S. Abutbul, J. Shapiro, I. Szaingurten-solodkin, N. Levy, Y. Carmy et al., TGF-? signaling through SMAD2/3 induces the quiescent microglial phenotype within the CNS environment, Glia, vol.60, pp.1160-1171, 2012.

T. Agalioti, G. Chen, and D. Thanos, Deciphering the transcriptional histone acetylation code for a human gene, Cell, vol.111, pp.381-392, 2002.

A. Barski, S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones et al., High-resolution profiling of histone methylations in the human genome, Cell, vol.129, pp.823-837, 2007.

B. E. Bernstein, J. A. Stamatoyannopoulos, J. F. Costello, B. Ren, A. Milosavljevic et al., The NIH Roadmap Epigenomics Mapping Consortium, vol.28, pp.1045-1048, 2010.

I. M. Boros, Histone modification in Drosophila, Brief Funct Genomics, vol.11, pp.319-331, 2012.

A. P. Boyle, S. Davis, H. P. Shulha, P. Meltzer, E. H. Margulies et al., High-resolution mapping and characterization of open chromatin across the genome, Cell, vol.132, pp.311-322, 2008.

E. Calo and J. Wysocka, Modification of enhancer chromatin: what, how, and why?, Mol Cell, vol.49, pp.825-837, 2013.

P. Carninci, A. Sandelin, B. Lenhard, S. Katayama, K. Shimokawa et al., Genomewide analysis of mammalian promoter architecture and evolution, Nat Genet, vol.38, pp.626-635, 2006.

X. Chen, H. Xu, P. Yuan, F. Fang, M. Huss et al., Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, vol.133, pp.1106-1117, 2008.

I. Chepelev, G. Wei, Q. Tang, and K. Zhao, Detection of single nucleotide variations in expressed exons of the human genome using RNA-seq, Nucleic Acids Res, vol.37, p.106, 2009.

R. C. Del-rosario, N. A. Rayan, and S. Prabhakar, Noncoding origins of anthropoid traits and a new null model of transposon functionalization, Genome Res, vol.24, pp.1469-1484, 2014.

R. C. Del-rosario, J. Poschmann, S. L. Rouam, E. Png, C. C. Khor et al., Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms, Nat Methods, vol.12, pp.458-464, 2015.

, An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, pp.57-74, 2012.

J. Ernst and M. Kellis, Discovery and characterization of chromatin states for systematic annotation of the human genome, Nat Biotechnol, vol.28, pp.817-825, 2010.

J. Ernst and M. Kellis, ChromHMM: automating chromatin-state discovery and characterization, Nat Methods, vol.9, pp.215-216, 2012.

J. Ernst, P. Kheradpour, T. S. Mikkelsen, N. Shoresh, L. D. Ward et al., Mapping and analysis of chromatin state dynamics in nine human cell types, Nature, vol.473, pp.43-49, 2011.

B. Feng, S. Cheng, W. S. Pear, and H. C. Liou, NF-kB inhibitor blocks B cell development at two checkpoints, Med Immunol, vol.3, p.1, 2004.

M. B. Gerstein, A. Kundaje, M. Hariharan, S. G. Landt, K. K. Yan et al., Architecture of the human regulatory network derived from ENCODE data, Nature, vol.489, pp.91-100, 2012.

D. C. Hargreaves, T. Horng, and R. Medzhitov, Control of inducible gene expression by signal-dependent transcriptional elongation, Cell, vol.138, pp.129-145, 2009.

R. D. Hawkins, G. C. Hon, L. K. Lee, Q. Ngo, R. Lister et al., Distinct epigenomic landscapes of pluripotent and lineage-committed human cells, Cell Stem Cell, vol.6, pp.479-491, 2010.

E. Ing-simmons, V. C. Seitan, A. J. Faure, P. Flicek, T. Carroll et al., Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin, Genome Res, vol.25, pp.504-513, 2015.

F. Jin, Y. Li, J. R. Dixon, S. Selvaraj, Z. Ye et al., A high-resolution map of the three-dimensional chromatin interactome in human cells, Nature, vol.503, pp.290-294, 2013.

V. Kumar, M. Muratani, N. A. Rayan, P. Kraus, T. Lufkin et al., Uniform, optimal signal processing of mapped deep-sequencing data, Nat Biotechnol, vol.31, pp.615-622, 2013.

A. Kundaje, W. Meuleman, J. Ernst, M. Bilenky, Y. A. Heravi-moussavi et al., Integrative analysis of 111 reference human epigenomes, Nature, vol.518, pp.317-330, 2015.

J. C. Kwasnieski, C. Fiore, H. G. Chaudhari, and B. A. Cohen, High-throughput functional testing of ENCODE segmentation predictions, Genome Res, vol.24, pp.1595-1602, 2014.

J. Lasserre, H. R. Chung, and M. Vingron, Finding associations among histone modifications using sparse partial correlation networks, PLoS Comput Biol, vol.9, p.1003168, 2013.

K. M. Loh, L. T. Ang, J. Zhang, V. Kumar, J. Ang et al., Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations, Cell Stem Cell, vol.14, pp.237-252, 2014.

C. Y. Mclean, D. Bristor, M. Hiller, S. L. Clarke, B. T. Schaar et al., GREAT improves functional interpretation of cis-regulatory regions, Nat Biotechnol, vol.28, pp.495-501, 2010.

T. S. Mikkelsen, M. Ku, D. B. Jaffe, B. Issac, E. Lieberman et al., Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, vol.448, pp.553-560, 2007.

M. Murtha, Z. Tokcaer-keskin, Z. Tang, F. Strino, X. Chen et al., FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells, Nat Methods, vol.11, pp.559-565, 2014.

J. H. Ng, V. Kumar, M. Muratani, P. Kraus, J. C. Yeo et al., In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures, Dev Cell, vol.24, pp.324-333, 2013.

M. Percharde, F. Lavial, J. H. Ng, V. Kumar, R. A. Tomaz et al., Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming, Genes Dev, vol.26, pp.2286-2298, 2012.

J. V. Price, S. Tangsombatvisit, G. Xu, J. Yu, D. Levy et al., On silico peptide microarrays for highresolution mapping of antibody epitopes and diverse protein-protein interactions, Nat Med, vol.18, pp.1434-1440, 2012.

A. Rada-iglesias, R. Bajpai, T. Swigut, S. A. Brugmann, R. A. Flynn et al., A unique chromatin signature uncovers early developmental enhancers in humans, Nature, vol.470, pp.279-283, 2011.

N. Rajagopal, W. Xie, Y. Li, U. Wagner, W. Wang et al., RFECS: a random-forest based algorithm for enhancer identification from chromatin state, PLoS Comput Biol, vol.9, p.1002968, 2013.

N. Rajagopal, J. Ernst, P. Ray, J. Wu, M. Zhang et al., Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies, G3 (Bethesda), vol.4, pp.2051-2063, 2014.

D. Reynaud, I. A. Demarco, K. L. Reddy, H. Schjerven, E. Bertolino et al., Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros, Nat Immunol, vol.9, pp.927-936, 2008.

A. C. Ross, Q. Chen, and Y. Ma, Vitamin A and retinoic acid in the regulation of B-cell development and antibody production, Vitam Horm, vol.86, pp.103-126, 2011.

A. Sanyal, B. R. Lajoie, G. Jain, J. Dekker, and . 2012, The long-range interaction landscape of gene promoters, Nature, vol.489, pp.109-113

Y. Shen, F. Yue, D. F. Mccleary, Z. Ye, L. Edsall et al., A map of the cis-regulatory sequences in the mouse genome, Nature, vol.488, pp.116-120, 2012.

T. J. Stasevich, Y. Hayashi-takanaka, Y. Sato, K. Maehara, Y. Ohkawa et al., Regulation of RNA polymerase II activation by histone acetylation in single living cells, Nature, vol.516, pp.272-275, 2014.

A. Suzumura, M. Sawada, H. Yamamoto, and T. Marunouchi, Transforming growth factor-? suppresses activation and proliferation of microglia in vitro, J Immunol, vol.151, pp.2150-2158, 1993.

M. Tan, H. Luo, S. Lee, J. F. Yang, J. S. Montellier et al., Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification, Cell, vol.146, pp.1016-1028, 2011.

A. Visel, S. Minovitsky, I. Dubchak, and L. A. Pennacchio, VISTA Enhancer Browser: a database of tissue-specific human enhancers, Nucleic Acids Res, vol.35, pp.88-92, 2007.

Z. Wang, C. Zang, J. A. Rosenfeld, D. E. Schones, A. Barski et al., Combinatorial patterns of histone acetylations and methylations in the human genome, Nat Genet, vol.40, pp.897-903, 2008.

A. Weiner, T. H. Hsieh, A. Appleboim, H. V. Chen, A. Rahat et al., High-resolution chromatin dynamics during a yeast stress response, Mol Cell, vol.58, pp.371-386, 2015.