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A map of the cis-regulatory sequences in the mouse genome

Author

Listed:
  • Yin Shen

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Feng Yue

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • David F. McCleary

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Zhen Ye

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Lee Edsall

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Samantha Kuan

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Ulrich Wagner

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Jesse Dixon

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
    Medical Scientist Training Program, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
    Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Leonard Lee

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

  • Victor V. Lobanenkov

    (Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Twinbrook I NIAID Facility, Room 1417, 5640 Fishers Lane, Rockville, Maryland 20852, USA)

  • Bing Ren

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
    Institute of Genomic Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA)

Abstract

A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences.

Suggested Citation

  • Yin Shen & Feng Yue & David F. McCleary & Zhen Ye & Lee Edsall & Samantha Kuan & Ulrich Wagner & Jesse Dixon & Leonard Lee & Victor V. Lobanenkov & Bing Ren, 2012. "A map of the cis-regulatory sequences in the mouse genome," Nature, Nature, vol. 488(7409), pages 116-120, August.
    • Handle: RePEc:nat:nature:v:488:y:2012:i:7409:d:10.1038_nature11243
    DOI: 10.1038/nature11243
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    Cited by:

    1. Victoria Honnell & Jackie L. Norrie & Anand G. Patel & Cody Ramirez & Jiakun Zhang & Yu-Hsuan Lai & Shibiao Wan & Michael A. Dyer, 2022. "Identification of a modular super-enhancer in murine retinal development," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Graeme J. Thorn & Christopher T. Clarkson & Anne Rademacher & Hulkar Mamayusupova & Gunnar Schotta & Karsten Rippe & Vladimir B. Teif, 2022. "DNA sequence-dependent formation of heterochromatin nanodomains," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Ravneet Jaura & Ssu-Yu Yeh & Kaitlin N. Montanera & Alyssa Ialongo & Zobia Anwar & Yiming Lu & Kavindu Puwakdandawa & Ho Sung Rhee, 2022. "Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Beatriz del Blanco & Sergio Niñerola & Ana M. Martín-González & Juan Paraíso-Luna & Minji Kim & Rafael Muñoz-Viana & Carina Racovac & Jose V. Sanchez-Mut & Yijun Ruan & Ángel Barco, 2024. "Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    5. Yiming Lu & Wubin Qu & Guangyu Shan & Chenggang Zhang, 2015. "DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-20, June.
    6. Takayoshi Matsumura & Haruhito Totani & Yoshitaka Gunji & Masahiro Fukuda & Rui Yokomori & Jianwen Deng & Malini Rethnam & Chong Yang & Tze King Tan & Tadayoshi Karasawa & Kazuomi Kario & Masafumi Tak, 2022. "A Myb enhancer-guided analysis of basophil and mast cell differentiation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    7. Xuelong Yao & Zongyang Lu & Zhanying Feng & Lei Gao & Xin Zhou & Min Li & Suijuan Zhong & Qian Wu & Zhenbo Liu & Haofeng Zhang & Zeyuan Liu & Lizhi Yi & Tao Zhou & Xudong Zhao & Jun Zhang & Yong Wang , 2022. "Comparison of chromatin accessibility landscapes during early development of prefrontal cortex between rhesus macaque and human," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Markus Götz & Olivier Messina & Sergio Espinola & Jean-Bernard Fiche & Marcelo Nollmann, 2022. "Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. Wei Vivian Li & Yiling Chen & Jingyi Jessica Li, 2017. "TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 105-136, June.
    10. Renata Bordeira-Carriço & Joana Teixeira & Marta Duque & Mafalda Galhardo & Diogo Ribeiro & Rafael D. Acemel & Panos. N. Firbas & Juan J. Tena & Ana Eufrásio & Joana Marques & Fábio J. Ferreira & Telm, 2022. "Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    11. Tomas Zelenka & Antonios Klonizakis & Despina Tsoukatou & Dionysios-Alexandros Papamatheakis & Sören Franzenburg & Petros Tzerpos & Ioannis-Rafail Tzonevrakis & George Papadogkonas & Manouela Kapsetak, 2022. "The 3D enhancer network of the developing T cell genome is shaped by SATB1," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    12. Yu Chen & Mengjiao Luo & Haixia Tu & Yaling Qi & Yueshuai Guo & Xiangzheng Zhang & Yiqiang Cui & Mengmeng Gao & Xin Zhou & Tianyu Zhu & Hui Zhu & Chenghao Situ & Yan Li & Xuejiang Guo, 2024. "STYXL1 regulates CCT complex assembly and flagellar tubulin folding in sperm formation," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    13. Takeshi Katsuda & Jonathan H. Sussman & Kenji Ito & Andrew Katznelson & Salina Yuan & Naomi Takenaka & Jinyang Li & Allyson J. Merrell & Hector Cure & Qinglan Li & Reyaz Ur Rasool & Irfan A. Asangani , 2024. "Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    14. Amir D. Hay & Noah J. Kessler & Daniel Gebert & Nozomi Takahashi & Hugo Tavares & Felipe K. Teixeira & Anne C. Ferguson-Smith, 2023. "Epigenetic inheritance is unfaithful at intermediately methylated CpG sites," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    15. Xuemeng Zhou & Tsz Wing Sam & Ah Young Lee & Danny Leung, 2021. "Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations," Nature Communications, Nature, vol. 12(1), pages 1-18, December.

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