.12.013 · Cited by 105
Cx3cr1- deficient microglia exhibit a premature aging transcriptome
Gyoneva, S., Hosur, R., Gosselin, D., Zhang, B., Ouyang, Z., Cotleur, A. C., Peterson, M., Allaire, N., Challa, R., Cullen, P., et al. (2019) · Life Science Alliance · doi:10.26508/lsa.201900453 · Cited by 103
“ChIP-seq library preparation, sequencing, and data analysis ChIP-seq libraries were prepared from recovered DNA by blunting, A-tailing, and adapter ligation using barcoded adapters (NextFlex; Bioo Scienti fi c) as previously described (Heinz et al, 2010; Gosselin et al, 2014).”
Self-citationChopin, M., Lun, A. T., Zhan, Y., Schreuder, J., Coughlan, H., D’Amico, A., Mielke, L. A., Almeida, F. F., Kueh, A. J., Dickins, R. A., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.11.010 · Cited by 104
Subramanian, S., Busch, C. J.-L., Molawi, K., Geirsdottir, L., Maurizio, J., Vargas Aguilar, S., Belahbib, H., Gimenez, G., Yuda, R. A. A., Burkon, M., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01146-w · Cited by 103
The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages
Daniel, B., Nagy, G., Hah, N., Horvath, A., Czimmerer, Z., Poliska, S., Gyuris, T., Keirsse, J., Gysemans, C., Van Ginderachter, J. A., et al. (2014) · Genes & Development · doi:10.1101/gad.242685.114 · Cited by 97
Gain-of-function mutation of microRNA-140 in human skeletal dysplasia
Grigelioniene, G., Suzuki, H. I., Taylan, F., Mirzamohammadi, F., Borochowitz, Z. U., Ayturk, U. M., Tzur, S., Horemuzova, E., Lindstrand, A., Weis, M. A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0353-2 · Cited by 103
Fong, N., Saldi, T., Sheridan, R. M., Cortazar, M. A., & Bentley, D. L. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.016 · Cited by 98
Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome
Martinez-Ara, M., Comoglio, F., van Arensbergen, J., & van Steensel, B. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.04.009 · Cited by 101
The Transcription Factor PU.1 is a Critical Regulator of Cellular Communication in the Immune System
Turkistany, S. A., & DeKoter, R. P. (2011) · Archivum Immunologiae et Therapiae Experimentalis · doi:10.1007/s00005-011-0147-9 · Cited by 96
Analytical tools and current challenges in the modern era of neuroepigenomics
Maze, I., Shen, L., Zhang, B., Garcia, B. A., Shao, N., Mitchell, A., Sun, H., Akbarian, S., Allis, C. D., & Nestler, E. J. (2014) · Nature Neuroscience · doi:10.1038/nn.3816 · Cited by 100
Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development
Rothenberg, E. V., Hosokawa, H., & Ungerbäck, J. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.00228 · Cited by 99
“1 binding partners are not the same in early T-cell precursors as in myeloid cells or B lineage cells (13, 80, 84, 85), a similar situation to its early role in erythroblasts (86).”
ResultWickramasinghe, V. O., Gonzàlez-Porta, M., Perera, D., Bartolozzi, A. R., Sibley, C. R., Hallegger, M., Ule, J., Marioni, J. C., & Venkitaraman, A. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0749-3 · Cited by 91
Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming
Malik, V., Zimmer, D., & Jauch, R. (2018) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-018-2748-5 · Cited by 98
Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells
Nakahara, F., Borger, D. K., Wei, Q., Pinho, S., Maryanovich, M., Zahalka, A. H., Suzuki, M., Cruz, C. D., Wang, Z., Xu, C., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0308-3 · Cited by 99
Karakaslar, E. O., Katiyar, N., Hasham, M., Youn, A., Sharma, S., Chung, C., Marches, R., Korstanje, R., Banchereau, J., & Ucar, D. (2023) · Aging Cell · doi:10.1111/acel.13792 · Cited by 98
Goldstein, I., Paakinaho, V., Baek, S., Sung, M.-H., & Hager, G. L. (2017) · Nature Communications · doi:10.1038/s41467-017-02055-5 · Cited by 97
Bulut-Karslioglu, A., Macrae, T. A., Oses-Prieto, J. A., Covarrubias, S., Percharde, M., Ku, G., Diaz, A., McManus, M. T., Burlingame, A. L., & Ramalho-Santos, M. (2018) · Cell Stem Cell · doi:10.1016/j.stem.2018.02.004 · Cited by 97
A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction
Ting, P. Y., Borikar, S., Kerrigan, J. R., Thomsen, N. M., Aghania, E., Hinman, A. E., Reyes, A., Pizzato, N., Fodor, B. D., Wu, F., et al. (2024) · Science · doi:10.1126/science.adk6129 · Cited by 97
Vitamin C-induced epigenomic remodelling in IDH1 mutant acute myeloid leukaemia
Mingay, M., Chaturvedi, A., Bilenky, M., Cao, Q., Jackson, L., Hui, T., Moksa, M., Heravi-Moussavi, A., Humphries, R. K., Heuser, M., et al. (2018) · Leukemia · doi:10.1038/leu.2017.171 · Cited by 94
Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility
Meijer, M., Agirre, E., Kabbe, M., van Tuijn, C. A., Heskol, A., Zheng, C., Mendanha Falcão, A., Bartosovic, M., Kirby, L., Calini, D., et al. (2022) · Neuron · doi:10.1016/j.neuron.2021.12.034 · Cited by 98
Guo, Y., Jardin, B. D., Zhou, P., Sethi, I., Akerberg, B. N., Toepfer, C. N., Ai, Y., Li, Y., Ma, Q., Guatimosim, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06347-2 · Cited by 96
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
Verfaillie, A., Svetlichnyy, D., Imrichova, H., Davie, K., Fiers, M., Kalender Atak, Z., Hulselmans, G., Christiaens, V., & Aerts, S. (2016) · Genome Research · doi:10.1101/gr.204149.116 · Cited by 82
A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients
Guéant, J.-L., Chéry, C., Oussalah, A., Nadaf, J., Coelho, D., Josse, T., Flayac, J., Robert, A., Koscinski, I., Gastin, I., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02306-5 · Cited by 93
Borggrewe, M., Grit, C., Den Dunnen, W. F. A., Burm, S. M., Bajramovic, J. J., Noelle, R. J., Eggen, B. J. L., & Laman, J. D. (2018) · Glia · doi:10.1002/glia.23517 · Cited by 91
Transcriptional regulation of Hepatic Stellate Cell activation in NASH
Marcher, A.-B., Bendixen, S. M., Terkelsen, M. K., Hohmann, S. S., Hansen, M. H., Larsen, B. D., Mandrup, S., Dimke, H., Detlefsen, S., & Ravnskjaer, K. (2019) · Scientific Reports · doi:10.1038/s41598-019-39112-6 · Cited by 95
Enhancing face validity of mouse models of Alzheimer’s disease with natural genetic variation
Onos, K. D., Uyar, A., Keezer, K. J., Jackson, H. M., Preuss, C., Acklin, C. J., O’Rourke, R., Buchanan, R., Cossette, T. L., Sukoff Rizzo, S. J., et al. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008155 · Cited by 93
Succinylation of H3K122 destabilizes nucleosomes and enhances transcription
Zorro Shahidian, L., Haas, M., Le Gras, S., Nitsch, S., Mourão, A., Geerlof, A., Margueron, R., Michaelis, J., Daujat, S., & Schneider, R. (2021) · The EMBO Reports · doi:10.15252/embr.202051009 · Cited by 92
PU.1 enforces quiescence and limits hematopoietic stem cell expansion during inflammatory stress
Chavez, J. S., Rabe, J. L., Loeffler, D., Higa, K. C., Hernandez, G., Mills, T. S., Ahmed, N., Gessner, R. L., Ke, Z., Idler, B. M., et al. (2021) · Journal of Experimental Medicine · doi:10.1084/jem.20201169 · Cited by 91
“S4F) at different timepoints post induction (Heinz et al., 2010).”
BackgroundMethodInfluentialHuang, D., Yi, X., Zhang, S., Zheng, Z., Wang, P., Xuan, C., Sham, P. C., Wang, J., & Li, M. J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky407 · Cited by 83
Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq
Bottini, S., Hamouda-Tekaya, N., Mategot, R., Zaragosi, L.-E., Audebert, S., Pisano, S., Grandjean, V., Mauduit, C., Benahmed, M., Barbry, P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01126-x · Cited by 89
Zhang, Y., Amaral, M. L., Zhu, C., Grieco, S. F., Hou, X., Lin, L., Buchanan, J., Tong, L., Preissl, S., Xu, X., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00719-6 · Cited by 89
Kutejova, E., Sasai, N., Shah, A., Gouti, M., & Briscoe, J. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.02.013 · Cited by 87
Determinants of transcription factor regulatory range
Chen, C.-H., Zheng, R., Tokheim, C., Dong, X., Fan, J., Wan, C., Tang, Q., Brown, M., Liu, J. S., Meyer, C. A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16106-x · Cited by 85
TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Seberg, H. E., Van Otterloo, E., Loftus, S. K., Liu, H., Bonde, G., Sompallae, R., Gildea, D. E., Santana, J. F., Manak, J. R., Pavan, W. J., et al. (2017) · PLOS Genetics · doi:10.1371/journal.pgen.1006636 · Cited by 85
Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops
Oh, H. J., Aguilar, R., Kesner, B., Lee, H.-G., Kriz, A. J., Chu, H.-P., & Lee, J. T. (2021) · Cell · doi:10.1016/j.cell.2021.11.012 · Cited by 84
Sensory experience remodels genome architecture in neural circuit to drive motor learning
Yamada, T., Yang, Y., Valnegri, P., Juric, I., Abnousi, A., Markwalter, K. H., Guthrie, A. N., Godec, A., Oldenborg, A., Hu, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1190-7 · Cited by 83
ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes
Blattler, A., Yao, L., Wang, Y., Ye, Z., Jin, V. X., & Farnham, P. J. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-13 · Cited by 82
Regulatory network control of blood stem cells
Göttgens, B. (2015) · Blood · doi:10.1182/blood-2014-08-570226 · Cited by 82
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
Kamimoto, K., Hoffmann, C. M., & Morris, S. A. (2020) · doi:10.1101/2020.02.17.947416 · Cited by 81
Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis
Shcherbina, A., Larouche, J., Fraczek, P., Yang, B. A., Brown, L. A., Markworth, J. F., Chung, C. H., Khaliq, M., de Silva, K., Choi, J. J., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107964 · Cited by 76
HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer
Kalisz, M., Bernardo, E., Beucher, A., Maestro, M. A., del Pozo, N., Millán, I., Haeberle, L., Schlensog, M., Safi, S. A., Knoefel, W. T., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019102808 · Cited by 77
Pundhir, S., Bratt Lauridsen, F. K., Schuster, M. B., Jakobsen, J. S., Ge, Y., Schoof, E. M., Rapin, N., Waage, J., Hasemann, M. S., & Porse, B. T. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.012 · Cited by 77
An evolutionary trade-off between host immunity and metabolism drives fatty liver in male mice
Nikkanen, J., Leong, Y. A., Krause, W. C., Dermadi, D., Maschek, J. A., Van Ry, T., Cox, J. E., Weiss, E. J., Gokcumen, O., Chawla, A., et al. (2022) · Science · doi:10.1126/science.abn9886 · Cited by 77
A macrophage-hepatocyte glucocorticoid receptor axis coordinates fasting ketogenesis
Loft, A., Schmidt, S. F., Caratti, G., Stifel, U., Havelund, J., Sekar, R., Kwon, Y., Sulaj, A., Chow, K. K., Alfaro, A. J., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.01.004 · Cited by 76
Ungerbäck, J., Hosokawa, H., Wang, X., Strid, T., Williams, B. A., Sigvardsson, M., & Rothenberg, E. V. (2018) · Genome Research · doi:10.1101/gr.231423.117 · Cited by 77
Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing
Saldi, T., Fong, N., & Bentley, D. L. (2018) · Genes & Development · doi:10.1101/gad.310896.117 · Cited by 66
Champhekar, A., Damle, S. S., Freedman, G., Carotta, S., Nutt, S. L., & Rothenberg, E. V. (2015) · Genes & Development · doi:10.1101/gad.259879.115 · Cited by 74
Daniel, B., Nagy, G., Horvath, A., Czimmerer, Z., Cuaranta-Monroy, I., Poliska, S., Hays, T. T., Sauer, S., Francois-Deleuze, J., & Nagy, L. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky157 · Cited by 73
TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation
Ferri, F., Parcelier, A., Petit, V., Gallouet, A.-S., Lewandowski, D., Dalloz, M., van den Heuvel, A., Kolovos, P., Soler, E., Squadrito, M. L., et al. (2015) · Nature Communications · doi:10.1038/ncomms9900 · Cited by 70
Functional characterization of Alzheimer’s disease genetic variants in microglia
Yang, X., Wen, J., Yang, H., Jones, I. R., Zhu, X., Liu, W., Li, B., Clelland, C. D., Luo, W., Wong, M. Y., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01506-8 · Cited by 71
Dedifferentiation and neuronal repression define familial Alzheimer’s disease
Caldwell, A. B., Liu, Q., Schroth, G. P., Galasko, D. R., Yuan, S. H., Wagner, S. L., & Subramaniam, S. (2020) · Science Advances · doi:10.1126/sciadv.aba5933 · Cited by 69
Pang, S. H. M., de Graaf, C. A., Hilton, D. J., Huntington, N. D., Carotta, S., Wu, L., & Nutt, S. L. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01264 · Cited by 60
“1 concentration is highest in myeloid cells where it functions as a pioneer factor to broadly promote lineage-specific gene expression (14).”
BackgroundPU.1 cooperates with IRF4 and IRF8 to suppress pre-B-cell leukemia
Pang, S. H. M., Minnich, M., Gangatirkar, P., Zheng, Z., Ebert, A., Song, G., Dickins, R. A., Corcoran, L. M., Mullighan, C. G., Busslinger, M., et al. (2016) · Leukemia · doi:10.1038/leu.2016.27 · Cited by 69
Vogel Ciernia, A., Careaga, M., LaSalle, J. M., & Ashwood, P. (2018) · Glia · doi:10.1002/glia.23261 · Cited by 69
Droplet-based single-cell joint profiling of histone modifications and transcriptomes
Xie, Y., Zhu, C., Wang, Z., Tastemel, M., Chang, L., Li, Y. E., & Ren, B. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01060-1 · Cited by 69
A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair
van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2020) · doi:10.1101/2020.01.04.894808 · Cited by 69
DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A
Leon, K. E., Buj, R., Lesko, E., Dahl, E. S., Chen, C.-W., Tangudu, N. K., Imamura-Kawasawa, Y., Kossenkov, A. V., Hobbs, R. P., & Aird, K. M. (2021) · Journal of Cell Biology · doi:10.1083/jcb.202008101 · Cited by 70
Sahu, B., Pihlajamaa, P., Dubois, V., Kerkhofs, S., Claessens, F., & Jänne, O. A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1401 · Cited by 66
Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs
Cates, K., McCoy, M. J., Kwon, J.-S., Liu, Y., Abernathy, D. G., Zhang, B., Liu, S., Gontarz, P., Kim, W. K., Chen, S., et al. (2021) · Cell Stem Cell · doi:10.1016/j.stem.2020.08.015 · Cited by 67
Rbpj expression in regulatory T cells is critical for restraining TH2 responses
Delacher, M., Schmidl, C., Herzig, Y., Breloer, M., Hartmann, W., Brunk, F., Kägebein, D., Träger, U., Hofer, A.-C., Bittner, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09276-w · Cited by 63
Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex
Wehrspaun, C. C., Haerty, W., & Ponting, C. P. (2015) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2015.04.008 · Cited by 64
Kumar, A., Karuppagounder, S. S., Chen, Y., Corona, C., Kawaguchi, R., Cheng, Y., Balkaya, M., Sagdullaev, B. T., Wen, Z., Stuart, C., et al. (2023) · Neuron · doi:10.1016/j.neuron.2023.06.013 · Cited by 64
Phosphoinositide 3-kinase signaling can modulate MHC class I and II expression
Chandrasekaran, S., Sasaki, M., Scharer, C. D., Kissick, H. T., Patterson, D. G., Magliocca, K. R., Seykora, J. T., Sapkota, B., Gutman, D. A., Cooper, L. A., et al. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-19-0545 · Cited by 61
A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors
Nishi, Y., Zhang, X., Jeong, J., Peterson, K. A., Vedenko, A., Bulyk, M. L., Hide, W. A., & McMahon, A. P. (2015) · Development · doi:10.1242/dev.124636 · Cited by 53
Andrysik, Z., Bender, H., Galbraith, M. D., & Espinosa, J. M. (2021) · Nature Communications · doi:10.1038/s41467-021-21687-2 · Cited by 63
Sen, M., Wang, X., Hamdan, F. H., Rapp, J., Eggert, J., Kosinsky, R. L., Wegwitz, F., Kutschat, A. P., Younesi, F. S., Gaedcke, J., et al. (2019) · Clinical Epigenetics · doi:10.1186/s13148-019-0690-5 · Cited by 61
Metabolic alterations mediated by STAT3 promotes drug persistence in CML
Patel, S. B., Nemkov, T., Stefanoni, D., Benavides, G. A., Bassal, M. A., Crown, B. L., Matkins, V. R., Camacho, V., Kuznetsova, V., Hoang, A. T., et al. (2021) · Leukemia · doi:10.1038/s41375-021-01315-0 · Cited by 56
Jia, Y., Li, L., Lin, Y.-H., Gopal, P., Shen, S., Zhou, K., Yu, X., Sharma, T., Zhang, Y., Siegwart, D. J., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2022.01.001 · Cited by 59
Self-citationPadmanabhan, A., Alexanian, M., Linares-Saldana, R., González-Terán, B., Andreoletti, G., Huang, Y., Connolly, A. J., Kim, W., Hsu, A., Duan, Q., et al. (2020) · Circulation · doi:10.1161/circulationaha.120.047753 · Cited by 60
Ng, N. H. J., Ghosh, S., Bok, C. M., Ching, C., Low, B. S. J., Chen, J. T., Lim, E., Miserendino, M. C., Tan, Y. S., Hoon, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48647-w · Cited by 57
Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils
Fischer, J., Walter, C., Tönges, A., Aleth, H., Jordão, M. J. C., Leddin, M., Gröning, V., Erdmann, T., Lenz, G., Roth, J., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0343-z · Cited by 56
Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression
Kong, N. R., Bassal, M. A., Tan, H. K., Kurland, J. V., Yong, K. J., Young, J. J., Yang, Y., Li, F., Lee, J. D., Liu, Y., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108574 · Cited by 56
Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
Montefiori, L., Hernandez, L., Zhang, Z., Gilad, Y., Ober, C., Crawford, G., Nobrega, M., & Jo Sakabe, N. (2017) · Scientific Reports · doi:10.1038/s41598-017-02547-w · Cited by 54
TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41
Carey, K. L., Paulus, G. L. C., Wang, L., Balce, D. R., Luo, J. W., Bergman, P., Ferder, I. C., Kong, L., Renaud, N., Singh, S., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108371 · Cited by 55
Taguchi, J., Shibata, H., Kabata, M., Kato, M., Fukuda, K., Tanaka, A., Ohta, S., Ukai, T., Mitsunaga, K., Yamada, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25249-4 · Cited by 46
Max deletion destabilizes MYC protein and abrogates Eµ- Myc lymphomagenesis
Mathsyaraja, H., Freie, B., Cheng, P.-F., Babaeva, E., Catchpole, J. T., Janssens, D., Henikoff, S., & Eisenman, R. N. (2019) · Genes & Development · doi:10.1101/gad.325878.119 · Cited by 54
Multifaceted role for p53 in pancreatic cancer suppression
Mello, S. S., Flowers, B. M., Mazur, P. K., Lee, J. J., Müller, F., Denny, S. K., Ferreira, S., Hanson, K., Kim, S. K., Greenleaf, W. J., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2211937120 · Cited by 55
Wontakal, S. N., Guo, X., Will, B., Shi, M., Raha, D., Mahajan, M. C., Weissman, S., Snyder, M., Steidl, U., Zheng, D., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001392 · Cited by 53
Optimized CRISPR-mediated gene knockin reveals FOXP3-independent maintenance of human Treg identity
Lam, A. J., Lin, D. T. S., Gillies, J. K., Uday, P., Pesenacker, A. M., Kobor, M. S., & Levings, M. K. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109494 · Cited by 52
Arid1a restrains Kras-dependent changes in acinar cell identity
Livshits, G., Alonso-Curbelo, D., Morris, J. P., Koche, R., Saborowski, M., Wilkinson, J. E., & Lowe, S. W. (2018) · eLife · doi:10.7554/elife.35216 · Cited by 48
Metadata
- Authors
- Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K.
- Affiliations
- University of California San Diego (US)
- University of Chicago (US)
- University of Leeds (GB)
- Genentech (US)
- Corresponding author
- Glass, Christopher K.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2010-05
- Volume
- 38
- Issue
- 4
- Pages
- 576-589
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC2898526
- OpenAlex
- W2014677321
- Cited by
- 13,382
- References
- 49
- Citations by year
- 2026: 1075 · 2025: 1447 · 2024: 1483 · 2023: 1473 · 2022: 1305 · 2021: 1435 · 2020: 1177 · 2019: 939 · 2018: 791 · 2017: 653 · 2016: 461 · 2015: 422 · 2014: 309 · 2013: 188 · 2012: 109
- FWCI
- 50.91
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (F32HL083752, HC088093)
- National Cancer Institute (R01CA078384, R01CA052599, R01CA054198, CA 52599)
- National Institute of General Medical Sciences (P50GM081892)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK063491, DK62434, U19DK062434, P30DK063491, R01DK091183)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- PU.1, cis-regulatory elements, macrophage identity, B cell identity, H3K4me1, H3K4 monomethylation, nucleosome remodeling, liver X receptor, transcription factor binding sites
- MeSH terms
- Proto-Oncogene Protein Spi-1, Animals, B-Lymphocytes, Binding Sites, Macrophages, Male, Mice, Inbred C57BL, Proto-Oncogene Proteins, Transcription Factors, Trans-Activators, Cell Lineage, Oligonucleotide Array Sequence Analysis, Regulatory Elements, Transcriptional, Mice
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
