Publications

Featured Publications

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated these data to develop a Registry of 0.9 million human and 300 thousand mouse candidate cis-Regulatory Elements (cCREs) annotated with potential functions1. We have expanded the Registry to include 2.35 million human and 927 thousand mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded Registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays like STARR-seq, MPRA, CRISPR perturbation, and transgenic mouse assays now cover over 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer/silencer roles in different cellular contexts. Integrating the Registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by discovering KLF1 as a novel causal gene for red blood cell traits. This expanded Registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Recent Publications

Deciphering the impact of genomic variation on function

IGFV Consortium. Nature (2024)

Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements

Pratt, H. E., Andrews, G., Shedd, N., Phalke, N., Li, T., Pampari, A., Jensen, M., Wen, C., Consortium, P., Gandal, M. J., Geschwind, D. H., Gerstein, M., Moore, J., Kundaje, A., Colubri, A. & Weng, Z.K. Science Advances (2024).

Multicenter integrated analysis of noncoding CRISPRi screens

Yao, D., Tycko, J., Oh, J. W., Bounds, L. R., Gosai, S. J., Lataniotis, L., Mackay-Smith, A., Doughty, B. R., Gabdank, I., Schmidt, H., Guerrero-Altamirano, T., Siklenka, K., Guo, K., White, A. D., Youngworth, I., Andreeva, K., Ren, X., Barrera, A., Luo, Y., Yardımcı, G. G., Tewhey, R., Kundaje, A., Greenleaf, W. J., Sabeti, P. C., Leslie, C., Pritykin, Y., Moore, J. E., Beer, M. A., Gersbach, C. A., Reddy, T. E., Shen, Y., Engreitz, J. M., Bassik, M. C. & Reilly, S. K. Nature Methods (2024).

Mammalian evolution of human cis-regulatory elements and transcription factor binding sites

Andrews, G., Fan, K., Pratt, H. E., Phalke, N., Zoonomia Consortium, Karlsson, E. K., Lindblad-Toh, K., Gazal, S., Moore, J. E., Weng, Z. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (2023).

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Rozowsky, J., Drenkow, J., Yang, Y. T., Gursoy, G., Galeev, T., Borsari, B., Epstein, C. B., Xiong, K., Xu, J., Gao, J., Yu, K., Berthel, A., Chen, Z., Navarro, F., Liu, J., Sun, M. S., Wright, J., Chang, J., Cameron, C. J. F., Shoresh, N., Gaskell, E., Adrian, J., Aganezov, S., Aguet, F., Balderrama-Gutierrez, G., Banskota, S., Corona, G. B., Chee, S., Chhetri, S. B., Martins, G. C. C., Danyko, C., Davis, C. A., Farid, D., Farrell, N. P., Gabdank, I., Gofin, Y., Gorkin, D. U., Gu, M., Hecht, V., Hitz, B. C., Issner, R., Kirsche, M., Kong, X., Lam, B. R., Li, S., Li, B., Li, T., Li, X., Lin, K. Z., Luo, R., Mackiewicz, M., Moore, J. E., Mudge, J., Nelson, N., Nusbaum, C., Popov, I., Pratt, H. E., Qiu, Y., Ramakrishnan, S., Raymond, J., Salichos, L., Scavelli, A., Schreiber, J. M., Sedlazeck, F. J., See, L. H., Sherman, R. M., Shi, X., Shi, M., Sloan, C. A., Seth Strattan, J., Tan, Z., Tanaka, F. Y., Vlasova, A., Wang, J., Werner, J., Williams, B., Xu, M., Yan, C., Yu, L., Zaleski, C., Zhang, J., Ardlie, K., Michael Cherry, J., Mendenhall, E. M., Noble, W. S., Weng, Z., Levine, M. E., Dobin, A., Wold, B., Mortazavi, A., Ren, B., Gillis, J., Myers, R. M., Snyder, M. P., Choudhary, J., Milosavljevic, A., Schatz, M. C., Guigó, R., Bernstein, B. E., Gingeras, T. R. & Gerstein, M. Cell (2023)

Downregulation of Hsp90 and the antimicrobial peptide Mtk suppresses poly (GR)-induced neurotoxicity in C9ORF72-ALS/FTD

Lee, S., Jun, Y.-W., Linares, G. R., Butler, B., Yuva-Adyemir, Y., Moore, J., Krishnan, G., Ruiz-Juarez, B., Santana, M., Pons, M., Silverman, N., Weng, Z., Ichida, J. K. & Gao, F.-B. Neuron (2023).

Building integrative functional maps of gene regulation

Xu, J., Pratt, H. E., Moore, J. E., Gerstein, M. B. & Weng, Z. Hum Mol Genet (2022).

FAVOR: functional annotation of variants online resource and annotator for variation across the human genome

Zhou, H., Arapoglou, T., Li, X., Li, Z., Zheng, X., Moore, J., Asok, A., Kumar, S., Blue, E. E., Buyske, S., Cox, N., Felsenfeld, A., Gerstein, M., Kenny, E., Li, B., Matise, T., Philippakis, A., Rehm, H., Sofia, H. J., Snyder, G., NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng, Z., Neale, B., Sunyaev, S. R. & Lin, X. Nucleic Acids Res (2022)

Preprints

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

Moore, J. E., Pratt, H. E., Fan, K., Phalke, N., Fisher, J., Elhajjajy, S. I., Andrews, G., Gao, M., Shedd, N., Fu, Y., Lacadie, M. C., Meza, J., Ganna, M., Choudhury, E., Swofford, R., Farrell, N. P., Pampari, A., Ramalingam, V., Reese, F., Borsari, B., Yu, M., Wattenberg, E., Ruiz-Romero, M., Razavi-Mohseni, M., Xu, J., Galeev, T., Beer, M. A., Guigó, R., Gerstein, M., Engreitz, J., Ljungman, M., Reddy, T. E., Snyder, M. P., Epstein, C. B., Gaskell, E., Bernstein, B. E., Dickel, D. E., Visel, A., Pennacchio, L. A., Mortazavi, A., Kundaje, A. & Weng, Z. bioRxiv (2024)

Currently Under Review

A consensus variant-to-function score to functionally prioritize variants for disease

Fabiha, T., Evergreen, I., Kundu, S., Pampari, A., Abramov, S., Boytsov, A., Strouse, K., Dura, K., Fang, W., Kerner, G., Butts, J., Ali, T., Gschwind, A., Mualim, K. S., Moore, J. E., Weng, Z., Ulirsch, J., Ji, H. E., Vierstra, J., Reddy, T. E., Montgomery, S. B., Engreitz, J., Kundaje, A., Tewhey, R., Price, A. & Dey, K. bioRxiv (2024)

Currently Under Review

An encyclopedia of enhancer-gene regulatory interactions in the human genome

Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R. N., Xi, W., Tan, A. S., Jones, H., Ma, X. R., Yao, D., Nasser, J., Avsec, Ž., James, B. T., Shamim, M. S., Durand, N. C., Rao, S. S. P., Mahajan, R., Doughty, B. R., Andreeva, K., Ulirsch, J. C., Fan, K., Perez, E. M., Nguyen, T. C., Kelley, D. R., Finucane, H. K., Moore, J. E., Weng, Z., Kellis, M., Bassik, M. C., Price, A. L., Beer, M. A., Guigó, R., Stamatoyannopoulos, J. A., Aiden, E. L., Greenleaf, W. J., Leslie, C. S., Steinmetz, L. M., Kundaje, A. & Engreitz, J. M. bioRxiv (2023)

Currently In Revision

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Reese, F., Williams, B., Balderrama-Gutierrez, G., Wyman, D., Çelik, M. H., Rebboah, E., Rezaie, N., Trout, D., Razavi-Mohseni, M., Jiang, Y., Borsari, B., Morabito, S., Liang, H. Y., McGill, C. J., Rahmanian, S., Sakr, J., Jiang, S., Zeng, W., Carvalho, K., Weimer, A. K., Dionne, L. A., McShane, A., Bedi, K., Elhajjajy, S. I., Upchurch, S., Jou, J., Youngworth, I., Gabdank, I., Sud, P., Jolanki, O., Strattan, J. S., Kagda, M. S., Snyder, M. P., Hitz, B. C., Moore, J. E., Weng, Z., Bennett, D., Reinholdt, L., Ljungman, M., Beer, M. A., Gerstein, M. B., Pachter, L., Guigó, R., Wold, B. J. & Mortazavi, A. bioRxiv (2023)

Currently In Revision

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